SUMMARY Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans. Whether such signatures are similar across multiple seasons and in diverse populations is unknown. We applied systems approaches to study immune responses in young, elderly, and diabetic subjects vaccinated with the seasonal influenza vaccine across five consecutive seasons. Signatures of innate immunity and plasmablasts correlated with and predicted influenza antibody titers at 1 month after vaccination with >80% accuracy across multiple seasons but were not associated with the longevity of the response. Baseline signatures of lymphocyte and monocyte inflammation were positively and negatively correlated, respectively, with antibody responses at 1 month. Finally, integrative analysis of microRNAs and transcriptomic profiling revealed potential regulators of vaccine immunity. These results identify shared vaccine-induced signatures across multiple seasons and in diverse populations and might help guide the development of next-generation vaccines that provide persistent immunity against influenza.

Through long-term laboratory selection (over 200 generations), we have generated Drosophila melanogaster populations that tolerate severe, normally lethal, levels of hypoxia. Because of initial experiments suspecting genetic mechanisms underlying this adaptation, we compared the genomes of the hypoxia-selected flies with those of controls using deep resequencing. By applying unique computing and analytical methods we identified a number of DNA regions under selection, mostly on the X chromosome. Several of the hypoxia-selected regions contained genes encoding or regulating the Notch pathway. In addition, previous expression profiling revealed an activation of the Notch pathway in the hypoxia-selected flies. We confirmed the contribution of Notch activation to hypoxia tolerance using a specific γ-secretase inhibitor, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT), which significantly reduced adult survival and life span in the hypoxiaselected flies. We also demonstrated that flies with loss-of-function Notch mutations or RNAi-mediated Notch knockdown had a significant reduction in hypoxia tolerance, but those with a gain-of-function had a dramatic opposite effect. Using the UAS-Gal4 system, we also showed that specific overexpression of the Notch intracellular domain in glial cells was critical for conferring hypoxia tolerance. Unique analytical tools and genetic and bioinformatic strategies allowed us to discover that Notch activation plays a major role in this hypoxia tolerance in Drosophila melanogaster.evolution | next-generation sequencing O xygen homoeostasis is essential for development, growth, and integrity of cells, tissues, and organisms. Limited oxygen supply to cells and tissues (hypoxia) has a wide range of physiologic and potentially pathologic consequences, ranging from ischemic/hypoxic heart disease, stroke, and pulmonary hypertension to a number of obstetrical/perinatal complications, to high-altitude illnesses, to organ transplantation, and finally to intratumor hypoxia and cancer progression. Despite the clinical importance and societal disease impact of such a wide range of disorders, the molecular underpinnings of susceptibility or tolerance of cells or tissues to lack of O 2 are not well understood. Many studies have investigated the mechanisms that lead to injury when cells are deprived of O 2 , but to potentially treat or prevent the consequences of hypoxia necessitates also the understanding of the inherent tissue mechanisms that are critical for tolerance and survival. To do so, we use a long-term laboratory selection strategy that unmasks mechanisms that play an important role in hypoxia tolerance in a genetic model, Drosophila melanogaster (1, 2). In this attempt, starting with 27 isofemale D. melanogaster strains, and applying decreasing levels of O 2 over >200 generations, we generated Drosophila populations that tolerate severe levels of hypoxia, which are lethal to the original parental lines. These hypoxia-adapted flies (AF) pass the tolerance trait ...

Human rhinovirus (HRV) infections are usually self-limited but may be associated with serious consequences, particularly in those with asthma and chronic respiratory disease. Effective antiviral agents are needed for preventing and treating HRV illnesses. Ruprintrivir (Agouron Pharmaceuticals, Inc., San Diego, Calif.) selectively inhibits HRV 3C protease and shows potent, broad-spectrum anti-HRV activity in vitro. We conducted three double-blind, placebo-controlled clinical trials in 202 healthy volunteers to assess the activity of ruprintrivir in experimental HRV infection. Subjects were randomized to receive intranasal ruprintrivir (8 mg) or placebo sprays as prophylaxis (two or five times daily [2؋/day or 5؋/day] for 5 days) starting 6 h before infection or as treatment (5؋/day for 4 days) starting 24 h after infection. Ruprintrivir prophylaxis reduced the proportion of subjects with positive viral cultures (for 5؋/day dosing groups, 44% for ruprintrivir treatment group versus 70% for placebo treatment group [P ‫؍‬ 0.03]; for 2؋/day dosing groups, 60% for ruprintrivir group versus 92% for placebo group [P ‫؍‬ 0.004]) and viral titers but did not decrease the frequency of colds. Ruprintrivir treatment reduced the mean total daily symptom score (2.2 for ruprintrivir treatment group and 3.3 for the placebo treatment group [P ‫؍‬ 0.014]) by 33%. Secondary endpoints, including viral titers, individual symptom scores, and nasal discharge weights, were also reduced by ruprintrivir treatment. Overall, ruprintrivir was well tolerated; blood-tinged mucus and nasal passage irritation were the most common adverse effects reported. Pharmacokinetic analysis of plasma and nasal ruprintrivir concentrations revealed intranasal drug residence with minimal systemic absorption. Results from these studies in experimental rhinoviral infection support continued investigation of intranasal ruprintrivir in the setting of natural HRV infection.Human rhinoviruses (HRV) account for 40 to 50% of common colds on an annual basis and up to 80% of the colds during the autumn months in the Northern Hemisphere (2, 16). In healthy individuals, these infections are generally selflimiting and mild, although acute respiratory infections may be associated with substantial morbidity, loss of productivity, excess antibiotic use, and frequent self-medication with nonprescription remedies. HRV infection may also be complicated by acute sinusitis and otitis media and may cause exacerbations of asthma, chronic bronchitis, and cystic fibrosis, requiring acute care and hospital admission (7,15,20,21,24). For both otherwise healthy and high-risk individuals, antiviral treatment or prophylaxis would be desirable.At this time, no antiviral agents are approved for the prevention or treatment of HRV infection. Several antiviral compounds with in vitro activity against HRV have been evaluated for the management of colds, including intranasal tremacamra, a soluble intercellular adhesion molecule 1 (ICAM-1); alpha interferon 2b; and the capsid binders, pirodavir a...

Mitogen Activated Protein Kinase (MAPK) pathways form the backbone of signal transduction within the mammalian cell. Here, we apply a systematic experimental and computational approach to map 2,269 interactions between human MAPK-related proteins and other cellular machinery and to assemble these data into functional modules. A core network of 641 interactions is supported by multiple lines of evidence including conservation with yeast. Using siRNA knockdowns, we reveal that a significant number of novel interactors can modulate MAPK mediated signaling. We uncover the Na-H exchanger NHE1 as a scaffold for a novel set of MAPKs, link HSP90 chaperones to MAPK pathways, and identify MUC12 as the human analogue to the yeast signaling mucin Msb2. This study makes available a large resource of MAPK interactions along with the accompanying clone libraries. It illustrates a methodology for probing signaling networks based on functional refinement of experimentally-derived protein interaction maps.