Environmental Restrictions: A New Concept Governing HIV-1 Spread Emerging from Integrated Experimental-Computational Analysis of Tissue-Like 3D Cultures

Abstract

HIV-1 can use cell-free and cell-associated transmission modes to infect new target cells, but how the virus spreads in the infected host remains to be determined. We recently established 3D collagen cultures to study HIV-1 spread in tissue-like environments and applied iterative cycles of experimentation and computation to develop a first in silico model to describe the dynamics of HIV-1 spread in complex tissue. These analyses (i) revealed that 3D collagen environments restrict cell-free HIV-1 infection but promote cell-associated virus transmission and (ii) defined that cell densities in tissue dictate the efficacy of these transmission modes for virus spread. In this review, we discuss, in the context of the current literature, the implications of this study for our understanding of HIV-1 spread in vivo, which aspects of in vivo physiology this integrated experimental–computational analysis takes into account, and how it can be further improved experimentally and in silico.

HCV Spread Kinetics Reveal Varying Contributions of Transmission Modes to Infection Dynamics

“…The consistent differences in the results observed when the different serum lots were utilized suggest that the contribution of each transmission mode may be influenced by the environmental conditions encountered. The observation that viral transmission modes were influenced by environmental conditions is in line with observations made for other viruses, such as HIV-1 [ 26 , 32 ], and highlights the utility of trying to incorporating more physiologically relevant conditions and altering other aspects of cell culture environments (e.g., concentrations of lipids, iron, and other components of serum) in future experiments when studying viral spread [ 33 ], as well as accounting for these factors within the mathematical models used to analyze these data.…”

HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics

“…These results suggest that the contribution of each transmission mode may be influenced by the environmental conditions encountered. The observation that viral transmission modes are influenced by environmental conditions is in line with observations made for other viruses, such as HIV-1 [20,21] and highlights the utility of trying to incorporating more physiologically relevant conditions in future experiments when studying viral spread [22]. Arguably, cell proliferation dynamics could have an impact on the efficacy of viral transmission modes.…”

“…The inoculum was then removed, and the wells were rinsed twice with warm cDMEM before adding 200µL fresh cDMEM with 10% FBS. Media and cell lysates were collected from triplicate wells at 0, 3,6,9,12,15,18,21,24,27,30,36,42,48, 72 and hours post inoculation (p.i.). To determine the amount of cell division, cells in parallel wells were counted at 0, 36, 72 and 96 hours post-inoculation.…”

Contact-dependent inhibition of HIV-1 replication in ex vivo human tonsil cultures by polymorphonuclear neutrophils

“…We first tested whether PMNs release NETs in this experimental system, as described to occur in response to high amounts of HIV 1 viral particles and to reduce HIV infectivity. 36 We therefore considered the possibility that HIV-1 particles released in the cell culture supernatant or the local high concentrations of HIV-1 particles at cell-cell contacts formed to transmit the virus from infected donor to uninfected target cells (virological synapse) 40 , 53 , 54 , 55 might trigger a similar response and contribute to the anti-HIV-1 activity in HLACs. Hence, we incubated PMNs with various amounts of HIV particles (between 1 × 10 7 –5 × 10 8 pU RT/μL) and stained these samples for DNA and MPO to detect NETs ( Figures 5 B and S5 A).…”

“… 36 , 37 , 38 Although these studies indicated that PMNs may be able to exert anti-HIV activity, they did not assess whether PMNs impair HIV-1 replication in physiologically relevant target cells and tissue, where virus spread occurs predominately via cell-associated transmission and not cell-free virus particles. 39 , 40 , 41 We therefore set out to study the effects of PMNs on HIV-1 replication in ex vivo cultures of human tonsil tissue and peripheral blood mononuclear cells (PBMCs). We find that PMNs exert immediate and potent anti-HIV-1 activity that requires direct cell-cell contact but is not mediated by any of the classic PMN effector functions described so far.…”