Characterization of Mesenchymal Cell from BAL of post COVID-19 patient whit fibrosis

Increasing number of severe COVID 19 patients develop pulmonary Fibrosis, but the management of this complication is still unclear due to a lack of clinical trials. Aim of this study was to characterize mesenchymal cells (MC) isolated from 10 broncho-alveolar lavage (BAL, at 2 months after discharge) from patients with COVID19 fibrosis (COVID19-f) and to compare them with those isolated from 8 patients with collagen tissue diseaseassociated interstitial fibrosis(CTD-ILD). BAL fluid (BALf) levels of TGFbeta, VEGF, TIMP2, RANTES, IL6, IL8, and PAI1 were assessed by ELISA. Primary MC foci were cultured and expanded in D-MEM +10% FBS, characterized by flow cytometry and osteogenic and adipogenic differentiation. Collagen 1 production (+/-TGF-beta) was tested by WB and mRNA expression. BALf cytokine and GF levels were comparable in the two groups. Efficiency of MC isolation from BAL was 100% in COVID-f compared to 65% in CTD-ILD. MC antigen surface expression of CD105, CD73, CD90 (>90%, respectively), CD45, CD34, CD19 and HLA-DR (<5%, respectively) was comparable. None of MC samples differentiated in adipocytes, while COVID19-f were positive for calcium deposition. COVID19-f MC showed at WB, higher Collagen 1 production with respect to CTD-ILD with TGF-beta stimulation. Our preliminary data suggest MC from COVID19-f share several features with CTD-ILD but might have a higher response to fibrogenic and differentiation signals.

A Method to Monitor Activity of SARS-CoV-2 Nsp3 from Cells

SARS-CoV-2 protease Nsp3 is a therapeutic target for developing anti-SARS-CoV-2 drugs. Nsp3 is a large multi-spanning membrane protein, and its characterization in vitro has been challenging. Here we describe an in vitro assay to characterize the biochemical activity of full-length Nsp3 isolated from cells. The assay can be used to evaluate Nsp3 inhibitors. © 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

B-cell ELISpot assay to analyze human memory B cell and plasmablast responses specific to SARS-CoV-2 receptor-binding domain.

B-cell ELISpot is an extremely sensitive assay based on the secretion of antibodies by B cells that requires the differentiation of B cells into antibody-secreting cells. Here, we describe the procedure to analyze both plasmablast (PB) and memory B cell (MBC) responses specific to SARS-CoV-2 receptor-binding domain (RBD) in the context of acute SARS-CoV-2 infection and vaccination. We detail steps for MBC stimulation, MBC and PB plating, detection, and counting of total IgG and RBD-specific spots. For complete details on the use and execution of this protocol, please refer to Tay et al. (2022).1.

Imaging tumor-infiltrating CD8+ T-cells in non-small cell lung cancer patients upon neo-adjuvant treatment with durvalumab

Aim/Introduction: Immune checkpoint inhibitors (ICI), like targeting programmed death receptor ligand 1 (PD-L1), have revolutionized anti-cancer treatments, including non-small cell lung cancer (NSCLC) [1, 2]. Assessment of PD-L1 expression on tumor biopsies is current practice, but there is a need for additional biomarkers correlating to the complex mechanism of action of ICI. The presence of tumorinfiltrating CD8+ T-cells (TILs) is a robust biomarker associated with immune therapy success [3]. Tools to track TILs in patients during ICI treatment allow further development of immune-oncology drugs. Material(s) and Method(s): This ongoing single-center prospective study (NCT03853187) includes patients with histologically proven T1b-3N0-1M0 NSCLC eligible for resection. Exclusion criteria are previous anti-cancer therapy and known immune disorders or suppression. Patients receive two courses neo-adjuvant durvalumab (750mg Q2W), after which TIL imaging is performed. Cohort 1 underwent apheresis and magnetic-activated cells sorting to isolate 100 x10e6 autologous CD8+ T-cells for cell labeling with 111In-oxine. Re-injection was followed by 4h post-injection (p.i.) planar imaging, 70h p.i. SPECT imaging, standard-of-care surgery and 78h p.i. uSPECT of the resected lobe. Patients in cohort 2 (ongoing) receive 1.5mg 89Zr-Df-crefmirlimab followed by PET/CT 24h p.i. Result(s): In cohort 1, 8/10 patients underwent apheresis and TIL imaging;one procedure was withdrawn due to COVID-19 restrictions and one due to unsuccessful T-cell isolation. Yield ranged 240-714 x10e6 CD8+ T-cells, purity 84%-97% and cell viability 92%-100%. Labeling efficacy of 100 x10e6 cells for re-injection ranged 42%-64% and injected activity 22,4-36,7 MBq In-111.TIL imaging was completed by 4/5 patients in cohort 2, one subject discontinued neo-adjuvant treatment due to post-obstruction pneumonia.Tumor-to-bloodpool were determined to quantify specific TIL accumulation in the tumor. Our results favor quantification of T-cells on PET over SPECT given its higher sensitivity and spatial resolution. Correlation of imaging findings with density of CD8+ T-cells in the resected tumor is currently ongoing. Conclusion(s): We implemented two methods for tracking CD8+ T-cells in earlystage NSCLC patients after neo-adjuvant durvalumab treatment. Although ex vivo cell labeling perhaps more specifically targets migrating TILs into the tumor, 89Zr-Df-crefmirlimab has the potential to also target residing cells. Quantitative correlation with presence of TILs in the resected tumor will help to determine the role of these imaging tools in the development of immune-oncology drugs.

Higher Post-COVID-19 Urinary Mitochondrial DNA Level: Serves a Biomarker of Mitochondrial Distress and Inducer of Inflammatory Cytokines Secretion in Peripheral Blood Mononuclear Cells (PBMCs)

Background: Severe acute respiratory corona virus-2(SARS-CoV-2) affected multiple organs including Kidney. SARS-CoV-2 open reading frame protein 3a induces necroptosis in infected cell leading release of mt-DNA, which binds to TLR9 and trigger innate immunity, which may lead to acute allograft injury. Method(s): Sixty-six live related renal allograft recipient previously hospitalized with SARS-CoV-2 infection were recruited after 2-3week of discharge. Patients were categorized either in non-AKI(n=47) or AKI(n=19) group, if hospitalization serum creatinine level was >30% of preCovid serum creatinine. A 50ml urine sample was collected for the umt-DNA gene NADH-ubiquinone oxidoreductase chain1(ND-1) and nuclear 36B4 gene quantification by RT-PCR and urine N-GAL measurement by ELISA. A 10ml blood sample from 10healthy volunteers was collected for PBMCs isolation. A 1x106 PBMCs were stimulated for 24hrs. with 1mug/ml of urinary DNA or CpG oligodeoxynucleotide(5'-tcgtcgttttcggcgc:gcgccg-3') in duplicate. Unstimulated PBMCs served as control. The gene expression of IL-10, IL-6, MYD88 was analyzed by the RT-PCR and IL-6, IL-10 level in supernatants by the ELISA. Result(s): The precovid creatinine in non-AKI vs AKI patient was 1.06+/-0.20vs0.97+/-0.27, p=.14;at hospitalization 1.27+/-0.18vs1.84 +/-0.37, p<.001;at discharge 1.09+/-0.20vs1.11+/-0.32mg/dl, p=0.73. The mean ND-1 gene Ct in non-AKI vs AKI was 21.77+/-3.60vs19.44+/-2.58a.u, p=.013. The normalized ND-1 Ct in non-AKI vs AKI was 0.89+0.14vs0.79+/-0.11a.u, P=0.007. The median urinary N-GAL level in non-AKI vs AKI group was 212.78 (range, 219.8-383.06) vs 453.5 (range, 320.2-725.02;p=0.015) ng/ml. The area under curve of ND-1 Ct gene was 0.73, normalized ND-1 Ct was 0.71, uNGAL was 0.66 and normalized uNGAL was 0.68 for detecting the AKI. The IL-10 gene expression was downregulated in umt-DNA treated PBMCs compared to control (-3.5+/-0.40vs1.02+/-0.02, p<0.001). IL-6 and Myd88 gene expression was upregulated. The culture supernatant IL-10 and IL-6 level in umt-DNA treatment PBMCs vs control was 10.65+/-2.02 vs 30.3+/-5.47, p=0.001;and 200.2+/-33.67 vs 47.6+/-12.83, p=0.001 respectively. Conclusion(s): Quantification of umt-DNA can detect the post covid19 mitochondrial distress with higher sensitivity compare to uNGAL. umt-DNA induces robust inflammatory response in PBMCs may exacerbate the post-Covid19 allograft injury.

Protocol for isolation and characterization of lung tissue resident memory T cells and airway trained innate immunity after intranasal vaccination in mice.

Vaccination route dictates the quality and localization of immune responses within tissues. Intranasal vaccination seeds tissue-resident adaptive immunity, alongside trained innate responses within the lung/airways, critical for superior protection against SARS-CoV-2. This protocol encompasses intranasal vaccination in mice, step-by-step bronchoalveolar lavage for both cellular and acellular airway components, lung mononuclear cell isolation, and detailed flow cytometric characterization of lung tissue-resident memory T cell responses, and airway macrophage-trained innate immunity. For complete details on the use and execution of this protocol, please refer to Afkhami et al. (2022).

Transcriptome profiling of PBMCs and formalin-fixed autopsy tissues from COVID-19 patients.

Here we present an optimized protocol for transcriptome profiling of COVID-19 patient samples, including peripheral blood mononuclear cells (PBMCs) and formalin-fixed paraffin-embedded tissue samples obtained from the lung, liver, heart, kidney, and spleen, with the matched controls. We describe RNA extraction and subsequent transcriptome analysis using NanoString technology of the patient samples. The protocol provides information about sample preparation, RNA extraction, and NanoString profiling and analysis. It can be also applied to differentiated Th17 and Treg subsets or formalin-fixed colon tissue samples. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

Optimization of antigen-specific CD8+ T cell activation conditions for infectious diseases including COVID-19.

Here, we describe the use of the artificial antigen-presenting cell (aAPC) system for the verification of T-cell epitopes. We purify and activate CD8+ T cells from blood samples from HLA-A2 that are negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). CD8+ T cells are combined with peptide-loaded T2-A2 cells, which are then stained with a SARS-CoV-2-specific MHC-1 tetramer to identify specific HLA-A2-restricted T-cell epitopes. The use of aAPC and healthy donors means that only BSL2 lab conditions are needed. For details of the use and implementation of this protocol, please refer to Deng et al. (2021).

Infecting human hematopoietic stem and progenitor cells with SARS-CoV-2.

Determining how hematopoietic stem and progenitor cells (HSPCs) can be infected by viruses is necessary to understand and predict how the immune system will drive the host response. We present here a protocol to analyze the capacity of SARS-CoV-2 to infect different subsets of human HSPCs, inlcuding procedures for SARS-CoV-2 production and titration, isolation of human HSPCs from different sources (bone marrow, umbilical cord, or peripheral blood), and quantification of SARS-Cov-2 infection capacity by RT-qPCR and colony forming unit assay. For complete details on the use and execution of this protocol, please refer to Huerga Encabo et al. (2021).

Ex vivo assay to evaluate the efficacy of drugs targeting sphingolipids in preventing SARS-CoV-2 infection of nasal epithelial cells.

This protocol enables the testing of drugs against infection of epithelial cells with SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), using pseudo-typed replication deficient vesicular stomatitis virus particles (pp-VSV) presenting the SARS-CoV-2 spike protein. After treating human volunteers with amitriptyline, an approved antidepressant and inhibitor of the acid sphingomyelinase, freshly isolated nasal epithelial cells were infected ex vivo and infection levels were quantified. This protocol offers the possibility to rapidly test the efficacy of potential drugs in the fight against COVID-19. For complete details on the use and execution of this protocol, please refer to Carpinteiro et al. (2020).