Single-cell analysis of innate cytokine responses to pattern recognition receptor stimulation in children across four continents.

Innate immunity instructs adaptive immunity, and suppression of innate immunity is associated with an increased risk for infection. We showed previously that whole-blood cellular components from a cohort of South African children secreted significantly lower levels of most cytokines following stimulation of pattern recognition receptors compared with whole blood from cohorts of Ecuadorian, Belgian, or Canadian children. To begin dissecting the responsible molecular mechanisms, we set out to identify the relevant cellular source of these differences. Across the four cohorts represented in our study, we identified significant variation in the cellular composition of whole blood; however, a significant reduction in the intracellular cytokine production on the single-cell level was only detected in South African children's monocytes, conventional dendritic cells, and plasmacytoid dendritic cells. We also uncovered a marked reduction in polyfunctionality for each of these cellular compartments in South African children compared with children from the other continents. Together, our data identify differences in cell composition, as well as profoundly lower functional responses of innate cells, in our cohort of South African children. A possible link between altered innate immunity and increased risk for infection or lower response to vaccines in South African infants needs to be explored.

Soluble ecto-5'-nucleotidase (5'-NT), alkaline phosphatase, and adenosine deaminase (ADA1) activities in neonatal blood favor elevated extracellular adenosine.

Extracellular adenosine, a key regulator of physiology and immune cell function that is found at elevated levels in neonatal blood, is generated by phosphohydrolysis of adenine nucleotides released from cells and catabolized by deamination to inosine. Generation of adenosine monophosphate (AMP) in blood is driven by cell-associated enzymes, whereas conversion of AMP to adenosine is largely mediated by soluble enzymes. The identities of the enzymes responsible for these activities in whole blood of neonates have been defined in this study and contrasted to adult blood. We demonstrate that soluble 5'-nucleotidase (5'-NT) and alkaline phosphatase (AP) mediate conversion of AMP to adenosine, whereas soluble adenosine deaminase (ADA) catabolizes adenosine to inosine. Newborn blood plasma demonstrates substantially higher adenosine-generating 5'-NT and AP activity and lower adenosine-metabolizing ADA activity than adult plasma. In addition to a role in soluble purine metabolism, abundant AP expressed on the surface of circulating neonatal neutrophils is the dominant AMPase on these cells. Plasma samples from infant observational cohorts reveal a relative plasma ADA deficiency at birth, followed by a gradual maturation of plasma ADA through infancy. The robust adenosine-generating capacity of neonates appears functionally relevant because supplementation with AMP inhibited whereas selective pharmacologic inhibition of 5'-NT enhanced Toll-like receptor-mediated TNF-α production in neonatal whole blood. Overall, we have characterized previously unrecognized age-dependent expression patterns of plasma purine-metabolizing enzymes that result in elevated plasma concentrations of anti-inflammatory adenosine in newborns. Targeted manipulation of purine-metabolizing enzymes may benefit this vulnerable population.

Measles Maternal Antibodies With Low Avidity Do Not Interfere With the Establishment of Robust Quantity and Quality Antibody Responses After the Primary Dose of Measles, Mumps, and Rubella Vaccine Administered at 12-Months of Age.

In this study, we illustrate, for the first time, that preexisting low-avidity neutralizing measles maternal antibodies do not interfere with the development of high concentrations of high-avidity measles antibodies in children immunized at age 12 months. This suggests that the quality of measles maternal antibodies, rather than the quantity, impacts immunogenicity of primary measles immunization.

Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy.

A challenge in the clinical adoption of cell-free DNA (cfDNA) liquid biopsies for cancer care is their high cost compared to potential reimbursement. The most common approach used in liquid biopsies to achieve high specificity detection of circulating tumor DNA (ctDNA) among a large background of normal cfDNA is to attach molecular barcodes to each DNA template, amplify it, and then sequence it many times to reach a low-error consensus. In applications where the highest possible specificity is required, error rate can be lowered further by independently detecting the sequences of both strands of the starting cfDNA. While effective in error reduction, the additional sequencing redundancy required by such barcoding methods can increase the cost of sequencing up to 100-fold over standard next-generation sequencing (NGS) of equivalent depth. We present a novel library construction and analysis method for NGS that achieves comparable performance to the best barcoding methods, but without the increase in sequencing and subsequent sequencing cost. Named Proximity-Sequencing (Pro-Seq), the method merges multiple copies of each template into a single sequencing read by physically linking the molecular copies so they seed a single sequencing cluster. Since multiple DNA copies of the same template are compared for consensus within the same cluster, sequencing accuracy is improved without the use of redundant reads. Additionally, it is possible to represent both senses of the starting duplex in a single cluster. The resulting workflow is simple, and can be completed by a single technician in a work day with minimal hands on time. Using both cfDNA and cell line DNA, we report the average per-mutation detection threshold and per-base analytical specificity to be 0.003% and >99.9997% respectively, demonstrating that Pro-Seq is among the highest performing liquid biopsy technologies in terms of both sensitivity and specificity, but with greatly reduced sequencing costs compared to existing methods of comparable accuracy.

Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers.

Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require complex and lengthy (sometimes multi-day) workflows that complicates their use in certain applications. In addition, small panels for high sequencing depth applications such as liquid biopsy typically have low on-target rates, resulting in unnecessarily high sequencing cost. We have developed a novel targeted sequencing library preparation method, named Linked Target Capture (LTC), which replaces typical multi-day target capture workflows with a single-day, combined 'target-capture-PCR' workflow. This approach uses physically linked capture probes and PCR primers and is expected to work with panel sizes from 100 bp to >10 Mbp. It reduces the time and complexity of the capture workflow, eliminates long hybridization and wash steps and enables rapid library construction and target capture. High on-target read fractions are achievable due to repeated sequence selection in the target-capture-PCR step, thus lowering sequencing cost. We have demonstrated this technology on sample types including cell-free DNA (cfDNA) and formalin-fixed, paraffin-embedded (FFPE) derived DNA, capturing a 35-gene pan-cancer panel, and therein detecting single nucleotide variants, copy number variants, insertions, deletions and gene fusions. With the integration of unique molecular identifiers (UMIs), variants as low as 0.25% abundance were detected, limited by input mass and sequencing depth. Additionally, sequencing libraries were prepared in less than eight hours from extracted DNA to loaded sequencer, demonstrating that LTC holds promise as a broadly applicable tool for rapid, cost-effective and high performance targeted sequencing.

Age of recipient and number of doses differentially impact human B and T cell immune memory responses to HPV vaccination.

Vaccination is one of the most effective medical interventions. However, optimization of existing as well as design of new vaccines is still mostly conducted empirically; a rational approach to vaccine design is largely prohibited by the lack of insight into the relevant mechanisms underlying immune-mediated protection. To delineate the impact of variables on immune memory formation following vaccination, we took advantage of a trial assessing the role of the age of the recipient and the number of administered doses of the quadrivalent HPV vaccine in a well-characterized longitudinal cohort of girls and young women. We found that age of the recipient and the number of doses administered differentially impact the development of B and T cell memory. Specifically, age of the recipient significantly impacted generation of HPV 18-specific B cell memory, while the number of vaccine doses displayed a significant effect on the development of HPV-specific T cell memory. Our data indicate that rational design of vaccines has to be tailored according to the desired induction of B and/or T cell memory.

Highly purified human peripheral blood monocytes produce IL-6 but not TNFalpha in response to angiotensin II.

HYPOTHESIS: Monocytes produce pro-inflammatory cytokines in response to Angiotensin II (AngII). INTRODUCTION: AngII has been suggested by many to be pro-inflammatory and likely to contribute to the migration of leukocytes in patients with cardiovascular conditions. MATERIALS AND METHODS: Monocytes were purified from peripheral blood mononuclear cells (PBMCs) by negative selection using antibodies conjugated to magnetic beads. Detection of CD14(+) and AT(1)R expression was achieved by double-labeling flow cytometry. Highly purified monocytes were then stimulated with AngII (6 and 24 h) to assess IL-6 and TNF-α transcript levels by qRT-PCR and protein secretion by ELISA. RESULTS: Monocytes comprised 9.7 ± 2.0% of the PBMCs. Monocyte isolation by negative selection yielded a purity of up to 99.8%. We demonstrated AT(1)R expression on 9.5 ± 0.3% of highly purifed CD14(+)/CD16(-) monocytes. Stimulation of highly purified monocytes with AngII resulted in increased transcript levels of IL-6 at 6 h but not at 24 h, and increased secretion of IL-6 in a dose-dependent manner compared with controls (p <0.01). Conversely, there was no increase in TNF-α mRNA transcripts or protein secretion. CONCLUSIONS: We provide evidence that a CD14(+)/CD16(-) subset of highly purified human monocytes express AT(1)R and respond to AngII exposure in vitro by producing IL-6 but not TNF-α.

Integrins and monocyte migration to the ischemic myocardium.

AIMS: Characterize mononuclear cell migration after acute-myocardial infarction (MI). MATERIAL AND METHODS: Male Lewis rats underwent a left thoracotomy and ligation of the left anterior descending coronary artery (MI group). Control animals underwent thoracotomy without ligation (Sham group). Animals were sacrificed at 0, 2, 4, or 24 hr after the onset of ischemia. Leukocyte migration was assessed using isolated and In(111) labeled mononuclear cells (injected at the onset of ischemia) and gamma-count determined at 24 hours. Inhibition of migration was evaluated with monoclonal anti alpha4 and/or beta2 antibodies. RESULTS: Serum troponin was significantly elevated in animals with MI as compared with Sham (p = .017). Labeled mononuclear cell migration was five-fold higher in MI-treated animals than in Sham (p = .006). ED-1 positive mononuclear cells were confirmed in the left myocardium after 24 hr of ischemia. MCP-1 mRNA was significantly elevated in the left myocardium at 2 hr and 4 hr and peaked at 24 hr (p <.05). In addition, alpha4 integrin blockade inhibited labeled mononuclear cell migration by 22%. Blockade of beta2 integrin inhibited mononuclear cell migration by 48%, while the combined alpha4+beta2 blockade resulted in 59% inhibition of labeled mononuclear cell migration compared with treatment with isotype control antibody (p = .001). CONCLUSIONS: Significant ED1+ mononuclear cell migration within 24 hr of MI correlated with peak MCP-1 mRNA. Monoclonal antibody blockade suggested that early mononuclear cell migration is dependent only in part on alpha4 and beta2 integrins.