Plant immunity protects plants from numerous potentially pathogenic microbes. The biological network that controls plant inducible immunity must function effectively even when network components are ...targeted and disabled by pathogen effectors. Network buffering could confer this resilience by allowing different parts of the network to compensate for loss of one another's functions. Networks rich in buffering rely on interactions within the network, but these mechanisms are difficult to study by simple genetic means. Through a network reconstitution strategy, in which we disassemble and stepwise reassemble the plant immune network that mediates Pattern-Triggered-Immunity, we have resolved systems-level regulatory mechanisms underlying the Arabidopsis transcriptome response to the immune stimulant flagellin-22 (flg22). These mechanisms show widespread evidence of interactions among major sub-networks-we call these sectors-in the flg22-responsive transcriptome. Many of these interactions result in network buffering. Resolved regulatory mechanisms show unexpected patterns for how the jasmonate (JA), ethylene (ET), phytoalexin-deficient 4 (PAD4), and salicylate (SA) signaling sectors control the transcriptional response to flg22. We demonstrate that many of the regulatory mechanisms we resolved are not detectable by the traditional genetic approach of single-gene null-mutant analysis. Similar to potential pathogenic perturbations, null-mutant effects on immune signaling can be buffered by the network.
Cells integrate complex cytokine cues and other inflammatory stimuli through activation of the signal transducers and activators of transcription (STAT) family of transcription factors to drive the ...appropriate anti-microbial, inflammatory, and resolving functions. Here, we discuss recent progress in our understanding of mechanisms supporting STAT functional diversity. Signaling component availability and the strength of receptor and STAT interactions emerge as important determinants of immune function. The resultant dynamics of STAT activation, together with stimulus-specific variation in STAT post-translationally modified states, will impact downstream binding partners to support transcription of distinct gene subsets. Understanding how context-dependent STAT function is encoded to dictate cytokine specificity, crosstalk, and control of inflammation will guide therapeutic efforts to selectively perturb STAT-regulated responses.
Renal transplantation from hepatitis C (HCV) nucleic acid amplification test-positive (NAAT-positive) donors to uninfected recipients has greatly increased the organ donation pool. However, there is ...concern for adverse outcomes in these recipients due to dysregulated immunologic activation secondary to active inflammation from acute viremia at the time of transplantation. This includes increased rates of cytomegalovirus (CMV) DNAemia and allograft rejection. In this study, we evaluate transcriptional responses in circulating leukocytes to define the character, timing, and resolution of this immune dysregulation and assess for biomarkers of adverse outcomes in transplant patients. We enrolled 67 renal transplant recipients (30 controls, 37 HCV recipients) and performed RNA sequencing on serial samples from one, 3-, and 6-months post-transplant. CMV DNAemia and allograft rejection outcomes were measured. Least absolute shrinkage and selection operator was utilized to develop gene expression classifiers predictive of clinical outcomes. Acute HCV incited a marked transcriptomic response in circulating leukocytes of renal transplant recipients in the acute post-transplant setting, despite the presence of immunosuppression, with 109 genes significantly differentially expressed compared to controls. These HCV infection-associated genes were reflective of antiviral immune pathways and generally resolved by the 3-month timepoint after sustained viral response (SVR) for HCV. Differential gene expression was also noted from patients who developed CMV DNAemia or allograft rejection compared to those who did not, although transcriptomic classifiers could not accurately predict these outcomes, likely due to sample size and variable time-to-event. Acute HCV infection incites evidence of immune activation and canonical antiviral responses in the human host even in the presence of systemic immunosuppression. After treatment of HCV with antiviral therapy and subsequent aviremia, this immune activation resolves. Changes in gene expression patterns in circulating leukocytes are associated with some clinical outcomes, although larger studies are needed to develop accurate predictive classifiers of these events.
Several discrete groups of feeding-regulated neurons in the nucleus of the solitary tract (
; NTS) suppress food intake, including avoidance-promoting neurons that express
(NTS
cells) and distinct
- ...and
-expressing neurons (NTS
and NTS
cells, respectively) that suppress food intake without promoting avoidance. To test potential synergies among these cell groups, we manipulated multiple NTS cell populations simultaneously. We found that activating multiple sets of NTS neurons (e.g. NTS
plus NTS
NTS
, or NTS
plus NTS
NTS
) suppressed feeding more robustly than activating single populations. While activating groups of cells that include NTS
neurons promoted conditioned taste avoidance (CTA), NTS
activation produced no CTA despite abrogating feeding. Thus, the ability to promote CTA formation represents a dominant effect but activating multiple non-aversive populations augments the suppression of food intake without provoking avoidance. Furthermore, silencing multiple NTS neuron groups augmented food intake and body weight to a greater extent than silencing single populations, consistent with the notion that each of these NTS neuron populations plays crucial and cumulative roles in the control of energy balance. We found that silencing NTS
neurons failed to blunt the weight-loss response to vertical sleeve gastrectomy (VSG) and that feeding activated many non-NTS
neurons, however, suggesting that as-yet undefined NTS cell types must make additional contributions to the restraint of feeding.
Primary care providers (PCPs) will play an important role in precision medicine. However, their lack of training and knowledge about genetics and genomics may limit their ability to advise patients ...or interpret or utilize test results. We evaluated PCPs' awareness of the role of genetics/genomics in health, knowledge about key concepts in genomic medicine, perception/attitudes towards direct-to-consumer (DTC) genetic testing, and their level of confidence/comfort in discussing testing with patients prior to and after undergoing DTC testing through the 23andMe Health + Ancestry Service. A total of 130 PCPs completed the study. Sixty-three percent were board-certified in family practice, 32% graduated between 1991 and 2000, and 88% had heard of 23andMe prior to the study. Seventy-two percent decided to participate in the study to gain a better understanding about testing. At baseline, 23% of respondents indicated comfort discussing genetics as a risk factor for common diseases, increasing to 59% after undergoing personal genetic testing (PGT) (
< 0.01). In summary, we find that undergoing PGT augments physicians' confidence, comfort, and interest in DTC testing.
Background Atopic dermatitis (AD) is a heterogeneous chronic inflammatory skin disease. Most AD during infancy resolves during childhood, but moderate-to-severe AD with allergic sensitization is more ...likely to persist into adulthood and more often occurs with other allergic diseases. Objective We sought to find susceptibility loci by performing the first genome-wide association study (GWAS) of AD in Korean children with recalcitrant AD, which was defined as moderate-to-severe AD with allergic sensitization. Methods Our study included 246 children with recalcitrant AD and 551 adult control subjects with a negative history of both allergic disease and allergic sensitization. DNA from these subjects was genotyped; sets of common single nucleotide polymorphisms (SNPs) were imputed and used in the GWAS after quality control checks. Results SNPs at a region on 13q21.31 were associated with recalcitrant AD at a genome-wide threshold of significance ( P < 2.0 × 10−8 ). These associated SNPs are more than 1 Mb from the closest gene, protocadherin ( PCDH )9. SNPs at 4 additional loci had P values of less than 1 × 10−6 , including SNPs at or near the neuroblastoma amplified sequence ( NBAS ; 2p24.3), thymus-expressed molecule involved in selection ( THEMIS ; 6q22.33), GATA3 (10p14), and S-phase cyclin A-associated protein in the ER ( SCAPER ; 15q24.3) genes. Further analysis of total serum IgE levels suggested 13q21.31 might be primarily an IgE locus, and analyses of published data demonstrated that SNPs at the 15q24.3 region are expression quantitative trait loci for 2 nearby genes, ISL2 and proline-serine-threonine phosphatase interacting protein 1 ( PSTPIP1 ), in immune cells. Conclusion Our GWAS of recalcitrant AD identified new susceptibility regions containing genes involved in epithelial cell function and immune dysregulation, 2 key features of AD, and potentially extend our understanding of their role in pathogenesis.
Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n ... = 285 patients) study of candidate genes coupled with population genetics and statistical methods to identify rare variants associated with Autism Spectrum Disorder and Schizophrenia. Three genes, MAP1A, GRIN2B, and CACNA1F, were consistently identified by different methods as having significant excess of rare missense mutations in either one or both disease cohorts. In a broader context, we also found that the overall site frequency spectrum of variation in these cases is best explained by population models of both selection and complex demography rather than neutral models or models accounting for complex demography alone. Mutations in the three disease-associated genes explained much of the difference in the overall site frequency spectrum among the cases versus controls. This study demonstrates that genes associated with complex disorders can be mapped using resequencing and analytical methods with sample sizes far smaller than those required by genome-wide association studies. Additionally, our findings support the hypothesis that rare mutations account for a proportion of the phenotypic variance of these complex disorders.
Aspirin has known effects beyond inhibiting platelet cyclooxygenase‐1 (COX‐1) that have been incompletely characterized. Transcriptomics can comprehensively characterize the on‐ and off‐target ...effects of medications. We used a systems pharmacogenomics approach of aspirin exposure in volunteers coupled with serial platelet function and purified platelet mRNA sequencing to test the hypothesis that aspirin's effects on the platelet transcriptome are associated with platelet function. We prospectively recruited 74 adult volunteers for a randomized crossover study of 81‐ vs. 325 mg/day, each for 4 weeks. Using mRNA sequencing of purified platelets collected before and after each 4‐week exposure, we identified 208 aspirin‐responsive genes with no evidence for dosage effects. In independent cohorts of healthy volunteers and patients with diabetes, we validated aspirin's effects on five genes: EIF2S3, CHRNB1, EPAS1, SLC9A3R2 and HLA‐DRA. Functional characterization of the effects of aspirin on mRNA as well as platelet ribosomal RNA demonstrated that aspirin may act as an inhibitor of protein synthesis. Database searches for small molecules that mimicked the effects of aspirin on platelet gene expression in vitro identified aspirin but no other molecules that share aspirin's known mechanisms of action. The effects of aspirin on platelet mRNA were correlated with higher levels of platelet function both at baseline and after aspirin exposure—an effect that counteracts aspirin's known antiplatelet effect. In summary, this work collectively demonstrates a dose‐independent effect of aspirin on the platelet transcriptome that counteracts the well‐known antiplatelet effects of aspirin.
Non-invasive monitoring of atherosclerosis remains challenging. Pulse Wave Imaging (PWI) is a non-invasive technique to measure the local stiffness at diastolic and end-systolic pressures and ...quantify the hemodynamics. The objective of this study is twofold, namely (1) to investigate the capability of (adaptive) PWI to assess progressive change in local stiffness and homogeneity of the carotid in a high-cholesterol swine model and (2) to assess the ability of PWI to monitor the change in hemodynamics and a corresponding change in stiffness. Nine (n=9) hypercholesterolemic swine were included in this study and followed for up to 9 months. A ligation in the left carotid was used to cause a hemodynamic disturbance. The carotids with detectable hemodynamic disturbance showed a reduction in wall shear stress immediately after ligation (2.12 ± 0.49 to 0.98 ± 0.47 Pa for 40-90% ligation (Group B) and 1.82 ± 0.25 to 0.49 ± 0.46 Pa for >90% ligation (Group C)). Histology revealed subsequent lesion formation after 8-9 months, and the type of lesion formation was dependent on the type of the induced ligation, with more complex plaques observed in the carotids with a more significant ligation (C: >90%). The compliance progression appears differed for groups B and C, with an increase in compliance to 2.09 ± 2.90×10
m
Pa
for group C whereas the compliance of group B remained low at 8 months (0.95 ± 0.94×10
m
Pa
). In summary, PWI appeared capable of monitoring a change in wall shear stress and separating two distinct progression pathways resulting in distinct compliances.
Gender-affirming surgical procedures, such as metoidioplasty and phalloplasty for those assigned female at birth, are complex and multistaged and involve risks. Individuals considering these ...procedures experience greater uncertainty or decisional conflict, compounded by difficulty finding trustworthy information.
(1) To explore the factors contributing to decisional uncertainty and the needs of individuals considering metoidioplasty and phalloplasty gender-affirming surgery (MaPGAS) and (2) to inform development of a patient-centered decision aid.
This cross-sectional study was based on mixed methods. Adult transgender men and nonbinary individuals assigned female at birth at various stages of MaPGAS decision making were recruited from 2 study sites in the United States to participate in semistructured interviews and an online gender health survey, which included measures of gender congruence, decisional conflict, urinary health, and quality of life. Trained qualitative researchers conducted all interviews with questions to explore constructs from the Ottawa decision support framework.
Outcomes included goals and priorities for MaPGAS, expectations, knowledge, and decisional needs, as well as variations in decisional conflict by surgical preference, surgical status, and sociodemographic variables.
We interviewed 26 participants and collected survey data from 39 (24 interviewees, 92%) at various stages of MaPGAS decision making. In surveys and interviews, affirmation of gender identity, standing to urinate, sensation, and the ability to "pass" as male emerged as highly important factors for deciding to undergo MaPGAS. A third of survey respondents reported decisional conflict. Triangulation of data from all sources revealed that conflict emerged most when trying to balance the strong desire to resolve gender dysphoria through surgical transition against the risks and unknowns in urinary and sexual function, appearance, and preservation of sensation post-MaPGAS. Insurance coverage, age, access to surgeons, and health concerns further influenced surgery preferences and timing.
The findings add to the understanding of decisional needs and priorities of those considering MaPGAS while revealing new complexities among knowledge, personal factors, and decisional uncertainty.
This mixed methods study was codeveloped by members of the transgender and nonbinary community and yielded important guidance for providers and individuals considering MaPGAS. The results provide rich qualitative insights for MaPGAS decision making in US contexts. Limitations include low diversity and sample size; both are being addressed in work underway.
This study increases understanding of the factors important to MaPGAS decision making, and results are being used to guide development of a patient-centered surgical decision aid and informed survey revision for national distribution.
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