The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

PLoS BIOLOGY Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor Jean-Philippe Coppe 1 , Christopher K. Patil 1[ , Francis Rodier 1,2[ , Yu Sun 3 , Denise P. Mun oz 1,2 , Joshua Goldstein 1¤ , Peter S. Nelson 3 , Pierre-Yves Desprez 1,4 , Judith Campisi 1,2* 1 Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 2 Buck Institute for Age Research, Novato, California, United States of America, 3 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, 4 California Pacific Medical Center Research Institute, San Francisco, California, United States of America Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA- damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial–mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment. Citation: Coppe JP, Patil CK, Rodier F, Sun Y, Mun oz DP, et al. (2008) Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor. PLoS Biol 6(12): e301. doi:10.1371/journal.pbio.0060301 Introduction Cancer is a multistep disease in which cells acquire increasingly malignant phenotypes. These phenotypes are acquired in part by somatic mutations, which derange normal controls over cell proliferation (growth), survival, invasion, and other processes important for malignant tumorigenesis [1]. In addition, there is increasing evidence that the tissue microenvironment is an important determinant of whether and how malignancies develop [2,3]. Normal tissue environ- ments tend to suppress malignant phenotypes, whereas abnormal tissue environments such at those caused by inﬂammation can promote cancer progression. Cancer development is restrained by a variety of tumor suppressor genes. Some of these genes permanently arrest the growth of cells at risk for neoplastic transformation, a process termed cellular senescence [4–6]. Two tumor suppressor pathways, controlled by the p53 and p16INK4a/pRB proteins, regulate senescence responses. Both pathways integrate multiple aspects of cellular physiology and direct cell fate towards survival, death, proliferation, or growth arrest, depending on the context [7,8]. Several lines of evidence indicate that cellular senescence is a potent tumor-suppressive mechanism [4,9,10]. Many poten- tially oncogenic stimuli (e.g., dysfunctional telomeres, DNA PLoS Biology | www.plosbiology.org damage, and certain oncogenes) induce senescence [6,11]. Moreover, mutations that dampen the p53 or p16INK4a/pRB pathways confer resistance to senescence and greatly increase cancer risk [12,13]. Most cancers harbor mutations in one or both of these pathways [14,15]. Lastly, in mice and humans, a senescence response to strong mitogenic signals, such as those delivered by certain oncogenes, prevents premalignant lesions from progressing to malignant cancers [16–19]. Academic Editor: Julian Downward, Cancer Research UK, United Kingdom Received June 27, 2008; Accepted October 22, 2008; Published December 2, 2008 Copyright: O 2008 Coppe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abbreviations: CM, conditioned medium; DDR, DNA damage response; ELISA, enzyme-linked immunosorbent assay; EMT, epithelial–mesenchymal transition; GSE, genetic suppressor element; IL, interleukin; MIT, mitoxantrone; PRE, presenescent; PrEC, normal human prostate epithelial cell; REP, replicative exhaustion; SASP, senescence-associated secretory phenotype; SEN, senescent; shRNA, short hairpin RNA; XRA, X-irradiation * To whom correspondence should be addressed. E-mail: jcampisi@lbl.gov [ These authors contributed equally to this work. ¤ Current address: Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America December 2008 | Volume 6 | Issue 12 | e301

Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

Tumours express a range of antigens, including self-antigens. Regulatory T cells are crucial for maintaining T-cell tolerance to self-antigens. Regulatory T cells are thought to dampen T-cell immunity to tumour-associated antigens and to be the main obstacle tempering successful immunotherapy and active vaccination. In this Review, I consider the nature and characteristics of regulatory T cells in the tumour microenvironment and their potential multiple suppressive mechanisms. Strategies for therapeutic targeting of regulatory T cells and the effect of regulatory T cells on current immunotherapeutic and vaccine regimens are discussed.

Regulatory T cells, tumour immunity and immunotherapy

https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1006&context=covid19

SARS-CoV-2

Erroneous communication between the innate and adaptive immune systems through cytokines results in exaggerated or attenuated immune response. It is not known whether the pathologic immune response in inflammatory bowel disease has its origin in a dysbalance of pro- and anti-inflammatory cytokine release or whether it is secondary in subsequence of a defective intestinal barrier or the destructive power of aggressive microbiota in the gut lumen.

Cytokines in inflammatory bowel disease

The basophil-IL-4-mast cell axis is required for food allergy.

79 Rapid and Intense Induction of Apoptosis in Human Eosinophils by Anti-CD30 Antibody Treatment In Vitro Maki Terakawa*, Kenji Matsumoto§, Kenju Miura*, Hirohisa Saito¥ *Suntory Biomed Research Limited, Osaka, Japan §National Children's Medical Research Center, Tokyo, Japan ~National Children's Hospital, Tokyo, Japan Apoptosis is an important cellular mechanism for controlling cell viability and proliferation. With respect to eosinophils, cytokines prolong their survival while corticosteroids reduce their survival in vitro. CD30, a member of the TNF/NGF receptor family, is reported to be expressed on the surface of many cell types including Hodgkin's lymphoma cells. CD30 is capable of inducing apoptosis after antibody treatment on some cell lines but not all. To determine whether this surface structure is involved in apoptosis of eosinophils, we examined the effect of anti-CD30 antibody treatment on the viability of human eosinophil. Eosinophils were purified from human peripheral blood with percoll density gradient centrifugation and negative selection with immunomagnetic beads. Purified eosinophils (> 99%) were suspended in RPMI-1640 medium supplemented with 10% FCS and 1 ng/ml IL-5 at a cell density of 5x105/ml. Expression of CD30 on eosinophils was examined by flow cytometry. Eosinophils were cultured in 24-well culture plate previously coated with various concentrations of anti-CD30 antibodies (1 to 1,000 ng/ml) or control antibody (irrelevant IgG 1 control mAb, 100 ng/ml), and cell viability was examined by FITC-conjugated Annexin V and propium iodide after 4 hrs of culture. Resting eosinophils expressed low but consistent amounts of CD30 (Mean Fluorescent Intensity: 8.9_+ 1.4 vs 2.6 _+ 0.2 for anti-CD30 (AC10) and irrelevant IgG1 mAb, respectively, n = 5, p 1 ng/ml anti-CD30 antibody in a concentrationand time-dependent manner. %Annexin V ÷ cells at 4 hrs was: 5.3 +0.9, 58.7 -+ 6.7", 64.2 _+ 4.6", or 3.8 _+ 0.7, for IgG1 control mAb, anti-CD30 (HRS-4), anti-CD30 (Bet-H8), or anti-CD30 (Ber-H2), respectively (Mean -+ SEM, n=6-8, * p < 0.001). By DNA fragmentation assay, there was evidence of ladder formation in anti-CD30 (HRS-4 or Ber-H8)-treated eosinophils, consistent with apoptosis. We conclude that eosinophil express low level of CD30, and that treatment with some anti-CD30 antibody shortened eosinophil survival. This suggests that CD30 on eosinophil regulates their survival, perhaps by inducing apoptosis.

https://www.jacionline.org/article/S0091-6749(02)81816-4/pdf

Rapid and intense induction of apoptosis in human eosinophils by anti-CD30 antibody treatment in vitro

Background: Respiratory syncytial virus (RSV) infection in infants with Th2 predisposition is thought to increase the risk of allergic sensitization, recurrent wheezing, and bronchial asthma during childhood. We attempted to clarify the molecular mechanisms by which Th1/Th2 predisposition in the host alters RSV infection and facilitates airway inflammation. Methods: A549 human airway epithelial cells were inoculated with live or UV-treated RSV after pretreatment with either a combination of tumor necrosis factor (TNF)-α and interferon-γ (Th1-primed) or a combination of TNF-α and interleukin-4 (Th2-primed) for 48 h. The gene and protein expression profiles of RSV-infected A549 cells were examined. Results: GeneChip analysis indicated that, at 96 h after inoculation with RSV, the expression of 62 genes was specifically enhanced (more than 2-fold by normalized data) in Th2-primed cells compared to that in unprimed or Th1-primed cells. An increase in mRNA and protein levels of monocyte chemoattractant protein (MCP)-1/CCL2 among those 62 genes was confirmed by real-time PCR and cytometric bead assay, respectively. RSV replication was markedly diminished in Th1-primed airway epithelial cells but not in Th2-primed cells, which was presumably caused at least in part by the early induction of antiviral genes. Conclusions: These results suggest that Th1/Th2 predisposition in the host prior to RSV infection critically regulates inflammatory reactions in the airways through alteration of gene expression, and that MCP-1/CCL2 plays an important role in the pathogenesis of severe RSV infection and the subsequent development of asthma in Th2-predisposed hosts.

/pdf/effect-of-th1-th2-cytokine-pretreatment-on-rsv-induced-gene-288izhfll8.pdf

Effect of Th1/Th2 Cytokine Pretreatment on RSV-Induced Gene Expression in Airway Epithelial Cells

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2801%2902477-2

Identification of novel mast cell genes by serial analysis of gene expression in cord blood-derived mast cells

Microarrays have attracted tremendous interest among biologists. However, questions have been raised regarding the reproducibility between experiments performed in different laboratories using different platforms. Here, we discuss these problems and reach the following conclusions. First, the reproducibility between different platforms of arrays is low, but bioinformatics may permit compensation at least among oligonucleotide microarrays. Second, it is hard to interpret microarray results generated using mixed cell populations. Hierarchical clustering may be applied to identify whether upregulated transcripts in an inflammatory tissue were caused simply by an increased number of inflammatory cells.

Kenji Matsumoto

Papers

The basophil-IL-4-mast cell axis is required for food allergy.

Rapid and intense induction of apoptosis in human eosinophils by anti-CD30 antibody treatment in vitro

Effect of Th1/Th2 Cytokine Pretreatment on RSV-Induced Gene Expression in Airway Epithelial Cells

Identification of novel mast cell genes by serial analysis of gene expression in cord blood-derived mast cells

Allergy-related genes in microarray: an update review.