Predominant DNMT and TET mediate effects of allergen on the human bronchial epithelium in a controlled air pollution exposure study

BackgroundEpidemiological data show that traffic-related air pollution contributes to the increasing prevalence and severity of asthma. DNA methylation (DNAm) changes may elucidate adverse health effects of environmental exposures.ObjectivesWe sought to assess the effects of allergen and diesel exhaust (DE) exposures on global DNAm and its regulation enzymes in human airway epithelium.MethodsA total of 11 participants, including 7 with and 4 without airway hyperresponsiveness, were recruited for a randomized, double-blind crossover study. Each participant had 3 exposures: filtered air + saline, filtered air + allergen, and DE + allergen. Forty-eight hours postexposure, endobronchial biopsies and bronchoalveolar lavages were collected. Levels of DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) enzymes, 5-methylcytosine, and 5-hydroxymethylcytosine were determined by immunohistochemistry. Cytokines and chemokines in bronchoalveolar lavages were measured by electrochemiluminescence multiplex assays.ResultsPredominant DNMT (the most abundant among DNMT1, DNMT3A, and DNMT3B) and predominant TET (the most abundant among TET1, TET2, and TET3) were participant-dependent. 5-Methylcytosine and its regulation enzymes differed between participants with and without airway hyperresponsiveness at baseline (filtered air + saline) and in response to allergen challenge (regardless of DE exposure). Predominant DNMT and predominant TET correlated with lung function. Allergen challenge effect on IL-8 in bronchoalveolar lavages was modified by TET2 baseline levels in the epithelium.ConclusionsResponse to allergen challenge is associated with key DNAm regulation enzymes. This relationship is generally unaltered by DE coexposure but is rather dependent on airway hyperresponsiveness status. These enzymes therefore warranted further inquiry regarding their potential in diagnosis, prognosis, and treatment of asthma

Federated Benchmarking of Medical Artificial Intelligence With MedPerf

Medical artificial intelligence (AI) has tremendous potential to advance healthcare by supporting and contributing to the evidence-based practice of medicine, personalizing patient treatment, reducing costs, and improving both healthcare provider and patient experience. Unlocking this potential requires systematic, quantitative evaluation of the performance of medical AI models on large-scale, heterogeneous data capturing diverse patient populations. Here, to meet this need, we introduce MedPerf, an open platform for benchmarking AI models in the medical domain. MedPerf focuses on enabling federated evaluation of AI models, by securely distributing them to different facilities, such as healthcare organizations. This process of bringing the model to the data empowers each facility to assess and verify the performance of AI models in an efficient and human-supervised process, while prioritizing privacy. We describe the current challenges healthcare and AI communities face, the need for an open platform, the design philosophy of MedPerf, its current implementation status and real-world deployment, our roadmap and, importantly, the use of MedPerf with multiple international institutions within cloud-based technology and on-premises scenarios. Finally, we welcome new contributions by researchers and organizations to further strengthen MedPerf as an open benchmarking platform

MedPerf : Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluation

Medical AI has tremendous potential to advance healthcare by supporting the evidence-based practice of medicine, personalizing patient treatment, reducing costs, and improving provider and patient experience. We argue that unlocking this potential requires a systematic way to measure the performance of medical AI models on large-scale heterogeneous data. To meet this need, we are building MedPerf, an open framework for benchmarking machine learning in the medical domain. MedPerf will enable federated evaluation in which models are securely distributed to different facilities for evaluation, thereby empowering healthcare organizations to assess and verify the performance of AI models in an efficient and human-supervised process, while prioritizing privacy. We describe the current challenges healthcare and AI communities face, the need for an open platform, the design philosophy of MedPerf, its current implementation status, and our roadmap. We call for researchers and organizations to join us in creating the MedPerf open benchmarking platform

The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition

<div><p>RNA polymerase II (RNAPII) contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the <i>rpb1-CTD11</i> mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of <i>STE12</i> and <i>TEC1</i> suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.</p></div

Loss of <i>STE12</i> or <i>TEC1</i> suppressed growth defects associated with <i>rpb1-CTD11</i> and the latter functioned in the same pathway as <i>CDK8</i>.

<p>(A-B) Sensitivity of the <i>rpb1-CTD11</i> mutant to growth under normal and low temperature conditions was suppressed by deletion of <i>STE12</i> or <i>TEC1</i>. Loss of <i>TEC1</i> also suppressed the growth defects of the <i>rpb1-CTD11</i> mutant upon exposure to high temperatures, formamide and hydroxyurea. Ten-fold serial dilutions of the indicated mutants were plated on YPD media at 16, 30 and 37°C or media containing the indicated concentrations of hydroxyurea or formamide. (C) Loss of <i>TEC1</i> and <i>CDK8</i> suppressed the sensitivity of the <i>rpb1-CTD11</i> mutant to growth under low and high temperatures and upon exposure to formamide and hydroxyurea. Ten-fold serial dilutions of the indicated mutants were plated and incubated on YPD media at 16, 30 and 37°C and media containing the indicated concentrations of hydroxyurea or formamide.</p

Paired t-test p values comparing RNAPII levels in wild type vs <i>rpb1-CTD11</i> at Ty1 and Ty1 retrotransposons and derived-LTRs.

<p>Paired t-test p values comparing RNAPII levels in wild type vs <i>rpb1-CTD11</i> at Ty1 and Ty1 retrotransposons and derived-LTRs.</p

Loss of <i>CDK8</i> decreased the elevated RNAPII-CTD S₅ phosphorylation levels at Ty1 retrotransposons observed in the <i>rpb1-CTD11</i> mutant.

<p>(A) Box plot showing differences in average RNAPII-CTD S₂ phosphorylation occupancy scores between the wild type and the <i>rpb1-CTD11</i>, <i>cdk8Δ</i> and <i>rpb1-CTD11 cdk8Δ</i> mutants at Ty1 or Ty2 retrotransposons. Average gene profiles of phospho-S₂ occupancy at Ty1 (B) or Ty2 (C) retrotransposons. (D) The elevated average RNAPII-CTD S₅ phosphorylation scores at Ty1 and Ty2 elements in the <i>rpb1-CTD11</i> mutant were reduced upon loss of <i>CDK8</i>. Average gene profiles of phospho-S₅ occupancy at Ty1 (E) or Ty2 (F) retrotransposons.</p