Virus Expression Database

GSE125686

Transcriptomic profiling of peripheral blood NK cells of chronic HBV, HCV and HIV patients

Submitted by Andre Boonstra (Erasmus MC, Netherlands) on Jan 25 2019

Platform: ngs – Illumina HiSeq 2500 (Homo sapiens)

Pubmed: 30185599

Summary Background: NK cells during chronic viral infection have been well studied over the last decade. We performed an unbiased next-generation RNA-sequencing approach to identify commonalities or differences of the effect of HIV, HCV and HBV viremia on NK cell transcriptomes.
Methods: Using cell sorting, we obtained CD3-CD56+ NK cells from blood of 6 HIV, 11 HCV, and 32 HBV infected and untreated patients. Library preparation and sequencing were done using Illumina mRNA-Seq Sample Prep Kit and the HiSeq 2000, HiSeq2500 or NextSeq 500, and further analysis by an in-house analytic pipeline.
Results: In NK cells from HIV, HCV and HBV patients, transcriptome analysis identified 272, 53, and 56 differentially expressed genes, respectively (fold change >1.5, q-value 0.2). Interferon stimulated genes were induced in NK cells from HIV/HCV patients, but not during HBV infection. HIV viremia downregulated ribosome assembly genes in NK cells. In HBV, viral load and ALT variation had little effect on genes related to NK effector function.
Conclusion: We compare, for the first time, NK cell transcripts of viremic HIV, HCV and HBV patients. We clearly demonstrate distinctive NK cell gene signatures in 3 different populations, suggestive for a different degree of functional alterations of the NK cell compartment as compared to healthy individuals.

62 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM3580276 102613-001-003 natural killer cell  chronic HBV Hepatitis B virus
GSM3580277 102613-001-010 natural killer cell  chronic HBV Hepatitis B virus
GSM3580278 102613-001-011 natural killer cell  chronic HBV Hepatitis B virus
GSM3580279 102613-001-004 natural killer cell  chronic HBV Hepatitis B virus
GSM3580280 102613-001-008 natural killer cell  chronic HBV Hepatitis B virus
GSM3580281 102613-001-012 natural killer cell  chronic HBV Hepatitis B virus
GSM3580282 102613-001-013 natural killer cell  chronic HBV Hepatitis B virus
GSM3580283 102613-001-009 natural killer cell  chronic HBV Hepatitis B virus
GSM3580284 103078-001-001 natural killer cell  chronic HCV Hepacivirus C
GSM3580285 102278-14 natural killer cell  chronic HCV Hepacivirus C
GSM3580286 102278-18 natural killer cell  chronic HCV Hepacivirus C
GSM3580287 102278-15 natural killer cell  chronic HCV Hepacivirus C
GSM3580288 102278-16 natural killer cell  chronic HCV Hepacivirus C
GSM3580289 102415-14 natural killer cell  chronic HCV Hepacivirus C
GSM3580290 102415-15 natural killer cell  chronic HCV Hepacivirus C
GSM3580291 102415-16 natural killer cell  chronic HCV Hepacivirus C
GSM3580292 102278-13 natural killer cell  healthy Uninfected
GSM3580293 102278-06 natural killer cell  healthy Uninfected
GSM3580294 102278-12 natural killer cell  healthy Uninfected
GSM3580295 102415-02 natural killer cell  healthy Uninfected
GSM3580296 103078-001-012 natural killer cell  healthy Uninfected
GSM3580297 102415-03 natural killer cell  healthy Uninfected
GSM3580298 102415-04 natural killer cell  healthy Uninfected
GSM3580299 103078-001-004 natural killer cell  healthy Uninfected
GSM3580300 103078-001-005 natural killer cell  healthy Uninfected
GSM3580301 103078-001-006 natural killer cell  healthy Uninfected
GSM3580302 103078-001-007 natural killer cell  healthy Uninfected
GSM3580303 102415-01 natural killer cell  healthy Uninfected
GSM3580304 102613-001-017 natural killer cell  healthy Uninfected
GSM3580305 102613-001-018 natural killer cell  healthy Uninfected
GSM3580306 102613-001-019 natural killer cell  healthy Uninfected
GSM3580307 102613-001-020 natural killer cell  healthy Uninfected
GSM3580308 103078-001-002 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580309 103078-001-003 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580310 103078-001-010 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580311 103078-001-008 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580312 103078-001-009 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580313 103078-001-011 natural killer cell  chronic HIV Human immunodeficiency virus 1
GSM3580314 102278-08 natural killer cell  chronic HBV Hepatitis B virus
GSM3580315 102415-07 natural killer cell  chronic HBV Hepatitis B virus
GSM3580316 102415-06 natural killer cell  chronic HBV Hepatitis B virus
GSM3580317 102415-05 natural killer cell  chronic HBV Hepatitis B virus
GSM3580318 102613-001-014 natural killer cell  chronic HBV Hepatitis B virus
GSM3580319 102613-001-016 natural killer cell  chronic HBV Hepatitis B virus
GSM3580320 102613-001-002 natural killer cell  chronic HBV Hepatitis B virus
GSM3580321 102613-001-015 natural killer cell  chronic HBV Hepatitis B virus
GSM3580322 102415-12 natural killer cell  chronic HBV Hepatitis B virus
GSM3580323 102278-10 natural killer cell  chronic HBV Hepatitis B virus
GSM3580324 102415-10 natural killer cell  chronic HBV Hepatitis B virus
GSM3580325 102415-09 natural killer cell  chronic HBV Hepatitis B virus
GSM3580326 102278-02 natural killer cell  chronic HBV Hepatitis B virus
GSM3580327 102278-03 natural killer cell  chronic HBV Hepatitis B virus
GSM3580328 102278-19 natural killer cell  chronic HBV Hepatitis B virus
GSM3580329 102278-20 natural killer cell  chronic HBV Hepatitis B virus
GSM3580330 102415-08 natural killer cell  chronic HBV Hepatitis B virus
GSM3580331 102278-07 natural killer cell  chronic HBV Hepatitis B virus
GSM3580332 102278-09 natural killer cell  chronic HBV Hepatitis B virus
GSM3580333 102278-11 natural killer cell  chronic HBV Hepatitis B virus
GSM3580334 102613-001-005 natural killer cell  chronic HBV Hepatitis B virus
GSM3580335 102613-001-001 natural killer cell  chronic HBV Hepatitis B virus
GSM3580336 102613-001-007 natural killer cell  chronic HBV Hepatitis B virus
GSM3580337 102613-001-006 natural killer cell  chronic HBV Hepatitis B virus