Multi-omics study reveals different pathogenesis of the generation of skin lesions in SLE and IDLE patients

Lupus erythematosus (LE) is a heterogeneous, antibody-mediated autoimmune disease. Isolate discoid LE (IDLE) and systematic LE (SLE) are traditionally regarded as the two ends of the spectrum, ranging from skin-limited damage to life-threatening multi-organ involvement. Both belong to LE, but IDLE and SLE differ in appearance of skin lesions, autoantibody panels, pathological changes, treatments, and immunopathogenesis. Is discoid lupus truly a form of LE or is it a completely separate entity? This question has not been fully elucidated. We compared the clinical data of IDLE and SLE from our center, applied multi-omics technology, such as immune repertoire sequencing, high-resolution HLA alleles sequencing and multi-spectrum pathological system to explore cellular and molecular phenotypes in skin and peripheral blood from LE patients. Based on the data from 136 LE patients from 8 hospitals in China, we observed higher damage scores and fewer LE specific autoantibodies in IDLE than SLE patients, more uCDR3 sharing between PBMCs and skin lesion from SLE than IDLE patients, elevated diversity of V-J recombination in IDLE skin lesion and SLE PBMCs, increased SHM frequency and class switch ratio in IDLE skin lesion, decreased SHM frequency but increased class switch ratio in SLE PBMCs, HLA-DRB1*03:01:01:01, HLA-B*58:01:01:01, HLA-C*03:02:02:01, and HLA-DQB1*02:01:01:01 positively associated with SLE patients, and expanded Tfh-like cells with ectopic germinal center structures in IDLE skin lesions. These findings suggest a significant difference in the immunopathogenesis of skin lesions between SLE and IDLE patients. SLE is a B cell-predominate systemic immune disorder, while IDLE appears limited to the skin. Our findings provide novel insights into the pathogenesis of IDLE and other types of LE, which may direct more accurate diagnosis and novel therapeutic strategies.

Intratumoral T cell clonality and survival in a randomized phase II study of preoperative autophagy inhibition in combination with gemcitabine and nab-paclitaxel treatment in patients with resectable pancreatic cancer

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Background: Autophagy is a cell survival mechanism that is upregulated in pancreatic ductal adenocarcinoma (PDAC). PDAC autophagy results in an altered metabolic phenotype that promotes tumor progression, chemotherapeutic resistance, and immune evasion. Methods: We previously completed a randomized phase II clinical trial of preoperative gemcitabine-nab-paclitaxel with (PGH n = 34) and without (PG, n = 30) autophagy inhibition in patients with resectable and borderline resectable PDAC, which demonstrated increased Evans Grade histopathologic and serum CA 19-9 response with autophagy inhibition (IRB 13-074, NCT01128296 ). Utilizing the resected FFPE tumor specimens from evaluable patients, we completed paired multiplex immunohistochemistry (CD4, CD8, FOXP3, CD20, CD68, Pan-CK) and T & B cell receptor RNA sequencing to assess the intratumoral adaptive immune response and correlates of outcome. Results: Autophagy inhibition increased the number of infiltrating CD8 T cells (1133±490 vs 712±460 average cells per high power field, p = 0.01), CD8:CD20 ratio (2.22±3.1 vs 0.96±1.1, p = 0.02) and reduced the CD4:CD8 ratio (2.04±0.87 vs 3.01±2.09, p = 0.03). No effect was observed on the number of immature or mature germinal center-like tertiary lymphoid structures (TLS), though the number of TLS correlated with increased infiltration of CD4 T cells (r = 0.40, p < 0.001), T-regulatory cells (r = 0.26, p = 0.03) and CD20 B cells (r = 0.65, p < 0.001). Although the total number of productive T and B cell receptors increased with autophagy inhibition (167217±105961 vs 97339±5,1628, p = 0.02), no apparent effects were observed on Vαβ TCR or BCR IgH, Igκ, Igλ clonality. Independent of treatment, intratumoral CD8 counts were associated with an improved CA 19-9 response (r = 0.32, p = 0.04) and in a subset of short term ( < 2 years, n = 17) and long term ( > 4 years, n = 10) survivors (LTS), a lowered CD4:CD8 ratio was identified in LTS (1.83±0.63 vs 2.8±0.90, p = 0.01). Dominance of B cell receptors was a prominent feature of the immune repertoire in all patients (average expression: Vα 0.6%, Vβ 0.8%, IgH 18.9%, Igκ 32.3%, Igλ 47.2%) with an IgA skewed immunoglobulin class switching (mean 63% of all BCRs). Increased αβ T cell receptor clonality above the median level was associated with a CA 19-9 response (r = 0.37, p = 0.06) and greater overall survival (median OS 38.3 vs 19.3 months, p = 0.02), indicative of possible tumor specific clonal expansion. Conclusions: Preoperative autophagy inhibition increased the number of tumor infiltrating CD8 T cells in patients with localized pancreatic cancer. Intratumoral αβ T cell receptor clonality was associated with CA 19-9 response and improved overall survival. Combination treatment regimens increasing PDAC specific CD8 responses are warranted. Clinical trial information: NCT01978184.

Corrigendum: Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients

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Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients

Severe COVID-19 is associated with profound lymphopenia and an elevated neutrophil to lymphocyte ratio. We applied a novel dimer avoidance multiplexed polymerase chain reaction next-generation sequencing assay to analyze T (TCR) and B cell receptor (BCR) repertoires. Surprisingly, TCR repertoires were markedly diminished during the early onset of severe disease but recovered during the convalescent stage. Monitoring TCR repertoires could serve as an indicative biomarker to predict disease progression and recovery. Panoramic concurrent assessment of BCR repertoires demonstrated isotype switching and a transient but dramatic early IgA expansion. Dominant B cell clonal expansion with decreased diversity occurred following recovery from infection. Profound changes in T cell homeostasis raise critical questions about the early events in COVID-19 infection and demonstrate that immune repertoire analysis is a promising method for evaluating emergent host immunity to SARS-CoV-2 viral infection, with great implications for assessing vaccination and other immunological therapies.

Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19

Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.

Full adaptome repertoire analysis of immunotherapy to predict responsiveness and correlation with CD8-LAG3, sLAG3, and hepatocyte growth factor levels in patients with renal cancer

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Background: Aldesleukin (recombinant interleukin-2, IL-2), the first checkpoint inhibitor overcoming Tregs, was FDA-approved for mRCC with a 5-10% rate of durable CRs and 25% ORR. Hydroxychloroquine (HCQ) inhibits autophagy, promoting tumor apoptosis. In murine models, IL-2 and HCQ is associated with diminished toxicity and increased efficacy. We hypothesized that a novel deep seven chain analysis of the TCR and BCR repertoire would correlate with sLAG3, CD8 cytosolic LAG3, and HGF levels, associated with outcomes in RCC patients treated with this regimen. Methods: Patients (pts) received high dose IL-2, 600,000 IU/kg, every 8 hours up to 14 doses/cycle. HCQ was administered orally, starting 2 weeks prior to IL-2 and continued up to one year. The HCQ dose was 600 mg (17pts) or 1200 mg (13pts) daily. A newly available seven chain TCR/BCR Adaptome dimer avoidance multiplex-PCR followed by NextGen Sequencing allowed identification of CDR3’s associated with response and increasing clonal diversity. Results: Of 30 pts in the study, 29 were evaluable for response (3CR, 3PR) with serum samples and seven chain analysis of PBMC with 330x106 total reads of the TCR αβ, TCR γδ, IgH, and κλ light chains. HGF (p < .009) was a significant negative predictor of OS at Day 1 after IL-2 and OS at Day -14 (p < .005). Surprisingly this correlated with the TCRδ/γ ratio (p < .01). Similarly serum sLAG3 and CD8LAG3+ both > median predicted improved PFS (p = 0.019) correlating with total TCRδγ expression, p < .01. Diversity of the TCR αβ but not the TCR γδ nor the IgH, and κλ light chains predicted response, p = .005. Conclusions: IL-2 plus HCQ was well tolerated and clinically active with encouraging increase in the PFS of > 17 months at the 600 mg HCQ dose ( > 4x greater than historical controls). Powerful new technology identifying enhanced responsiveness correlating significantly with diversity of the TCR αβ identifies a novel method for predicting responsiveness to immunotherapy. This unbiased examination of the full repertoire ('Adaptome') measured in the same bioassay correlates with other novel biomarkers and should be widely applicable in the further evolution of immunotherapy. NCT01550367 ; approved as IRB 11-074. Clinical trial information: NCT01550367.

High throughput sequencing of T-cell receptor repertoire using dry blood spots

Background

Immunology research, particularly next generation sequencing (NGS) of the immune T-cell receptor β (TCRβ) repertoire, has advanced progression in several fields, including treatment of various cancers and autoimmune diseases. This study aimed to identify the TCR repertoires from dry blood spots (DBS), a method that will help collecting real-world data for biomarker applications.

Methods

Finger-prick blood was collected onto a Whatman filter card. RNA was extracted from DBS of the filter card, and fully automated multiplex PCR was performed to generate a TCRβ chain library for next generation sequencing (NGS) analysis of unique CDR3s (uCDR3).

Results

We demonstrated that the dominant clonotypes from the DBS results recapitulated those found in whole blood. According to the statistical analysis and laboratory confirmation, 40 of 2-mm punch disks from the filter cards were enough to detect the shared top clones and have strong correlation in the uCDR3 discovery with whole blood. uCDR3 discovery was neither affected by storage temperatures (room temperature versus − 20 °C) nor storage durations (1, 14, and 28 days) when compared to whole blood. About 74–90% of top 50 uCDR3 clones of whole blood could also be detected from DBS. A low rate of clonotype sharing, 0.03–1.5%, was found among different individuals.

Conclusions

The DBS-based TCR repertoire profiling method is minimally invasive, provides convenient sampling, and incorporates fully automated library preparation. The system is sensitive to low RNA input, and the results are highly correlated with whole blood uCDR3 discovery allowing study scale-up to better understand the relationship and mutual influences between the immune and diseases.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1796-4) contains supplementary material, which is available to authorized users.

Identification of paired heavy and light chains from single B-cells from immunized Malian adults with rapid functional confirmation using iPair-BCR™, NGS, and iScreen™

Information about the cognate pairing of TCR alpha-beta chains and BCR IgH and IgKL chains encoded by individual T and B cells is key to understanding adaptive immune responses and developing therapeutic applications. We have previously reported the development of a sensitive technology that allows the amplification and identification of the paired human TCR alpha and beta chains from single T cells, termed iPair-TCR. Here, we report the extension of this technology to identify paired human BCR IgH and IgKL chains from antigen-specific single B cells. In this proof of concept study, we identified paired-VDJ-receptors from antigen-specific B-cells from nine Pfs230-EPA immunized Malian adults using the iPair-BCR method. Next, we developed a method to rapidly generate Fab fragments and demonstrate the binding of several of these single cell targets to the original Pfs230 antigen. Single cells of interest were identified based upon their repeated frequency on the plate, which indicates a clonal selection. The corresponding heavy and light chains were PCR amplified from selected wells. Using overlap extension PCR, all necessary elements for in vitro transcription and translation and either the CH1 or C-kappa-domain were added to both the 5′ and 3′ ends of the single cell VDJ. After in vitro transcription and translation, four out of five tested Fab fragments demonstrated binding through a colorimetric ELISA assay. The overall process after VDJ identification can be performed in under a week indicating the utility of our technology for rapid identification of antigen-specific BCRs and functional binding characteristics.

Recombinant production, crystallization and preliminary X-ray analysis of PCNA from the psychrophilic archaeon Methanococcoides burtonii DSM 6242

Proliferating cell nuclear antigen (PCNA) is a DNA-clamping protein that is responsible for increasing the processivity of the replicative polymerases during DNA replication and repair. The PCNA from the eurypsychrophilic archaeon Methanococcoides burtonii DSM 6242 (MbPCNA) has been targeted for protein structural studies. A recombinant expression system has been created that overproduces MbPCNA with an N-terminal hexahistidine affinity tag in Escherichia coli. As a result, recombinant MbPCNA with a molecular mass of 28.3 kDa has been purified to at least 95% homogeneity and crystallized by vapor-diffusion equilibration. Preliminary X-ray analysis revealed a trigonal hexagonal R3 space group, with unit-cell parameters a = b = 102.5, c = 97.5 angstrom. A singleMbPCNA crystal was subjected to complete diffraction data-set collection using synchrotron radiation and reflections were measured to 2.40 angstrom resolution. The diffraction data were of suitable quality for indexing and scaling and an unrefined molecular-replacement solution has been obtained.

Expression, purification and preliminary X-ray analysis of proliferating cell nuclear antigen from the archaeon Thermococcus thioreducens

Proliferating cell nuclear antigen (PCNA) is a DNA sliding clamp which confers processivity on replicative DNA polymerases. PCNA also acts as a sliding platform that enables the association of many DNA-processing proteins with DNA in a non-sequence-specific manner. In this investigation, the PCNA from the hyperthermophilic archaeon Thermococcus thioreducens (TtPCNA) was cloned, overexpressed in Escherichia coli and purified to greater than 90% homogeneity. TtPCNA crystals were obtained by sitting-drop vapor-diffusion methods and the best ordered crystal diffracted to 1.86 A resolution using synchrotron radiation. The crystals belonged to the hexagonal space group P6(3), with unit-cell parameters a = b = 89.0, c = 62.8 A. Crystals of TtPCNA proved to be amenable to complete X-ray analysis and future structure determination.

PCR-based gene synthesis to produce recombinant proteins for crystallization

BACKGROUND

Gene synthesis technologies are an important tool for structural biology projects, allowing increased protein expression through codon optimization and facilitating sequence alterations. Existing methods, however, can be complex and not always reproducible, prompting researchers to use commercial suppliers rather than synthesize genes themselves.

RESULTS

A PCR-based gene synthesis method, referred to as SeqTBIO, is described to efficiently assemble the coding regions of two novel hyperthermophilic proteins, PAZ (Piwi/Argonaute/Zwille) domain, a siRNA-binding domain of an Argonaute protein homologue and a deletion mutant of a family A DNA polymerase (PolA). The gene synthesis procedure is based on sequential assembly such that homogeneous DNA products can be obtained after each synthesis step without extensive manipulation or purification requirements. Coupling the gene synthesis procedure to in vivo homologous recombination techniques allows efficient subcloning and site-directed mutagenesis for error correction. The recombinant proteins of PAZ and PolA were subsequently overexpressed in E. coli and used for protein crystallization. Crystals of both proteins were obtained and they were suitable for X-ray analysis.

CONCLUSION

We demonstrate, by using PAZ and PolA as examples, the feasibility of integrating the gene synthesis, error correction and subcloning techniques into a non-automated gene to crystal pipeline such that genes can be designed, synthesized and implemented for recombinant expression and protein crystallization.