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Series GSE265785

Query DataSets for GSE265785

Status

Public on Jul 31, 2024

Title

Characterization of HBV and co-infection with HDV and HIV through spatial transcriptomics

Organism

Homo sapiens

Experiment type

Other

Summary

Background and aims: The intrahepatic processes associated with chronic hepatitis B (CHB), especially in the context of HDV and HIV co-infection, require a better understanding. Spatial transcriptomics can provide new insights into the complex intrahepatic biological processes, guiding new personalized treatments. Our aim is to evaluate this method to characterize the hepatic transcriptional landscape, cellular composition and biological pathways in liver biopsy samples from patients infected with HBV and HDV or HIV co-infection. Method: The GeoMx nanostring Digital Spatial Profiling (DSP) platform was employed to assess expression of HBsAg and CD45 in formalin fixed paraffin embedded (FFPE) biopsies from three treatment-naïve patients with chronic HBV and HDV or HIV co-infection. The GeoMx whole transcriptome human atlas assay quantified the expression of genes enriched in specific regions of interest (ROIs). Cell type proportions within ROIs were deconvoluted using a training matrix from the human liver cell atlas. A weighted gene correlation network analysis (WGCNA) evaluated transcriptomic signatures across sampled regions. Results: We identified spatially discrete transcriptomic signatures and distinct biological pathways that associate with HBV infection/disease status and immune responses. Shared features including cytotoxicity and B cell receptor signaling were consistent across patients, suggesting common elements alongside individual traits. HDV/HBV co-infection exhibited upregulated genes linked to apoptosis and immune cell recruitment, whereas HIV/HBV co-infection featured genes related to interferon response regulation. Varied cellular characteristics and immune cell populations, with an abundance of T cells in the HDV/HBV sample, were observed within analyzed regions. Transcriptional differences in hepatocyte function suggest disrupted metabolic processes in HDV/HBV co-infection potentially impacting disease progression. Conclusion: This proof-of-principle study shows the value of this platform in investigating the complex immune landscape highlighting relevant host pathways to disease pathogenesis.

Overall design

Archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from three patients with chronic HBV (PT1), one with HDV/HBV co-infection (PT2) and one patient with HIV/HBV (PT3) co-infection were analyzed in this study. Participants were recruited at The Royal London Hospital, Barts Health NHS Trust and samples were obtained during routine diagnostic procedures following written informed consent. Slides were submitted for Digital Spatial Profiling (DSP) and whole transcriptome sequencing, according to the manufacturer’s recommendations for GeoMx-NGS RNA BOND RX slide preparation (manual no. MAN-10131-02). The panel of morphology markers was designed to include HBsAg ((Polyclonal) 488 1:200 from Bioss #bs-1557G-A488), CD45 (D9M8I) 594 1:100 from Cell Signaling Technology #13917BF, CD3 (clone UMAB54; Origene #UM500048CF) and a DNA dye (Syto83dye; Invitrogen). Deparaffinization, rehydration, heat-induced epitope retrieval (for 20 minutes at 100°C), and enzymatic digestion (1 μg/mL proteinase K for 15 minutes at 37°C) were carried on the Leica BOND-RX. Tissues were incubated with 10% neutral buffered formalin for 5 minutes and for 5 minutes with NBF Stop buffer. The tissue sections were hybridized with the oligonucleotide probe mix (whole Transcriptome Atlas) overnight, then blocked and incubated with the four fluorescently labelled markers for 1 hour. Tissue sections were loaded into the GeoMx platform and scanned for an immunofluorescent signal.

*** FASTQ raw data files have been requested. ***

Contributor(s)

Peppa D

Citation(s)

39149129

Submission date

Apr 24, 2024

Last update date

Aug 21, 2024

Contact name

Dimitra Peppa

Organization name

University College London