Human study participants
Patients undergoing orthotopic liver transplantation at Emory Transplant Center of Emory University Hospital were enrolled in the study in accordance with the Emory University Institutional Review Board (IRB) approval (IRB #00100485). HCV-infected samples utilized in the current study are from individuals chronically infected with HCV without HIV coinfection. Patient characteristics with clinical information and relevant biological variables are summarized in Supplementary Table 1. Written informed consent was obtained from each individual and IRB #00100485 conforms to the guidelines of the 1975 Declaration of Helsinki (revised 2013). Additional human liver samples were obtained in accordance with the protocol approved by the Mass General Brigham IRB, protocol nos. 1999P004983 and 2004P000793.
Animals and ethics statement
C57BL/6J and B6.129P2-Aicdatm1(cre)Mnz/J (AIDcre/cre) mice were obtained from Jackson Laboratories. B6.129P2[C]-Ightm2Cgn/J (B1-8i) mice were obtained from J. Jacob. Predetermined sample size calculations and blinding were not performed, as number of individual data points and experimental design were determined based on experiment type to generate interpretable, reproducible conclusions. Regarding randomization, age-matched mice of identical strains ordered from commercial vendors were randomly divided into cages by animal care staff upon arrival at vivarium facilities. Mice were six to ten weeks of age at the time of study initiation. All biohazard and animal experiments were carried out in accordance with approved protocols from the Emory Institutional Animal Care and Use Committee (IACUC #201700372).
Viruses and infections
RHV inoculum was generated in vivo following serial passage and adaptation to the mouse host. Mice were infected with RHV via retroorbital injection unless otherwise specified with 105 viral genome equivalents. Lymphocytic choriomeningitis virus (LCMV) Armstrong was infected intraperitoneally with 2 × 105 plaque-forming units (PFU) per mouse and LCMV clone 13 was infected via retroorbital injection with 2 × 106 PFU per mouse.
FTY720 treatment and CD40L blockade
To prevent lymphocyte egress from SLOs, FTY720 (Sigma) was administered at a final concentration of 1 mg kg−1 and injected intraperitoneally three times weekly. To disrupt CD40–CD40L signalling, 250 μg anti-CD154 (CD40L, clone MR1, InVivoMab) was injected intraperitoneally 3 times weekly.
Disruption of associative anchor molecules
For assessing the functional role of cognate associa designated slide area. These slides were processed tive anchoring pairs on intrahepatic plasma cell retention, interventional treatments were acutely administered intraperitoneally at 200 μg each on days 26 and day 27 post-infection, after which ASC enumeration was conducted at day 28 post-infection. Such interventions included specified combinations of anti-CD49d (VLA-4, clone PS/2, InVivoMab), anti-CD11a (LFA-1, clone M17/4, InVivoMab), anti-SPP1 (osteopontin, clone 103D6, InVivoMab), and AMD3100 octahydrochloride (Tocris Bioscience). Persistent disruption of such factors was achieved via administration of such treatment at 100 μg 3 times weekly beginning at day 11 post-infection, again being assessed for intrahepatic ASC generation at day 28 post-infection.
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