Unmasking two stages of interferon signaling in dendritic cells infected with HIV-1

Myeloid dendritic cells (DCs) have the innate capacity to sense pathogens and mount counteroffensive responses, which include the production of type I and type III interferons (IFN). In the case of HIV-1 infection, DCs can internalize and present viral antigens, but the majority of DCs are not productively infected due to restriction at the level of reverse transcription. Consequently, DCs do not efficiently ‘sense’ HIV-1, fail to produce IFN, do not mature, and cannot program appropriate adaptive immune responses. To improve our understanding of how IFN and cell maturation are regulated in monocyte-derived DCs, we have used systems analyses to study how DCs respond to HIV-1 after removing the block to reverse transcription with the lentiviral protein Vpx. We have profiled changes in open chromatin during infection using an assay for transposase-accessible chromatin (ATAC-seq), and have tracked the kinetics of gene expression in parallel. Using antiretroviral drugs and virus mutants to separate stages of the life cycle, we have determined that at least two signals cooperate to drive innate immune responses during HIV-1 infection: the first coming from the cytoplasmic sensor, cGAS, which is known to recognize reverse transcribed HIV cDNA, and the second from an unrelated pathway engaged after virus integration. Moreover, by interrogating infection in combination with a battery of classic innate agonists we have found that HIV-1 primes DCs to produce IFN, even in the presence of certain antiretroviral drugs. Our studies demonstrate that robust IFN production in response to HIV-1 infection depends on the coordinated action of distinct transcription factors and illuminate key pathways that regulate innate immunity in myeloid cells.

Determining transcriptional networks regulating the response of alveolar macrophages to Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) continues to be a major global health problem, infecting nearly one-third of the world’s population and leading to around 1.5 million deaths each year. Current drug regimens last 6–9 months and there is still no effective vaccine for adults. It is still not fully understood how innate immune cells first respond to Mtb within the lung.

Alveolar macrophages (AMs) are the first cells in the lung to become infected with Mtb after aerosol exposure. Therefore, these macrophages play a crucial role in establishing the initial inflammatory response to Mtb and the priming environment of the adaptive response. Previously, technical limitations in cell isolation and RNA sequencing restricted gene expression studies of Mtb-infected macrophages to in vitro culture systems. These studies may have missed crucial signaling pathways unique to the immunoregulatory lung environment surrounding AMs.

To investigate the in situ response of AMs to Mtb, we developed a high-dose aerosol murine infection model with fluorescent-tagged bacteria to isolate Mtb-infected AMs at early time points after infection by fluorescence-activated cell sorting. We have now measured the global gene expression profiles of both naïve and Mtb-infected AMs by RNA-seq. Preliminary data has revealed numerous regulatory and immune pathways that are altered in response to Mtb infection. Pathway enrichment analysis identified the oxidative stress response as one of the most altered pathways and promoter scanning has identified Nrf2, a master transcription factor of the oxidative stress response, as a predicted regulator. Further network analysis of these pathways and their effects on subsequent disease outcome is currently being undertaken.

Safety and Immunogenicity of the Recombinant BCG Vaccine AERAS-422 in Healthy BCG-naïve Adults: A Randomized, Active-controlled, First-in-human Phase 1 Trial

BACKGROUND

We report a first-in-human trial evaluating safety and immunogenicity of a recombinant BCG, AERAS-422, over-expressing TB antigens Ag85A, Ag85B, and Rv3407 and expressing mutant perfringolysin.

METHODS

This was a randomized, double-blind, dose-escalation trial in HIV-negative, healthy adult, BCG-naïve volunteers, negative for prior exposure to Mtb, at one US clinical site. Volunteers were randomized 2:1 at each dose level to receive a single intradermal dose of AERAS-422 (>10(5)-<10(6)CFU=low dose, ≥10(6)-<10(7)CFU=high dose) or non-recombinant Tice BCG (1-8×10(5)CFU). Randomization used an independently prepared randomly generated sequence of treatment assignments. The primary and secondary outcomes were safety and immunogenicity, respectively, assessed in all participants through 182days post-vaccination. ClinicalTrials.gov registration number: NCT01340820.

FINDINGS

Between Nov 2010 and Aug 2011, 24 volunteers were enrolled (AERAS-422 high dose, n=8; AERAS-422 low dose, n=8; Tice BCG, n=8); all were included in the safety and immunogenicity analyses. All 24 subjects had at least one adverse event, primarily expected local reactions. High dose AERAS-422 vaccination induced Ag85A- and Ag85B-specific lymphoproliferative responses and marked anti-mycobacterial activity in a whole blood bactericidal activity culture assay (WBA), but was associated with varicella zoster virus (VZV) reactivation in two vaccinees. These volunteers displayed high BCG-specific IFN-γ responses pre- and post-vaccination possibly predisposing them to autocrine/paracrine negative regulation of immune control of latent VZV. A systems biology transcriptomal approach identified positive correlations between post-vaccination T cell expression modules and WBA, and negative correlations between post-vaccination monocyte expression modules and WBA. The expression of one key macrophage marker (F4/80) was constitutively elevated in the two volunteers with zoster.

INTERPRETATION

The unexpected development of VZV in two of eight healthy adult vaccine recipients resulted in discontinuation of AERAS-422 vaccine development. Immunological and transcriptomal data identified correlations with the development of TB immunity and VZV that require further investigation.

FUNDING

Aeras, FDA, Bill and Melinda Gates Foundation.

Plant macrofossil evidence for an early onset of the Holocene summer thermal maximum in northernmost Europe

Holocene summer temperature reconstructions from northern Europe based on sedimentary pollen records suggest an onset of peak summer warmth around 9,000 years ago. However, pollen-based temperature reconstructions are largely driven by changes in the proportions of tree taxa, and thus the early-Holocene warming signal may be delayed due to the geographical disequilibrium between climate and tree populations. Here we show that quantitative summer-temperature estimates in northern Europe based on macrofossils of aquatic plants are in many cases ca. 2 °C warmer in the early Holocene (11,700–7,500 years ago) than reconstructions based on pollen data. When the lag in potential tree establishment becomes imperceptible in the mid-Holocene (7,500 years ago), the reconstructed temperatures converge at all study sites. We demonstrate that aquatic plant macrofossil records can provide additional and informative insights into early-Holocene temperature evolution in northernmost Europe and suggest further validation of early post-glacial climate development based on multi-proxy data syntheses.

A geographical disequilibrium between climate and tree populations may bias northern European pollen-based temperature reconstructions for the early Holocene. Here, the authors compare pollen- and macrofossil-based temperature reconstructions, showing that macrofossils reveal warmer July temperatures.

A targeted proteomics-based pipeline for verification of biomarkers in plasma

High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.

[Restriction endonuclease analysis of Pomona serogroup of Leptospira interrogans]

Restriction Endonuclease Analysis (REA) was performed on DNAs from the type strains of the Pomona serogroup of Leptospira interrogans by using EcoRI and HhaI restriction enzyme, and the electrophoretic patterns obtained were compared with patterns obtained from 27 isolates from pig kidneys collected at abattoirs in Victoria, which belong to Pomona serogroup previous identified by MAT. All of the isolates were identified as serovar Pomona.