SLE: a cognitive step forward-a synthesis of rethinking theories, causality, and ignored DNA structures

Abstract

Systemic lupus erythematosus (SLE) is classified by instinctual classification criteria. A valid proclamation is that these formally accepted SLE classification criteria legitimate the syndrome as being difficult to explain and therefore enigmatic. SLE involves scientific problems linked to etiological factors and criteria. Our insufficient understanding of the clinical condition uniformly denoted SLE depends on the still open question of whether SLE is, according to classification criteria, a well-defined one disease entity or represents a variety of overlapping indistinct syndromes. Without rational hypotheses, these problems harm clear definition(s) of the syndrome. Why SLE is not anchored in logic, consequent, downstream interdependent and interactive inflammatory networks may rely on ignored predictive causality principles. Authoritative classification criteria do not reflect consequent causality criteria and do not unify characterization principles such as diagnostic criteria. We need now to reconcile legendary scientific achievements to concretize the delimitation of what SLE really is. Not all classified SLE syndromes are "genuine SLE"; many are theoretically "SLE-like non-SLE" syndromes. In this study, progressive theories imply imperative challenges to reconsider the fundamental impact of "the causality principle". This may offer us logic classification and diagnostic criteria aimed at identifying concise SLE syndromes as research objects. Can a systems science approach solve this problem?

Keywords: SLE; SLE classification criteria; lupus nephritis; system science; systemic lupus erythematosus; the causality principle; unique DNA structures.

Figure 1

Transcriptionally active DNA expresses distinct DNA structures—each structure is a unique antigen. (i) The B DNA helix is opened by single-stranded binding proteins (SSBPs; which stabilize ssDNA and polymerize, which are involved in replication and repair). (ii) Z DNA is a left-handed, high-energy, double helix. Z DNA forms during transcription as a result of torsional strains that depend on interaction with mobile polymerases. Z DNA is associated with linker DNA. (iii) Elongated (linker) DNA is a relaxed and stable, right-handed, low-energy form of B DNA. Cruciform DNA is another dsDNA structure (iv) and is different from B and Z DNA. Its formation requires that sequences (palindromes) in one strand are repeated on the other strand in opposite directions. The cruciform structures are, like Z DNA, higher-energy structures. Compacted B DNA as in core nucleosomes is defined as bent B DNA (v). Bent DNA is a compacted structure influenced by the histone octamer and histone H1. These structures (i–iv) are unique in terms of inducing highly specific antibodies with potential pathogenic impact if chromatin fragments are exposed in situ (see Figure 2 ). This figure demonstrates the unique immunogenic DNA structures [revised from Reference (2)].

Figure 2

Induction of anti-chromatin antibodies (A) and anti-DNA structure-specific antibodies (B)—demonstration of Sercarz’s hapten-carrier theorem involving expression of polyomavirus T antigen as immunogenic carrier protein. (A) Injection of non-autoimmune mice with plasmids expressing polyomavirus DNA-binding T antigen induces production of antibodies to DNA, T antigen, mammalian histones, and certain transcription factors like TATA-binding protein (TBP) and cAMP-responsive element-binding protein (CREB) by cognate interaction between chromatin specific B cells and polyomavirus T antigen peptide-specific helper T cells. (B) These antibodies bind chromatin-antigens exposed in GBM and promote nephritis. (C) Identical immunization regimes induce autoantibodies against elongated B DNA, bent B DNA, Z DNA, cruciform DNA, and ssDNA. (D) The anti-DNA structure-specific antibodies promote nephritis by binding exposed DNA antigens in GBM. Autoimmune B cells and operational immune T cells cooperate in this model. (E) All the induced anti-chromatin antibodies have pathogenic potentials if binding exposed chromatin, as is demonstrated in GBM as electron-dense structures (EDS in panels F, G). The induced autoantibodies (stained with 5-nm gold particles; F) bind chromatin fragments. Chromatin fragments are surrounded by GBM structures that bind anti-laminin antibodies added to the section in vitro (10-nm gold particles; G). (A–D) Modified from Reference (25).

Figure 3

Theoretical disease profiles differ due to the molecular specificities of the autoantibodies. (A) Anti-dsDNA antibodies form immune complexes with assumed circulating small chromatin fragments that accumulate in glomerulus mesangium (121). This promotes mild, early mono-phasic, and transient lupus nephritis (Phase 1). Under certain conditions, mesangial inflammation promotes silencing of the renal DNase 1 endonuclease (121). In reflection of loss of DNase 1 enzyme activity, chromatin released from dead cells accumulates as undigested chromatin fragments in complex with anti-chromatin antibodies in mesangial matrix and in GBM [see Figure 2 (121)]. This promotes end-stage nephritis (B; Phase 2)—a second-phased progression of lupus nephritis. This model contrasts with the cross-reacting model (described in panel C). Here, a cross-reacting anti-DNA antibody binds inherent membrane antigens (like laminin, collagen, and entactin) shared between the mesangial matrix and GBM. Therefore, the nephritis profile is mono-phasic, as the mesangium and GBM are simultaneously affected by antibodies. This mono-phasic nephritis is complementary to nephritis in Goodpasture syndrome (D). Goodpasture-type nephritis is caused by anti-collagen IV antibodies that bind collagen structures shared by the mesangial matrix and the GBM. The antibodies therefore promote a mono-phasic profile of the nephritis in cross-reacting lupus nephritis models and Goodpasture syndrome.

Figure 4

Severe proteinuria correlates positively with chromatin fragment deposits [observed as electron-dense structures (EDS) in GBM] and inversely with renal Dnase 1 mRNA levels. Renal tissue was collected from female (NZBxNZW)F1 (BW) and female age-matched BALB/c mice (Jackson Laboratory, Bar Harbor, ME, USA) sacrificed approximately every second week (n   = 3) from the age of 4 weeks until development of end-stage disease in the BW mice, clinically defined when severe proteinuria developed (≥20 g/L). Tissue was snap-frozen for protein extraction, preserved according to Tokuyasu for immune electron microscopy (138), or preserved in RNAlater (Ambion Inc., Austin, TX, USA) for mRNA analyses. Serum and urine samples were collected at 2–3-week intervals and stored at −80°C. No correlation between degree of proteinuria and levels of anti-dsDNA antibody titers was observed (A). To analyze if loci for electron-dense structure (EDS) deposits had impact on proteinuria, data on proteinuria and presence of EDS in the mesangial matrix (weighted 1 in B) or in the GBM (weighted 2 to make a visual distinction from mesangial deposits) were combined for each mouse and sorted by ascending values of proteinuria. Severe proteinuria (≥20 g/L) was, except for one mouse with intermediate proteinuria (≤3 g/L), exclusively observed in mice with EDS in GBM (B), while intermediate or mild proteinuria was observed in mice with mesangial matrix deposits only (B). In panel C, the degree of proteinuria and renal Dnase 1 mRNA levels were paired and sorted by ascending proteinuria levels. Severe proteinuria (≥20 g/L) correlated with a substantial loss of Dnase 1 mRNA (and enzyme activity; (C). Thus, in mice selected for proteinuria ≥20 g/L, renal Dnase 1 mRNA was nearby lost in all mice but one (C), and deposits of chromatin–IgG complexes (observed as EDS) in GBM were observed only in these mice. This instructive figure is copied from Reference (121). For statistical analyses, see Table 1 in Reference (121).