Class A scavenger receptors regulate tolerance against apoptotic cells, and autoantibodies against these receptors are predictive of systemic lupus

Apoptotic cells are considered to be a major source for autoantigens in autoimmune diseases such as systemic lupus erythematosus (SLE). In agreement with this, defective clearance of apoptotic cells has been shown to increase disease susceptibility. Still, little is known about how apoptotic cell–derived self-antigens activate autoreactive B cells and where this takes place. In this study, we find that apoptotic cells are taken up by specific scavenger receptors expressed on macrophages in the splenic marginal zone and that mice deficient in these receptors have a lower threshold for autoantibody responses. Furthermore, antibodies against scavenger receptors are found before the onset of clinical symptoms in SLE-prone mice, and they are also found in diagnosed SLE patients. Our findings describe a novel mechanism where autoantibodies toward scavenger receptors can alter the response to apoptotic cells, affect tolerance, and thus promote disease progression. Because the autoantibodies can be detected before onset of disease in mice, they could have predictive value as early indicators of SLE

Invariant NKT cells limit activation of autoreactive CD1d-positive B cells

Faulty activation of autoreactive B cells is a hallmark of autoimmune diseases like systemic lupus erythematosus (SLE). An important feature restricting activation of autoreactive B cells is efficient removal of apoptotic material. Mounting evidence also connects a primary defect in invariant natural killer T (iNKT) cells to autoimmune disease development. However, exactly how this unconventional T cell subset is involved remains to be defined. Here, we identify a suppressive role for iNKT cells in a model where autoantibody production is triggered by an increased load of circulating apoptotic cells, resembling the situation in SLE patients. Absence or reduction of iNKT cells as well as absence of CD1d-expression on B cells, needed for direct iNKT–B cell interaction, leads to increased autoreactive B cell activation and symptoms of disease. The suppression mediated by the iNKT cells is observed before B cell entry into germinal centers and can be rescued by transferring iNKT cells to deficient mice. This links iNKT cells to handling of dying cells and identifies a novel peripheral tolerance checkpoint relevant for autoimmune disease. Thus, these observations connect two clinical observations in SLE patients previously considered to be unrelated and define a new target for immunotherapy

A Role for the Transcription Factor Arid3a in Mouse B2 Lymphocyte Expansion and Peritoneal B1a Generation

The initiation, commitment, and terminal differentiation of the B cell lineage is stringently controlled by the coordinated action of various transcription factors. Among these, Arid3a has previously been implicated in regulating early B lymphopoiesis, humoral immune responses to phosphocholine, and furthermore to promote the B1 over the B2 cell lineage. We have now interrogated the function of Arid3a in the adult mouse using conditional mutagenesis. We demonstrate that loss of Arid3a does not affect early B cell development or lineage commitment but rather loss of this transcription factor results in a broad expansion of bone marrow B lymphopoiesis in a manner that reflects its developmental expression pattern. Furthermore, loss of Arid3a resulted in expanded splenic B cell numbers with the exception of the B1 lineage that was maintained at normal numbers. However, B1a lymphoyctes were reduced in the peritoneal cavity. In addition, antibody responses to phosphocholine were attenuated in the absence of Arid3a. Hence, functional Arid3a is required in mature B cells for specific immune responses and for generating normal numbers of B cells in a subset dependent manner

A rapid CRISPR competitive assay for in vitro and in vivo discovery of potential drug targets affecting the hematopoietic system

CRISPR/Cas9 can be used as an experimental tool to inactivate genes in cells. However, a CRISPR-targeted cell population will not show a uniform genotype of the targeted gene. Instead, a mix of genotypes is generated - from wild type to different forms of insertions and deletions. Such mixed genotypes complicate analysis of the role of the targeted gene in the studied cell population. Here, we present a rapid and universal experimental approach to functionally analyze a CRISPR-targeted cell population that does not involve generating clonal lines. As a simple readout, we leverage the CRISPR-induced genetic heterogeneity and use sequencing to identify how different genotypes are enriched or depleted in relation to the studied cellular behavior or phenotype. The approach uses standard PCR, Sanger sequencing, and a simple sequence deconvoluting software, enabling laboratories without specific in-depth experience to perform these experiments. As proof of principle, we present examples studying various aspects related to hematopoietic cells (T cell development in vivo and activation in vitro, differentiation of macrophages and dendritic cells, as well as a leukemia-like phenotype induced by overexpressing a proto-oncogene). In conclusion, we present a rapid experimental approach to identify potential drug targets related to mature immune cells, as well as normal and malignant hematopoiesis.Nanyang Technological UniversityPublished versionWe are grateful to Drs. Helena Malmgren, Lisa Westerberg, Taras Kreslavskiy, Laura Plant and Sudeepta Panda for valuable discussions and input. The ER-Hoxb8 construct was a gift from Mark P. Kamps, University of California, San Diego. The pSIRV-NF-jBeGFP construct was a gift from Peter Steinberger, Medical University of Vienna. This research was partly funded by grants from the Swedish Research Council, the Swedish Cancer Society, Karolinska Institutet, Magnus Bergvalls stiftelse, Stiftelsen Professor Nanna Svartz fond, Felix Mindus contribution to Leukemia Research (to FW), the China Scholarship Council (to LJ and YS), and the Nanyang Y. Shen, L. Jiang, Vaishnavi Srinivasan Iyer et al. Computational and Structural Biotechnology Journal 19 (2021) 5360–5370 5369 Technological University–Karolinska Institutet Joint PhD Programme (to VSI)

CRISPR/Cas9-induced DNA damage enriches for mutations in a p53-linked interactome: implications for CRISPR-based therapies

Inactivating p53 mutations are the most abundant genetic alterations found in cancer. Here we show that CRISPR/Cas9-induced double-stranded DNA breaks enrich for cells deficient in p53 and in genes of a core CRISPR-p53 tumor suppressor interactome. Such enrichment could predispose to cancer development and thus pose a challenge for clinical CRISPR use. Transient p53 inhibition could suppress the enrichment of cells with these mutations. The level of DNA damage response induced by an sgRNA influenced the enrichment of p53-deficient cells and could be a relevant parameter in sgRNA design to limit cellular enrichment. Furthermore, a dataset of >800 human cancer cell lines identified additional factors influencing the enrichment of p53-mutated cells, including strong baseline CDKN1A expression as a predictor for an active CRISPR-p53 axis. Taken together, these data provide details about p53 biology in the context of CRISPR-induced DNA damage and identify strategies to enable safer CRISPR use. SIGNIFICANCE: CRISPR-mediated DNA damage enriches for cells with escape mutations in a core CRISPR-p53 interactome, which can be suppressed by transient inhibition of p53.Published versionThe authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for AdvancedComputational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. This research was partly funded by grants from the Swedish Research Council (to F. Wermeling and D.P. Lane) , the Swedish Cancer Society, Karolinska Institutet and Magnus Bergvalls stiftelse (to F. Wermeling) , the China Scholarship Council (to L. Jiang and Y. Shen) , and the Nanyang Technological University-Karolinska Institutet Joint PhD Program (to V.S. Iyer)

WASP confers selective advantage for specific hematopoietic cell populations and serves a unique role in marginal zone B-cell homeostasis and function

Development of hematopoietic cells depends on a dynamic actin cytoskeleton. Here we demonstrate that expression of the cytoskeletal regulator WASP, mutated in the Wiskott-Aldrich syndrome, provides selective advantage for the development of naturally occurring regulatory T cells, natural killer T cells, CD4+ and CD8+ T lymphocytes, marginal zone (MZ) B cells, MZ macrophages, and platelets. To define the relative contribution of MZ B cells and MZ macrophages for MZ development, we generated wild-type and WASP-deficient bone marrow chimeric mice, with full restoration of the MZ. However, even in the presence of MZ macrophages, only 10% of MZ B cells were of WASP-deficient origin. We show that WASP-deficient MZ B cells hyperproliferate in vivo and fail to respond to sphingosine-1-phosphate, a crucial chemoattractant for MZ B-cell positioning. Abnormalities of the MZ compartment in WASP−/− mice lead to aberrant uptake of Staphylococcus aureus and to a reduced immune response to TNP-Ficoll. Moreover, WASP-deficient mice have increased levels of “natural” IgM antibodies. Our findings reveal that WASP regulates both development and function of hematopoietic cells. We demonstrate that WASP deficiency leads to an aberrant MZ that may affect responses to blood-borne pathogens and peripheral B-cell tolerance

Modulating T-cell activation with antisense oligoucleotides targeting lymphocyte cytosolic protein 2

Dysregulated T-cell activation is a hallmark of several autoimmune diseases such as rheumatoid arthritis (RA) and multiple sclerosis (MS). The lymphocyte cytosolic protein 2 (LCP2), also known as SLP-76, is essential for the development and activation of T cells. Despite the critical role of LCP2 in T-cell activation and the need for developing drugs that modify T-cell activation, no LCP2 inhibitors have been developed. This can be explained by the "undruggable" nature of LCP2, lacking a structure permissive to standard small molecule inhibitor modalities. Here, we explored an alternative drug modality, developing antisense oligonucleotides (ASOs) targeting LCP2 mRNAs, and evaluated its activity in modulating T-cell activation. We identified a set of 3' UTR targeting LCP2 ASOs, which knocked down LCP2 in a human T-cell line and primary human T cells and found that these suppressed T-cell receptor mediated activation. We also found that the ASOs suppressed FcεR1-mediated mast cell activation, in line with the role of LCP2 in mast cells. Taken together, our data provide examples of how immunomodulatory ASOs that interfere with undruggable targets can be developed and propose that such drug modalities can be used to treat autoimmune diseases.Nanyang Technological UniversityPublished versionThis research was funded by grants from the Karolinska Institutet, Swedish Research Council, Swedish Cancer Society, Stiftelsen Professor Nanna Svartz Fond, the China Scholarship Council, and the Nanyang Technological University–Karolinska Institutet Joint PhD Programme. This work has additionally received support via the European Union/ European Federation of Pharmaceutical Industries and Associations (EU/EFPIA) Innovative Medicines Initiative Joint Undertaking (RTCure Grant 777357)