De novo identification of CD4+ T cell epitopes

CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.

Living in Syn: T Cell Antigen Identification Based on Synapse Sequencing

The pivotal role of T cell responses has been well studied in both protective and destructive scenarios. T cells recognize peptide epitopes presented on Human Leukocyte Antigens (HLA) through their surface T cell receptors (TCR). Advances in single-cell RNA sequencing have identified millions of TCRs, but only a minuscule fraction of them have known epitopes. Recently, cell-based T cell antigen discovery platforms have emerged onto the landscape. Here, Jin and colleagues, report a novel antigen discovery platform called Tsyn-seq that relies on sequencing TCR-peptide-HLA-induced synapses for genome-wide epitope screening. See related article by Jin et al., p. xxxx.

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

Modern multiomic technologies can generate deep multiscale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make analyses and integration of high-dimensional omic datasets challenging. Here we present Significant Latent Factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, and has rigorous false discovery rate control. Using SLIDE on single-cell and spatial omic datasets, we uncovered significant interacting latent factors underlying a range of molecular, cellular and organismal phenotypes. SLIDE outperforms/performs at least as well as a wide range of state-of-the-art approaches, including other latent factor approaches. More importantly, it provides biological inference beyond prediction that other methods do not afford. Thus, SLIDE is a versatile engine for biological discovery from modern multiomic datasets.

The beta cell-immune cell interface in type 1 diabetes (T1D)

BACKGROUND

T1D is an autoimmune disease in which pancreatic islets of Langerhans are infiltrated by immune cells resulting in the specific destruction of insulin-producing islet beta cells. Our understanding of the factors leading to islet infiltration and the interplay of the immune cells with target beta cells is incomplete, especially in human disease. While murine models of T1D have provided crucial information for both beta cell and autoimmune cell function, the translation of successful therapies in the murine model to human disease has been a challenge.

SCOPE OF REVIEW

Here, we discuss current state of the art and consider knowledge gaps concerning the interface of the islet beta cell with immune infiltrates, with a focus on T cells. We discuss pancreatic and immune cell phenotypes and their impact on cell function in health and disease, which we deem important to investigate further to attain a more comprehensive understanding of human T1D disease etiology.

MAJOR CONCLUSIONS

The last years have seen accelerated development of approaches that allow comprehensive study of human T1D. Critically, recent studies have contributed to our revised understanding that the pancreatic beta cell assumes an active role, rather than a passive position, during autoimmune disease progression. The T cell-beta cell interface is a critical axis that dictates beta cell fate and shapes autoimmune responses. This includes the state of the beta cell after processing internal and external cues (e.g., stress, inflammation, genetic risk) that that contributes to the breaking of tolerance by hyperexpression of human leukocyte antigen (HLA) class I with presentation of native and neoepitopes and secretion of chemotactic factors to attract immune cells. We anticipate that emerging insights about the molecular and cellular aspects of disease initiation and progression processes will catalyze the development of novel and innovative intervention points to provide additional therapies to individuals affected by T1D.

Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment

The use of probiotics by cancer patients is increasing, including among those undergoing immune checkpoint inhibitor (ICI) treatment. Here, we elucidate a critical microbial-host crosstalk between probiotic-released aryl hydrocarbon receptor (AhR) agonist indole-3-aldehyde (I3A) and CD8 T cells within the tumor microenvironment that potently enhances antitumor immunity and facilitates ICI in preclinical melanoma. Our study reveals that probiotic Lactobacillus reuteri (Lr) translocates to, colonizes, and persists within melanoma, where via its released dietary tryptophan catabolite I3A, it locally promotes interferon-γ-producing CD8 T cells, thereby bolstering ICI. Moreover, Lr-secreted I3A was both necessary and sufficient to drive antitumor immunity, and loss of AhR signaling within CD8 T cells abrogated Lr's antitumor effects. Further, a tryptophan-enriched diet potentiated both Lr- and ICI-induced antitumor immunity, dependent on CD8 T cell AhR signaling. Finally, we provide evidence for a potential role of I3A in promoting ICI efficacy and survival in advanced melanoma patients.

Profiling transcriptomes, TCR repertoires, and antigenic specificities of islet-infiltrating T cells in Non-Obese Diabetic mice

Type 1 Diabetes (T1D) is an autoimmune disease caused by progressive destruction of pancreatic β-cells, resulting in reduced insulin production. The role of islet-infiltrating CD4+ T cells in mediating β-cell destruction and autoantibody formation is well established. However, many of the antigen specificities of CD4+ T cells which initiate disease are undefined. In this project, we performed single cell RNA sequencing of pancreatic islet infiltrating T cells from 6-, 8- , and 10-week-old Non-Obese Diabetic (NOD) mice. NOD mice recapitulate many immunologic features of T1D and share many autoantigens with human T1D patients. Analysis of TCR repertoires revealed clonal expansion in activated and pre-exhausted effector CD4+ T cells as well as regulatory T cells. Despite subtle differences, expanded effector CD4+ T cells showed a well-defined cell state. We cloned 40 TCRs from the top expanded T cells and expressed them in Jurkat cells. We performed antigen discovery assays on these TCRs using our lab’s Signaling and Antigen-presenting Bifunctional Receptor (SABR) platform. We constructed a SABR library of 4,075 I-Ag7-restricted epitopes based on published datasets. We identified several previously reported and novel autoantigens. Surprisingly, antigenic specificities did not influence the shared phenotype dramatically. These results identify several potential autoantigens that will be valuable for diagnostic, preventative, and therapeutic purposes. Moreover, these results suggest that the islet microenvironment is a major determinant of infiltrating CD4+ T cell states. Similar studies focused on CD8+ T cells in NOD mice and CD4+ and CD8+ T cells in humans are underway.

dkNET New investigator Pilot Program in Bioinformatics (PI: Joglekar) NIDDK New Investigator Gateway Award 1R03DK127447 (PI: Joglekar) PACER Innovative Discovery Award (PI: Joglekar)

Developmental dynamics and genomic programming of GC-derived precursors that give rise to long lived plasma cells

Plasma cell (PC) precursors are generated during a germinal center (GC) response and migrate to the bone marrow (BM) where they undergo terminal differentiation into short-lived (SL) or long-lived (LL) antibody secreting cells. The developmental dynamics and genomic states of PC precursors remain to be elucidated1. We utilize a novel experimental system, involving CD138+ splenocytes isolated from NP-KLH immunized C57Bl/6J mice (21–42 dpi) and their adoptive transfer into B cell deficient mMT mice, to analyze developmental dynamics of antigen-specific PC precursors and their progeny at single-cell resolution. We demonstrate that SLPC precursors are generated earlier (d21), whilst LLPC precursors are generated later (d35) during a GC response. scRNA-seq analyses reveals increased frequency of a novel cluster of transitional cells expressing both B-lineage and plasma cell-specific genes. Coupled analyses using BCR-seq shows that NP-specific transitional cells express cell cycle genes and undergo greater clonal expansion on d35 to give rise to proliferating and quiescent PCs. Antigen-specific clonal tracking in the spleen and BM compartments suggests that the transitional cells emanating from the GC, differentiate into proliferating PCs before migrating to the BM. CITE-seq analyses and reconstitution experiments demonstrate that proliferating PCs are contained within the B220− CD138+ CD44+ CD11a+ subset and are enriched for BMPC precursors. These results reveal novel GC-derived transitional cells that generate precursors of both SLPCs and LLPCs with differing developmental and proliferation dynamics in a humoral immune response.

People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden

Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in people critically ill with COVID-19. Here, we present high-dimensional profiling of blood and respiratory samples from people with severe COVID-19 to examine the association between cell-linked molecular features and mortality outcomes. Peripheral transcriptional profiles by single-cell RNA sequencing (RNA-seq)-based deconvolution of immune states are associated with COVID-19 mortality. Further, persistently high levels of an interferon signaling module in monocytes over time lead to subsequent concerted upregulation of inflammatory cytokines. SARS-CoV-2-infected myeloid cells in the lower respiratory tract upregulate CXCL10, leading to a higher risk of death. Our analysis suggests a pivotal role for viral-infected myeloid cells and protracted interferon signaling in severe COVID-19.

Bifurcated monocyte states are predictive of mortality in severe COVID-19

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection presents with varied clinical manifestations1, ranging from mild symptoms to acute respiratory distress syndrome (ARDS) with high mortality2,3. Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in severe COVID-19. We performed high-dimensional cellular and molecular profiling of blood and respiratory samples from critically ill COVID-19 patients to define immune cell genomic states that are predictive of outcome in severe COVID-19 disease. Critically ill patients admitted to the intensive care unit (ICU) manifested increased frequencies of inflammatory monocytes and plasmablasts that were also associated with ARDS not due to COVID-19. Single-cell RNAseq (scRNAseq)-based deconvolution of genomic states of peripheral immune cells revealed distinct gene modules that were associated with COVID-19 outcome. Notably, monocytes exhibited bifurcated genomic states, with expression of a cytokine gene module exemplified by CCL4 (MIP-1β) associated with survival and an interferon signaling module associated with death. These gene modules were correlated with higher levels of MIP-1β and CXCL10 levels in plasma, respectively. Monocytes expressing genes reflective of these divergent modules were also detectable in endotracheal aspirates. Machine learning algorithms identified the distinctive monocyte modules as part of a multivariate peripheral immune system state that was predictive of COVID-19 mortality. Follow-up analysis of the monocyte modules on ICU day 5 was consistent with bifurcated states that correlated with distinct inflammatory cytokines. Our data suggests a pivotal role for monocytes and their specific inflammatory genomic states in contributing to mortality in life-threatening COVID-19 disease and may facilitate discovery of new diagnostics and therapeutics.

Reprogramming T Cell Specificity to Suppress Autoreactive T Cells in Type 1 Diabetes

Effector T cells (Teff) in Type 1 Diabetes (T1D) recognize antigenic targets on pancreatic β cells, thereby killing them. Insulin-derived epitopes are targeted first, followed by rapid epitope spreading, leading to progressive destruction of pancreatic islets, causing insulitis and T1D. Curbing these autoimmune responses is key to the development of immunotherapies to treat T1D. In this study, we tested the proof-of-concept of two strategies to treat T1D by reprogramming T cell specificity. We have developed cell-surface receptors called SABRs (Signaling and Antigen-presenting Bifunctional Receptors), which present a peptide-MHC complex on the extracellular domain and link it with a CD28-CD3ζ signaling domain. The intracellular signaling domains in SABRs are capable of activating T cell function. The extracellular domains can recognize TCRs specifically. We successfully demonstrated that SABRs presenting peptide epitopes on human and mouse, class I and class II MHC complexes are able to induce a functional signal through the NFAT pathway. We tested two complementary approaches to use SABRs to engineer T cells. In the first approach, we transduced human Treg cells with SABRs. SABR-armed Treg cells were able to secrete IL-10 in response to T cells bearing a diabetogenic TCR. In the second approach, we transduced human CD8+ T cells with SABRs. SABR-modified CD8+ T cells were able to specifically lyse target cells bearing a diabetogenic TCR. Ongoing studies will determine if Treg-mediated suppression or CD8+ T cell-mediated elimination of diabetogenic Teff cells will be an efficient strategy for immunotherapy for T1D. If successful, these approaches will also be applicable to other autoimmune diseases such as Multiple Sclerosis.

Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome

X-linked hyper-immunoglobulin M (hyper-IgM) syndrome (XHIM) is a primary immunodeficiency due to mutations in CD40 ligand that affect immunoglobulin class-switch recombination and somatic hypermutation. The disease is amenable to gene therapy using retroviral vectors, but dysregulated gene expression results in abnormal lymphoproliferation in mouse models, highlighting the need for alternative strategies. Here, we demonstrate the ability of both the transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) platforms to efficiently drive integration of a normal copy of the CD40L cDNA delivered by Adeno-Associated Virus. Site-specific insertion of the donor sequence downstream of the endogenous CD40L promoter maintained physiologic expression of CD40L while overriding all reported downstream mutations. High levels of gene modification were achieved in primary human hematopoietic stem cells (HSCs), as well as in cell lines and XHIM-patient-derived T cells. Notably, gene-corrected HSCs engrafted in immunodeficient mice at clinically relevant frequencies. These studies provide the foundation for a permanent curative therapy in XHIM.

T cell antigen discovery via trogocytosis

T cell receptor (TCR) ligand discovery is essential for understanding and manipulating immune responses to tumors. We developed a cell-based selection platform for TCR ligand discovery that exploits a membrane transfer phenomenon called trogocytosis. We discovered that T cell membrane proteins are transferred specifically to target cells that present cognate peptide-major histocompatibility complex (MHC) molecules. Co-incubation of T cells expressing an orphan TCR with target cells collectively presenting a library of peptide-MHCs led to specific labeling of cognate target cells, enabling isolation of these target cells and sequencing of the cognate TCR ligand. We validated this method for two clinically employed TCRs and further used the platform to identify the cognate neoepitope for a subject-derived neoantigen-specific TCR. Thus, target cell trogocytosis is a robust tool for TCR ligand discovery that will be useful for studying basic tumor immunology and identifying new targets for immunotherapy.

T cell antigen discovery via signaling and antigen-presenting bifunctional receptors

CD8+ T cells recognize and eliminate tumors in an antigen-specific manner. Despite progress in characterizing the antitumor T cell repertoire and function, identifying their target antigens remains a challenge. Here, we describe the use of chimeric receptors called Signaling and Antigen-presenting Bifunctional Receptors (SABRs) in a novel cell-based platform for T Cell Receptor (TCR) antigen discovery. SABRs present an extracellular peptide-MHC complex and induce intracellular signaling via a TCR-like signal upon binding with a cognate TCR. We devised a strategy for antigen discovery using SABR libraries to screen thousands of antigenic epitopes. We validated this platform by identifying the targets recognized by public TCRs of known specificities. Moreover, we extended this approach for personalized neoantigen discovery. The antigen discovery platform reported here will provide a scalable and versatile way to develop novel targets for immunotherapy.

Dissecting the mechanism of histone deacetylase inhibitors to enhance the activity of zinc finger nucleases delivered by integrase-defective lentiviral vectors

Integrase-defective lentiviral vectors (IDLVs) have been of limited success in the delivery of zinc finger nucleases (ZFNs) to human cells, due to low expression. A reason for reduced gene expression has been proposed to involve the epigenetic silencing of vector genomes, carried out primarily by histone deacetylases (HDACs). In this study, we tested valproic acid (VPA), a known HDAC inhibitor (HDACi), for its ability to increase transgene expression from IDLVs, especially in the context of ZFN delivery. Using ZFNs targeting the human adenosine deaminase (ADA) gene in K562 cells, we demonstrated that treatment with VPA enhanced ZFN expression by up to 3-fold, resulting in improved allelic disruption at the ADA locus. Furthermore, three other U.S. Food and Drug Administration-approved HDACis (vorinostat, givinostat, and trichostatin-A) exhibited a similar effect on the activity of ZFN-IDLVs in K562 cells. In primary human CD34(+) cells, VPA- and vorinostat-treated cells showed higher levels of expression of both green fluorescent protein (GFP) as well as ZFNs from IDLVs. A major mechanism for the effects of HDAC inhibitors on improving expression was from their modulation of the cell cycle, and the influence of heterochromatinization was determined to be a lesser contributing factor.

Integrase-defective lentiviral vectors as a delivery platform for targeted modification of adenosine deaminase locus

We investigated the use of integrase-defective lentiviral vectors (IDLVs) for transient delivery of zinc finger nucleases (ZFNs) and donor templates for site-specific modification of the human adenosine deaminase (hADA) gene. Initially, we constructed IDLVs carrying ZFN monomers (Single-IDLVs) and found them to be able to deliver their gene-editing payload to K562 cells successfully upon cotransduction, with minimal cytotoxicity. To simplify delivery, we designed an IDLV construct to deliver both ZFN monomers from the same vector (Double-IDLV). However, this construct in its original state was prone to rearrangements of the vector genome, resulting in greatly reduced functionality; this was due to recombination between highly similar ZFN monomers arranged in tandem. We modified the Double-IDLV constructs to reduce recombination and restored simultaneous delivery of both ZFNs. We also tested an IDLV construct for delivery of donor templates and demonstrated its efficacy for gene modification. In summary, we highlighted the importance of modifying vector design for co-delivery of highly similar sequences inherent to genome-editing nucleases, and demonstrated significant improvement in the use of IDLVs for delivery of ZFNs and donor templates for genome modification.

Studies on cellulase production by a mutant-penicillium funiculosum uv-49

In search of hypercellulolytic microorganisms, ultraviolet irradiation carried out with Penicillium funiculosum has yielded a superior mutant. The investigations reported in this article are shake flask studies on some important nutritional requirements of the mutant, namely, nitrogen source, carbon source, and inducers. The mutant shows an ability to metabolize inorganic nitrogen sources like urea and sodium nitrate both for growth and enzyme production. A comparison of the long-term saccharification ability and the utilization efficiency of the mutant enzyme with those reported in the literature is also carried out, showing the superior performance of the mutant enzyme.

Snail and slug mediate radioresistance and chemoresistance by antagonizing p53-mediated apoptosis and acquiring a stem-like phenotype in ovarian cancer cells

The transcriptional repressors Snail and Slug contribute to cancer progression by mediating epithelial-mesenchymal transition (EMT), which results in tumor cell invasion and metastases. We extend this current understanding to demonstrate their involvement in the development of resistance to radiation and paclitaxel. The process is orchestrated through the acquisition of a novel subset of gene targets that is repressed under conditions of stress, effectively inactivating p53-mediated apoptosis, while another subset of targets continues to mediate EMT. Repressive activities are complemented by a concurrent derepression of specific genes resulting in the acquisition of stem cell-like characteristics. Such cells are bestowed with three critical capabilities, namely EMT, resistance to p53-mediated apoptosis, and a self-renewal program, that together define the functionality and survival of metastatic cancer stem cells. EMT provides a mechanism of escape to a new, less adverse niche; resistance to apoptosis ensures cell survival in conditions of stress in the primary tumor; whereas acquisition of "stemness" ensures generation of the critical tumor mass required for progression of micrometastases to macrometastases. Our findings, besides achieving considerable expansion of the inventory of direct genes targets, more importantly demonstrate that such elegant cooperative modulation of gene regulation mediated by Snail and Slug is critical for a cancer cell to acquire stem cell characteristics toward resisting radiotherapy- or chemotherapy-mediated cellular stress, and this may be a determinative aspect of aggressive cancer metastases.