Patients and Ethics
This prospective study was conducted at Peking Union Medical College Hospital during October 2023 to July 2024. A total of 41 healthy donors with age-and sex-matched were enrolled as HCs group. Those with any of the following circumstances were excluded: 1) chronic cardiac, liver, renal, lung, immunodeficiency disease; 2) infection in the last three months; 3) history of tumor disease; 4) Pregnant or lactating women.
Patients aged between 18 and 70 years old who met the diagnosis of septic shock according to sepsis 3.0 criteria were included in this study[29]. Exclusion criteria included any of the following: 1) patients diagnosed with septic shock more than 48 hours on admission; 2) the maximum dose of norepinephrine less than 0.1ug/kg/min; 3) patients with other types of shock (such as cardiogenic shock, hypovolemic shock or anaphylactic shock) at the same time; 4) patients suffering from hematological malignancies, solid organ tumors, hematopoietic stem cell transplantation, solid organ transplantation, immunodeficiency diseases, autoimmune diseases, chronic allergic diseases, or systemic chronic inflammation; 5) use of any kind of immunomodulators or immunosuppressive drugs, cytotoxic drugs or corticosteroids within the past 3 months; 6) patients with acute infection or acute allergy within the past 3 months; 7) female patients who are pregnant or breastfeeding.
Approval was obtained from Ethics Committee of Peking Union Medical College Hospital (JS-3480D). Informed consent was obtained from the participants or their authorized individuals. ln this study, all processes comply with the 1964 Declaration of Helsinki and its later amendments.
B cell Isolation
PBMCs were isolated by Ficoll-Hypaque density-gradient centrifugation and labeled with CD19 Microbeads (Miltenyi Biotec). B cells were isolated by positive selection using LS column and magnetic bead separator. The viability of isolated B cells > 90%.
Bulk RNA-sequencing and data analysis
Total RNA was extracted from CD19+ B cells of three patients with septic shock and four age-, sex- matched HCs. RNA sequencing was performed by Biomarker Technologies on an Illumina NovaSeq platform (Beijing, China). The raw reeds were processed with BMKCloud (www.biocloud.net) online platform using a bioinformatic pipelinetool. Packages limma (V3.58.1) was used to analyzed DEGs in the R environment. DEGs were determined by absolute (log2Foldchange) > 1.5 and adjusted p value < 0.05. The package clusterProfiler (V4.10.0) was used to conduct the KEGG pathway analysis[30]. Data was visualized with the packages ggplot2 (V3.4.4) in the R environment.
Flow cytometry
For surface staining, 2×106/100 µl cells were stained with surface antibody for 20 minutes at room temperature. The antibody was used as follows: FITC-conjugated anti-human CD38, APC-conjugated anti-human CD27, PE-Cy7-conjugated anti-human CD19 (Biolegend, USA). After surface staining, cells were washed twice with PBS and the Foxp3 Transcription Factor Staining Buffer Set (Invitrogen) was used for PE-conjugated anti-human Ki67 (Biolegend, USA) for intracellular staining. Cell apoptosis rate was measured using a FITC/PE Annexin V Apoptosis Detection Kit (BD, Biosciences) following the manufacturer’s instructions. Samples were analyzed on BD LSRFortessa (BD Biosciences) and data was analyzed using FlowJo software (TreeStar, USA).
Single-cell data sequencing and data analysis
Purified CD19+ B cells from five patients with septic shock and five age-, sex-matched HCs were collected for scRNA-seq using the V3.1 single-cell reagent kit (10 × Genomics) and sequenced by Biomarker Technologies on an Illumina NovaSeq platform (Beijing, China). Raw data were processed following the standard Chromium Cell Ranger pipeline (V4.0.0) against the GRCh38 human reference genome. Samples were merged and data analysis were conducted using the Seurat package (V5.0.1) in the R (V4.3.2) environment as described previously[31, 32]. We utilized the scRepertoire (V1.12.0) for BCR analysis in the dataset. Paired scBCR-seq data were integrated with scRNA-seq based on their matched unique cell barcodes.
Western blotting
Cells were lysed with RIPA lysis buffer mixed with protease inhibitor cocktail (Beyotime, China). The total protein concentration was quantified using a BCA protein assay kit (ThermoFisher, USA). After separation by SDS-PAGE, the proteins were transferred onto a PVDF membrane (Millipore, USA). The membrane was then blocked with 5% bovine serum albumin (BSA) for 1 hour at room temperature and incubated with primary antibodies overnight at 4°C. Subsequently, the membrane was washed three times and incubated with horseradish peroxidase (HRP)-conjugated secondary antibody (1:5000) for 1 hour at room temperature. The results were visualized by enhanced chemiluminescence (Peirce) and signals were read and analyzed using Image Lab software (Bio-Rad). Primary antibody was used as follows: ADM (Proteintech, Cat#10778-1-AP); DEPDC1 (Abcepta, Cat#AP5428a); KIF18B (Immunoway, Cat#YN5266); SOCS3 (Abcam, Cat#ab280884); CA8 (Proteintech, Cat#12391-1-AP); RRM2 (Proteintech, Cat#11661-1-AP); MMP2 (Abcam, Cat#ab92536); Akt (Abcam, Cat#ab32505); p-Akt (Abcam, Cat#ab192623).
RNA interference
Small interfering RNA was purchased from RIBOBIO (Guangzhou, China): RRM2 targeting siRNA (5’-CGUCGAUAUUCUGGCUCAATT-3’; 5’-UUGAGCCAGAAUAUCGACGTT-3’), CA8 targeting siRNA (5’- GCACACGGUUAAUUUCAAATT-3’; 5’-UUUGAAAUUAACCGUGUGCTT-3’). SF Cell Line 4D-Nucleofector X Kit L was used (Lonza, V4XC-2024) and transfection was conducted on Lonza 4D Nucleofection System (Lonza, Germany) following the manufacturer’s guidelines.
Cell counting kit-8
ARH77 cell lines were seeded in a 96-well plate (Corning Life Sciences, USA) and 10 µl CCK8 reagent (Dojindo, China) was added for 2 h of incubation. The absorbance at 450 nm was measured using a microplate reader (Biorad, USA).
Transmission Electron Microscopy
CD19+ B cells were freshly isolated and fixed with 2.5% glutaraldehyde in 0.1 M Sorenson’s buffer for 3 hours, the images were examined under the TME-1400 plus electron microscope at 5,000–50,000-fold magnification.
Statistical analysis
The graphs and statistical analysis in this study was conducted in Graphpad Prism (V9.0). Data were present as mean ± standard deviation. Normal distribution was tested. Student’s t test was used for normal distributed data, otherwise the Mann-Whitney test was used. P < 0.05 was considered statistically significant.