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Zimmerman, N.

Publications and source records attributed to Zimmerman, N..

5 recordsLinked to original sources

Methane oxidation genes are only present in bioaerosols at sites with high methane concentrations

Airborne microorganisms connect Earth's habitats, yet a central question in microbial ecology remains: do airborne communities simply reflect what is released from the surfaces below, or does local environmental context shape them? Methane oxidation offers a tractable test, because methane monooxygenase genes are restricted to defined bacterial lineages and methane is directly measurable. Pairing aerosol and underlying soil or water metagenomes across a 35-fold methane range, we show that these genes were present in every soil and water sample, yet detected in aerosols only above the landfill and dairy farm, and not above the three wetlands. The soil did not predict the air; instead, gene detection tracked local methane availability. Aerosol cell concentrations spanned 1,000 to 1,000,000 cells per cubic metre, and bacterial communities tracked their sources whereas eukaryotes were enriched in spore-dispersing fungi. Predicting what airborne microbiomes carry will therefore require accounting for local environmental context, not passive dispersal alone.

microbiology↗

CAR-engineered lymphocyte persistence is governed by a FAS ligand/FAS auto-regulatory circuit

Chimeric antigen receptor (CAR)-engineered T and NK cells can cause durable remission of B-cell malignancies; however, limited persistence restrains the full potential of these therapies in many patients. The FAS ligand (FAS-L)/FAS pathway governs naturally-occurring lymphocyte homeostasis, yet knowledge of which cells express FAS-L in patients and whether these sources compromise CAR persistence remains incomplete. Here, we constructed a single-cell atlas of diverse cancer types to identify cellular subsets expressing FASLG, the gene encoding FAS-L. We discovered that FASLG is limited primarily to endogenous T cells, NK cells, and CAR-T cells while tumor and stromal cells express minimal FASLG. To establish whether CAR-T/NK cell survival is regulated through FAS-L, we performed competitive fitness assays using lymphocytes modified with or without a FAS dominant negative receptor ({Delta}FAS). Following adoptive transfer, {Delta}FAS-expressing CAR-T and CAR-NK cells became enriched across multiple tissues, a phenomenon that mechanistically was reverted through FASLG knockout. By contrast, FASLG was dispensable for CAR-mediated tumor killing. In multiple models, {Delta}FAS co-expression by CAR-T and CAR-NK enhanced antitumor efficacy compared with CAR cells alone. Together, these findings reveal that CAR-engineered lymphocyte persistence is governed by a FAS-L/FAS auto-regulatory circuit.

immunology↗

Quantitative imaging reveals PI3Kδ inhibition reduces rhinovirus-induced damage of small airway epithelia in ex vivo cultured human precision cut lung slices from COPD patients

Chronic obstructive pulmonary disease (COPD) is one of the major causes of disability and death worldwide and a significant risk factor for respiratory infections. Rhinoviral infections are the most common trigger of COPD exacerbations which lead to a worsening of disease symptoms, decline in lung function and increased mortality. The lack of suitable disease models to study the relevant cellular and molecular mechanism hinders the discovery of novel medicines that prevent disease progression in exacerbating COPD patients. We used quantitative multi-color imaging of COPD and control patient derived human precision-cut lung slices (hPCLS) to study the impact of rhinovirus infection on the structure and function of the small airway epithelium. Data analysis highlighted that COPD-derived hPCLS have a higher cellular density and basal cell hyperplasia, more unciliated airway surface areas with mucus overproduction, and shorter cilia length compared to control hPCLS. In response to rhinovirus 16 infection, COPD-derived hPCLS secreted higher amounts of pro-inflammatory cytokines and displayed decreased epithelial integrity and reduced airway ciliation. Finally, treatment with a selective PI3K{delta} inhibitor reduced secretion of rhinovirus-induced cytokines and ameliorated rhinovirus-induced damage to COPD small airway epithelia. Thus, these data demonstrate the potential of quantitative imaging to assess complex airway functions in a patient-derived lung tissue model system, and indicate that targeting PI3K{delta} might be a promising therapeutic opportunity to limit rhinovirus-induced airway damage in exacerbating COPD patients. SummaryPI3K{delta} inhibition reduces rhinovirus-mediated damage of small airway epithelia from chronic obstructive pulmonary disease (COPD) patients

pathology↗

Blockade of LAG-3 in PD-L1-deficient mice enhances clearance of blood stage malaria independent of humoral responses

T cells expressing high levels of inhibitory receptors such as PD-1 and LAG-3 are a hallmark of chronic infections and cancer. Checkpoint blockade therapies targeting these receptors have been largely validated as promising strategies to restore exhausted T cell functions and clearance of chronic infections and tumors. The inability to develop long-term natural immunity in malaria-infected patients has been proposed to be at least partially accounted for by sustained expression of high levels of inhibitory receptors on T and B lymphocytes. While blockade or lack of PD-1/PD-L1 and/or LAG-3 was reported to promote better clearance of Plasmodium parasites in mice, how exactly these pathways contributes to protection is not known. Herein, using a mouse model of non-lethal P. yoelii (Py) infection, we reveal that the kinetics of blood parasitemia is indistinguishable between PD-1-/-, PD-L1-/- and WT mice. Yet, monoclonal antibody (mAb) blockade of LAG-3 in PD-L1-/- mice promoted accelerated control of blood parasite growth and clearance. We also report that i) the majority of LAG-3+ cells are T cells, ii) selective depletion of CD8+ T cells did not prevent anti-LAG-3-mediated protection, and iii) production of effector cytokines by CD4+ T cells is increased in anti-LAG-3-treated versus control mice. In addition, parasite-specific Ab serum titers and their ability to transfer protection from both groups of mice was comparable and depletion of CD4+ T cells prevented protection. Thus, taken together, these results are consistent with a model in which disruption of PD-L1 and LAG-3 on parasite-specific CD4+ T cells unleashes their ability to effectively clear blood parasites, independently from humoral responses. Author SummaryMalaria, caused by Plasmodium parasites, is a global burden for which an efficacious vaccine is urgently needed. The development of long-term immunity against malaria is unclear, but we know that both T and B (that produce antibodies, Ab) lymphocytes, that are subsets of white blood cells, are required. Studies in mouse models of malaria have suggested that sets of inhibitory receptors, namely LAG-3 and PD-1, expressed on cytotoxic and helper T lymphocytes hamper the development of effective immunity against malaria. Therapeutic blockade of these receptors was reported to enhance blood parasite clearance through the development of more protective parasite-specific helper T lymphocytes and Abs. Herein, we reveal that, while mice genetically deficient for the PD-1 pathway fail to clear blood parasites better than WT counterparts, anti-LAG-3 treatment does. Importantly, we found comparable parasite-specific Ab responses between all mouse groups, and Ab transfers conferred similar protection to newly infected mice. We also show that LAG-3 is mostly expressed on T lymphocytes, and that cytotoxic T lymphocytes are not involved in anti-LAG-3 accelerated clearance of parasites. Our results suggest that LAG-3 blockade acts on helper T lymphocytes to unleash their effector responses and enhance the control of blood-stage malaria, independently from parasite-specific Abs.

immunology↗

Designing robust N-of-1 studies for precision medicine

Recent advances in molecular biology, sensors, and digital medicine have led to an explosion of products and services for high-resolution monitoring of individual health. The N-of-1 study has emerged as an important methodological tool for harnessing these new data sources, enabling researchers to compare the effectiveness of health interventions at the level of a single individual. We have developed a stochastic time series model that simulates an N-of-1 study, facilitating rapid optimization of N-of-1 study designs and increasing the likelihood of study success while minimizing participant burden. Using simulation, we demonstrate how the number of treatment blocks, ordering of treatments within blocks, duration of each treatment, and sampling frequency affect our ability to detect true differences in treatment efficacy. We provide a set of recommendations for study designs based on treatment, outcome, and instrument parameters, and provide our simulation software as a supplement to the paper.

bioinformatics↗