Gene Expression
Nebulas
Gene Expression NebulasSummary: Regulatory KIR+RA+ T cells accumulate with age and are highly activated during viral respiratory disease
Overall Design: Severe respiratory viral infectious diseases such as influenza and COVID- 19 espe-cially affect the older population. This is partly ascribed to diminished CD8+ T- cell re-sponses a result of aging. The phenotypical diversity of the CD8+ T- cell population has made it difficult to identify the impact of aging on CD8+ T- cell subsets associated with diminished CD8+ T- cell responses. Here we identify a novel human CD8+ T- cell subset characterized by expression of Killer- cell Immunoglobulin-l ike Receptors (KIR+) and CD45RA (RA+). These KIR+RA+ T cells accumulated with age in the blood of healthy individuals (20– 82 years of age, n = 50), expressed high levels of aging- related mark-ers of T- cell regulation, and were functionally capable of suppressing proliferation of other CD8+ T cells. Moreover, KIR+RA+ T cells were a major T- cell subset becoming activated in older adults suffering from an acute respiratory viral infection (n = 36), including coronavirus and influenza virus infection. In addition, older adults with influ-enza A infection showed that higher activation status of their KIR+RA+ T cells associ-ated with longer duration of respiratory symptoms. Together, our data indicate that KIR+RA+ T cells are a unique human T- cell subset with regulatory properties that may explain susceptibility to viral respiratory disease at old age.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | FACS- sorted TNAIVE, TEMRA, KIR+RA+, and NKG2A+RA+ T- cell sub-sets of six healthy donors (ages: 30, 57, 61, 63, 65, 66 years) were centrifuged at 485 g for 15 min and lysed in buffer RLT (Qiagen) containing 1% β- mercaptoethanol. Total RNA was extracted from the cell lysates by using the RNeasy kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed by using the RNA 6000 Pico kit (Agilent Technologies) on a 2100 BioAnalyzer (Agilent Technologies). All RNA Integrity Number (RIN) scores were >7 DNA synthesis and amplification were performed by using the SMART- Seq® v4 Ultra® Low Input RNA kit for sequencing (Takara) and AMPure XP beads (Beckman Coulter) were used to purify the samples. Proper size distribution of the fragments acquired was veri-fied using the High Sensitivity DNA kit (Agilent Technologies). Next, 1 ng of cDNA was used to prepare a Nextera XT DNA library accord-ing to the manufacturer’s instruction (Illumina). |
| Library Construction Protocol: | Libraries were sub-sequently validated for fragment size using QIAxcel DNA Screening Kit (Qiagen) and quantified using RT- qPCR with a KAPA Library Quantification kit (KK4824, Roche/KAPA Biosystems). 23 librar-ies were pooled at equimolar concentrations and sequenced using the Illumina NextSeq 500/550 High Output Kit v2.5 (single- end, 75 cycles) |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | SINGLE |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NextSeq 500 |
| Strand-Specific: | unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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