Epigenetic memory of coronavirus infection in innate immune cells and their progenitors

Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.

Functional inference of gene regulation using single-cell multi-omics

Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.

Single-cell methods for measuring chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) are rapidly evolving, but tools to integrate data and infer gene-regulatory relationships remain limited. Here we generate multi-omics data of resting and stimulated human blood cells and present a new computational framework for constructing gene-regulatory networks (GRNs). Specifically, we describe functional inference of gene regulation (FigR), a workflow to (1) pair scATAC-seq with scRNA-seq, (2) connect cis-regulatory elements to target genes, and (3) identify TF-gene relationships.

Abstract 4607: Androgen signaling is essential for prostate cancer development initiated from prostatic basal cells

Emerging evidence has shown that both prostatic basal and luminal cells are able to initiate oncogenic transformation. However, despite the diversity of tumor initiating cells, most prostate cancer cells express the androgen receptor (AR) and depend on androgens for their growth and expansion, implicating an essential role of androgen signaling in prostate tumorigenesis. Prostatic basal cells express p63 and are able to differentiate into luminal, neuroendocrine, and basal cells. In this study, we used a variety of relevant mouse models and in vivo systems to directly address the significance of androgen signaling in oncogenic transformation and tumor development initiated from prostatic p63-expressing cells. We demonstrate that activating Wnt oncogenic signaling by expressing stabilized b-catenin in prostatic p63-expressing cells is able to induce cell proliferation and the formation of atypical cell clusters in different prostatic lobes at embryonic, prepubescent, and adult stages. Intriguingly, despite the androgen insensitive nature of prostatic p63-expressing cells, androgens are still essential for these cells to grow and develop to androgen-dependent, luminal cell type prostate tumors. These findings are consistent with what have been observed in human prostate cancers, in which the majority of tumor cells are androgen-sensitive and possess luminal cell properties, providing new insight into the molecular mechanisms for prostate cancer initiation and progression.

Citation Format: Yongfeng He, Erika Hooker, Eun-Jeong Yu, Gerald R. Cunha, Lan Liao, Jianming Xu, Andrew Earl, Huiqing Wu, Michael L. Gonzalgo, Zijie Sun. Androgen signaling is essential for prostate cancer development initiated from prostatic basal cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4607.

Androgen signaling is essential for development of prostate cancer initiated from prostatic basal cells

Emerging evidence has shown that both prostatic basal and luminal cells are able to initiate oncogenic transformation. However, despite the diversity of tumor-initiating cells, most prostate cancer cells express the androgen receptor (AR) and depend on androgens for their growth and expansion, implicating an essential role of androgen signaling in prostate tumorigenesis. Prostatic basal cells express p63 and are able to differentiate into luminal, neuroendocrine, and basal cells. Here, we directly assessed the essential role of androgen signaling in prostatic p63-expressing cell initiated oncogenic transformation and tumor formation. Using novel and relevant mouse models, we demonstrated that, with stabilized β-catenin expression, prostatic p63-expressing cells possess the ability to initiate oncogenic transformation and, in the presence of androgens, they further transdifferentiate into luminal-like tumor cells and develop adenocarcinomas. Castration prior to activating stabilized β-catenin sensitizes p63-expressing cells and increases their sensitivity to androgens, resulting in aggressive and fast growing tumor phenotypes. These findings are consistent with what have been observed in human prostate cancers, demonstrating an essential role for androgen signaling in prostate cancer initiation and progression. This study also provides fresh insight into developing new therapeutic strategies for better treating prostate cancer patients.

Care of HIV-infected patients: nurses' concerns, opinions, and precautions

The purpose of this study was to describe nurses' concerns, opinions, and precautions related to nursing patients infected with the human immunodeficiency virus (HIV). Of special interest was a comparison of responses by nurses who reported exposure to the HIV through broken skin or mucous membranes with the responses of nurses who reported no such exposure. The sample included all staff nurses employed in either the ambulatory/home health care unit or in one of seven inpatient critical care units of a large urban medical center. Of the 323 respondents, 64 (20%) reported HIV exposure, 77 (24%) reported no exposure, and 180 (56%) reported not knowing if they had been exposed. A 15-item Likert-type scale was used. More HIV-exposed nurses than non-exposed nurses reported: (a) worrying about becoming HIV-infected; (b) considering a change of specialty or profession because of the acquired immunodeficiency syndrome (AIDS) risk; and (c) favoring selected HIV-related policies. Of the total sample, nearly all subjects agreed that staff nurses should be involved in developing HIV-related policies affecting nurses; and over one-half said that, if the agency gave them the option, they would refuse assignment to HIV-infected patients. Nearly 30% said that they had considered changing their profession because of the AIDS risk. Some implications are that nursing administrators should involve well-informed staff nurses in formulating HIV-related policies that affect nurses. The HIV-exposed nurses may need support in dealing with their concerns resulting from HIV-exposure, and they may need more information about HIV-infection control and seroconversion rates of HIV-exposed nurses.

Mitochondrial control of cell surface characteristics in Saccharomyces cerevisiae

Defects in the inner mitochondrial membrane of petite mutants of yeast resulted not only in respiratory deficiency, but also in changes in cell surface characteristics. These were (1) concanavalin A agglutinability, (2) cell movement in a biphasic polymer system, (3) cell adhesion. Genetic analysis indicated that the control exerted by the mitochondria was on nuclear genes or on the products of these genes which were presumably specifying cell surface components. These findings ascribe a new role to mitochondria but also have implications for neoplastic transformation.