Global landscape of mouse and human cytokine transcriptional regulation

Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through three decades of studies to generate a comprehensive database, CytReg, reporting 843 and 647 interactions between TFs and cytokine genes, in human and mouse respectively. By integrating CytReg with other functional datasets, we determined general principles governing the transcriptional regulation of cytokine genes. In particular, we show a correlation between TF connectivity and immune phenotype and disease, we discuss the balance between tissue-specific and pathogen-activated TFs regulating each cytokine gene, and cooperativity and plasticity in cytokine regulation. We also illustrate the use of our database as a blueprint to predict TF–disease associations and identify potential TF–cytokine regulatory axes in autoimmune diseases. Finally, we discuss research biases in cytokine regulation studies, and use CytReg to predict novel interactions based on co-expression and motif analyses which we further validated experimentally. Overall, this resource provides a framework for the rational design of future cytokine gene regulation studies.National Institutes of Health (NIH) [R00 GM114296 and R35 GM128625 to J.I.F.B., 5T32HL007501-34 to J.A.S.]; National Science Foundation [NSF-REU BIO-1659605 to M.M.]. Funding for open access charge: NIH [R35 GM128625]. (R00 GM114296 - National Institutes of Health (NIH); R35 GM128625 - National Institutes of Health (NIH); 5T32HL007501-34 - National Institutes of Health (NIH); NSF-REU BIO-1659605 - National Science Foundation; R35 GM128625 - NIH)Published versio

A scoping review

Funding Information: LA is funded by King Abdul-Aziz University Hospital (KAU), Jeddah, Kingdom of Saudi Arabia. DH and MS are funded through the National Institute for Health and Care Research (NIHR) Biomedical Research Centre programme. The views expressed are those of the authors and not necessarily those of the NIHR, the NHS, the Department of Health, and Social Care. CC is funded by UNICAMP University of Campinas, Brazil, HH is funded by ENT Department, Hospital Cuf Tejo—Nova Medical School, Lisbon, Portugal and finally RD is funded by Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, United Kingdom. The funders had no role in preparation of the manuscript. Publisher Copyright: Copyright © 2022 Alzahrani, Sereda, Chamouton, Haider, Dewey and Hoare.Background: Tinnitus is defined as the subjective perception of sound in the absence of an external stimulus, and tinnitus disorder becomes relevant when it is associated with emotional distress, cognitive dysfunction, and/or autonomic arousal. Hearing loss is recognized as the main risk factor for the pathogenesis of tinnitus. However, clinical guidelines for tinnitus disorder provide little direction for those who have severe-to-profound hearing loss including those who are pre-lingually Deaf. The aim of this scoping review was to catalogue what is known from the existing literature regarding the experience and management of tinnitus in adults who have a severe-to-profound hearing loss. Summary: A scoping review was conducted following the Preferred Reporting Item for Systematic Reviews and Meta-analysis extension for Scoping Reviews. Records were included if they reported an evaluation of tinnitus in adults who had severe-to-profound hearing loss. The online databases Ovid (MEDLINE, EMBASE and PsycINFO), CINAHL, ProQuest, Scopus, and Google Scholar were searched using the search terms ‘tinnitus’ (as a MESH term) and ‘deaf’ OR ‘profound hearing loss. Thirty-five records met the inclusion criteria for this review and were cataloged according to three major themes: Impact of tinnitus in deaf adults; Primary treatment of tinnitus in deaf adults; and Cochlear implant studies where tinnitus was a secondary outcome. Tinnitus symptom severity was assessed before and after intervention using tinnitus validated questionnaires in 29 records, with six further records using other assessment tools to measure tinnitus severity. Participants using cochlear implants were included in 30 studies. Medication, repetitive transcranial magnetic stimulation (rTMS), electrical promontory stimulation, and behavioral self-control therapy were each reported in single records. Key messages: This scoping review cataloged the experience, assessment, and treatment of tinnitus in adults who have severe-to-profound hearing loss. It is shown that there is very limited research reported in this field. Although this review included many records, most focused on the provision of cochlear implants for severe-to-profound hearing loss, with assessment and measurement of tinnitus as a baseline or secondary outcome. Largely missing in the literature are empirical studies that seek firstly to understand the nature of the experience of tinnitus by people with no or little residual access to external sound.publishersversionpublishe

The lysosomal proteome of senescent cells contributes to the senescence secretome

Senescent cells accumulate in tissues over time, favoring the onset and progression of multiple age-related diseases. Senescent cells present a remarkable increase in lysosomal mass and elevated autophagic activity. Here, we report that two main autophagic pathways macroautophagy (MA) and chaperone-mediated autophagy (CMA) are constitutively upregulated in senescent cells. Proteomic analyses of the subpopulations of lysosomes preferentially engaged in each of these types of autophagy revealed profound quantitative and qualitative changes in senescent cells, affecting both lysosomal resident proteins and cargo proteins delivered to lysosomes for degradation. These studies have led us to identify resident lysosomal proteins that are highly augmented in senescent cells and can be used as novel markers of senescence, such as arylsulfatase ARSA. The abundant secretome of senescent cells, known as SASP, is considered their main pathological mediator; however, little is known about the mechanisms of SASP secretion. Some secretory cells, including melanocytes, use the small GTPase RAB27A to perform lysosomal secretion. We found that this process is exacerbated in the case of senescent melanoma cells, as revealed by the exposure of lysosomal membrane integral proteins LAMP1 and LAMP2 in their plasma membrane. Interestingly, a subset of SASP components, including cytokines CCL2, CCL3, CXCL12, cathepsin CTSD, or the protease inhibitor SERPINE1, are secreted in a RAB27A-dependent manner in senescent melanoma cells. Finally, proteins previously identified as plasma biomarkers of aging are highly enriched in the lysosomes of senescent cells, including CTSD. We conclude that the lysosomal proteome of senescent cells is profoundly reconfigured, and that some senescent cells can be highly active in lysosomal exocytosis.© 2022 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd

Sexual and reproductive health and human rights of women living with HIV

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138378/1/jia20834-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138378/2/jia20834.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138378/3/jia20834-sup-0002.pd