TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells

Common genetic variants in the repressive GATA-family transcription factor (TF) TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over 80 percent of TRPS1 from chromatin within 30 minutes of inducing degradation. We find that TRPS1 regulates transcription of hundreds of genes, including those related to estrogen signaling. TRPS1 directly regulates chromatin structure, which causes estrogen receptor alpha (ER) to redistribute in the genome. ER redistribution leads to both repression and activation of dozens of ER target genes. Downstream from these primary effects, TRPS1 depletion represses cell cycle-related gene sets and reduces cell doubling rate. Finally, we show that high TRPS1 activity, calculated using a gene expression signature defined by primary TRPS1-regulated genes, is associated with worse breast cancer patient prognosis. Taken together, these data suggest a model in which TRPS1 modulates the genomic distribution of ER, both activating and repressing transcription of genes related to cancer cell fitness.

The Androgen Receptor Does Not Directly Regulate the Transcription of DNA Damage Response Genes

The clinical success of combined androgen deprivation therapy (ADT) and radiotherapy (RT) in prostate cancer created interest in understanding the mechanistic links between androgen receptor (AR) signaling and the DNA damage response (DDR). Convergent data have led to a model where AR both regulates, and is regulated by, the DDR. Integral to this model is that the AR regulates the transcription of DDR genes both at a steady state and in response to ionizing radiation (IR). In this study, we sought to determine which immediate transcriptional changes are induced by IR in an AR-dependent manner. Using PRO-seq to quantify changes in nascent RNA transcription in response to IR, the AR antagonist enzalutamide, or the combination of the two, we find that enzalutamide treatment significantly decreased expression of canonical AR target genes but had no effect on DDR gene sets in prostate cancer cells. Surprisingly, we also found that the AR is not a primary regulator of DDR genes either in response to IR or at a steady state in asynchronously growing prostate cancer cells.

IMPLICATIONS

Our data indicate that the clinical benefit of combining ADT with RT is not due to direct AR regulation of DDR gene transcription, and that the field needs to consider alternative mechanisms for this clinical benefit.

TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells

Breast cancer is the most frequently diagnosed cancer in women. The most common subtype is luminal breast cancer, which is typically driven by the estrogen receptor α (ER), a transcription factor (TF) that activates many genes required for proliferation. Multiple effective therapies target this pathway, but individuals often develop resistance. Thus, there is a need to identify additional targets that regulate ER activity and contribute to breast tumor progression. TRPS1 is a repressive GATA-family TF that is overexpressed in breast tumors. Common genetic variants in the TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. However, we do not know how TRPS1 regulates target genes to mediate these breast cancer patient and cellular outcomes. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over eighty percent of TRPS1 from chromatin within 30 minutes of inducing degradation. We find that TRPS1 regulates transcription of hundreds of genes, including those related to estrogen signaling. TRPS1 directly regulates chromatin structure, which causes ER to redistribute in the genome. ER redistribution leads to both repression and activation of dozens of ER target genes. Downstream from these primary effects, TRPS1 depletion represses cell cycle-related gene sets and reduces cell doubling rate. Finally, we show that high TRPS1 activity, calculated using a gene expression signature defined by primary TRPS1-regulated genes, is associated with worse breast cancer patient prognosis. Taken together, these data suggest a model in which TRPS1 modulates the activity of other TFs, both activating and repressing transcription of genes related to cancer cell fitness.

ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels

Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological system under study remains intact and functional until perturbation, a feature that necessitates that the endogenous levels of the protein are maintained. However, endogenous tagging of genes with auxin‐inducible degrons (AID) can result in chronic, auxin‐independent proteasome‐mediated degradation. The ARF‐AID (auxin‐response factor–auxin‐inducible degron) system is a re‐engineered auxin‐inducible protein degradation system. The additional expression of the ARF‐PB1 domain prevents chronic, auxin‐independent degradation of AID‐tagged proteins while preserving rapid auxin‐induced degradation of tagged proteins. Here, we describe the protocol for engineering human cell lines to implement the ARF‐AID system for specific and inducible protein degradation. These methods are adaptable and can be extended from cell lines to organisms. © 2020 The Authors.

Basic Protocol 1: Generation of ARF‐P2A‐TIR1 progenitor cells

Basic Protocol 2: Designing, cloning, and testing of a gene‐specific sgRNA

Basic Protocol 3: Design and amplification of a homology‐directed repair construct (C‐terminal tagging)

Alternate Protocol 1: Design and amplification of a homology‐directed repair construct (N‐terminal tagging)

Basic Protocol 4: Tagging of a gene of interest with AID

Alternate Protocol 2: Establishment of an ARF‐AID clamp system

Basic Protocol 5: Testing of auxin‐mediated degradation of the AID‐tagged protein

Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition

Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.

Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition

Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.

Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma

Amplification of the locus encoding the oncogenic transcription factor MYCN is a defining feature of high-risk neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of MYCN perturbation in neuroblastoma. At oncogenic levels, MYCN associates with E-box binding motifs in an affinity-dependent manner, binding to strong canonical E-boxes at promoters and invading abundant weaker non-canonical E-boxes clustered at enhancers. Loss of MYCN leads to a global reduction in transcription, which is most pronounced at MYCN target genes with the greatest enhancer occupancy. These highly occupied MYCN target genes show tissue-specific expression and are linked to poor patient survival. The activity of genes with MYCN-occupied enhancers is dependent on the tissue-specific transcription factor TWIST1, which co-occupies enhancers with MYCN and is required for MYCN-dependent proliferation. These data implicate tissue-specific enhancers in defining often highly tumor-specific 'MYC target gene signatures' and identify disruption of the MYCN enhancer regulatory axis as a promising therapeutic strategy in neuroblastoma.

BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

Processive elongation of RNA Polymerase II from a proximal promoter paused state is a rate-limiting event in human gene control. A small number of regulatory factors influence transcription elongation on a global scale. Prior research using small-molecule BET bromodomain inhibitors, such as JQ1, linked BRD4 to context-specific elongation at a limited number of genes associated with massive enhancer regions. Here, the mechanistic characterization of an optimized chemical degrader of BET bromodomain proteins, dBET6, led to the unexpected identification of BET proteins as master regulators of global transcription elongation. In contrast to the selective effect of bromodomain inhibition on transcription, BET degradation prompts a collapse of global elongation that phenocopies CDK9 inhibition. Notably, BRD4 loss does not directly affect CDK9 localization. These studies, performed in translational models of T cell leukemia, establish a mechanism-based rationale for the development of BET bromodomain degradation as cancer therapy.

BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen

Chemical inhibition of epigenetic regulatory proteins BrdT and Brd4 is emerging as a promising therapeutic strategy in contraception, cancer, and heart disease. We report an easily synthesized dihydropyridopyrimidine pan-BET inhibitor scaffold, which was uncovered via a virtual screen followed by testing in a fluorescence anisotropy assay. Dihydropyridopyimidine 3 was subjected to further characterization and is highly selective for the BET family of bromodomains. Structure-activity relationship data and ligand deconstruction highlight the importance of the substitution of the uracil moiety for potency and selectivity. Compound 3 was also cocrystallized with Brd4 for determining the ligand binding pose and rationalizing subsequent structure-activity data. An additional series of dihydropyridopyrimidines was synthesized to exploit the proximity of a channel near the ZA loop of Brd4, leading to compounds with submicromolar affinity and cellular target engagement. Given these findings, novel and easily synthesized inhibitors are being introduced to the growing field of bromodomain inhibitor development.

Design and characterization of bivalent BET inhibitors

Cellular signaling is often propagated by multivalent interactions. Multivalency creates avidity, allowing stable biophysical recognition. Multivalency is an attractive strategy for achieving potent binding to protein targets, as the affinity of bivalent ligands is often greater than the sum of monovalent affinities. The BET family of transcriptional coactivators features tandem bromodomains, through which BET proteins naturally bind acetylated histones and transcription factors. All reported BRD4 antagonists bind in a monovalent fashion. Here, we report the first bivalent BET bromodomain inhibitor, MT1 that has unprecedented potency. Biophysical and biochemical studies suggest MT1 is an intramolecular bivalent BRD4 binder that is over 100-fold more potent in cellular assays compared to the corresponding monovalent antagonist, JQ1. MT1 significantly delayed leukemia progression in mice (Mus musculus) compared to JQ1. These data qualify a powerful chemical probe for BET bromodomains and extensible rationale for further development of multidomain epigenetic reader protein inhibitors.

Acute hepatitis B in Edinburgh 1975-92: a retrospective study in a population where human immunodeficiency virus is highly prevalent

A retrospective study of notified hepatitis B virus (HBV) infection in Edinburgh during 1975-92 identified 525 acute cases. For 343 where a probable transmission route could be determined, 215 were due to shared equipment by injection drug users (IDUs), 29 to homosexual intercourse, 25 to heterosexual or household contact with IDUs, 21 to heterosexual contact with infected non-IDU partners and 53 to various other or multiple routes. Cases were unevenly distributed geographically, particularly those among IDUs. The highest incidence within a post code district was approximately 2.5 times that for all Edinburgh. Annual cases peaked in 1984 then declined to low levels in the early 1990s. This reduction was most marked among IDUs, and may be ascribed both to changed injecting behaviour and decreased susceptibility within this group. The latter factor implies that HBV infections may be an unreliable guide to human immunodeficiency virus (HIV) infection in populations where HBV is highly prevalent.

Electron microscopy of adhesive interactions between Gardnerella vaginalis and vaginal epithelial cells, McCoy cells and human red blood cells

Exfoliated vaginal epithelial cells with attached bacteria, termed 'clue cells', which were procured from a patient with non-specific vaginitis, were stained with ruthenium red and examined by transmission electron microscopy. The attached bacteria appeared to adhere by means of an outer fibrillar coat. An epithelial tissue culture cell line (McCoy) and human red blood cells to which strains of Gardnerella vaginalis attached were similarly examined. The adherence of G. vaginalis to the epithelial cell line appeared to be mediated by an outer fibrillar coat while adherence to red cells appeared to be mediated by fimbriae. Transmission electron microscopy was performed on the Gardnerella strains used. Thin sections of tissue-culture-adherent strains revealed a dense outer fibrillar coat whereas the surface of the haemagglutinating strains showed fine fimbriae. Negative staining of haemagglutinating strains demonstrated fimbriae on a minority of organisms.

Haemagglutination and tissue culture adhesion of Gardnerella vaginalis

Six strains of Gardnerella vaginalis were studied to examine the adhesin-receptor mechanism involved in their attachment to human red blood cells and an epithelial tissue culture cell line (McCoy). The adhesins involved in the attachment of the bacteria to each of these cells were proteinaceous but showed marked differences after various chemical or physical treatments, indicating that separate adhesins were present. Haemagglutinating strains were more hydrophobic than tissue-culture-adherent strains. Haemagglutination of human red blood cells by strains of G. vaginalis was inhibited by galactose, lactose, N-acetylneuraminic acid and phosphatidylserine. In contrast, the tissue-culture adherence of strains was not inhibited by these substances.

In vitro adhesiveness and biotype of Gardnerella vaginalis strains in relation to the occurrence of clue cells in vaginal discharges

Haemagglutination and tissue culture adherence tests using a McCoy cell line were used to examine the adherence characteristics of 105 strains of Gardnerella vaginalis. Each strain represented one isolate per patient. For each patient, a direct smear of vaginal discharge was examined for clue cells. The relation between in vitro adherence and the presence of clue cells was examined. There seemed to be no appreciable relation between the presence of clue cells in smears and the haemagglutinating activity of strains. In contrast, adherence as judged by the McCoy tissue culture system showed a significant relation to the presence of clue cells (p less than 0.001). Though both adhesive characteristics were not inhibited by mannose, the mechanism of haemagglutination of human red cells appeared to differ from that of adherence of tissue culture cells. The findings imply that the clue cell phenomenon is due to attachment of adherent strains of G vaginalis to epithelial cells. Adherent strains of G vaginalis may play a part in the pathogenesis of bacterial vaginosis.

A pilot study of the reference values for the commoner haematological and biochemical parameters in Saudi nationals

A study of 16 haematological and 24 biochemical parameters in healthy, adult, male, volunteer Saudi blood donors was made, and enabled a preliminary determination of the reference values for these parameters to be made for Saudi Arabia. Statistically significant low means were observed for all the haematological parameters except the mean corpuscular haemoglobin concentration which was raised above Western levels and the mean corpuscular haemoglobin which was normal. A low total leucocyte count was seen to be due largely to a low neutrophil count, but accompanied by a raised lymphocyte count. The main biochemical differences were raised concentrations of serum albumin, alkaline phosphatase, conjugated bilirubin, aspartate aminotransferase, "liver" lactate dehydrogenase and alanine aminotransferase. Decreased concentrations of serum globulin, unconjugated bilirubin and calcium were also found. These changes are discussed in relation to putative endemic disease, ethnic origins and environmental factors.

Water-borne typhoid fever caused by an unusual Vi-phage type in Edinburgh

Investigation of a small series of cases of typhoid fever infected in a river between 1963 and 1970 revealed that all were caused by a single source, a carrier of a rare phage type of Salmonella typhi. The contamination of the river resulted from an incorrect sewage connexion with a surface water drain outfall into the river.

The specificity of 5'-nucleotidase in the brain of the mouse

5'-Nucleotidase in the brain of the mouse was examined histochemically. By means of various fixatives, substrate omission, heat effects, pH variation, ionic activators and inhibitors, an antigenic inhibitor (cobra venom antiserum) and substrate specificity, it was shown that the histochemical technique is specific for 5'-nucleotidase, and that it did not depend upon non-specific phosphatases. The enzyme was also show to hydrolyze seven different mononucleotides, but not a dinucleotide, two trinucleotides nor ribose 5-phosphate. Evidence is presented that the hydrolysis of the various mononucleotide substrates may be due either to separate 5'-nucleotidases or to isoenzymes.

Sex Ratios and Age Ratios in North American Ducks

The sex classes and age classes of various species of ducks constitute measurable elements of the populations. The present study deals primarily with sex ratios and age ratios and the ways in which they relate to population productivity. The present study is an evaluation of sex and age ratios in North American duck populations and the ways in which, in waterfowl management, these ratios can be used to measure productivity. Drakes occurred in relatively greater numbers among diving ducks than among dabblers; however, examination of the available knowledge on the reproductive biology characterizing these two subfamilies revealed nothing which suggests that extra drakes may be more important to the maintenance of populations of diving ducks than of dabblers. Juveniles were found to be more vulnerable to hunting than adults; the vulnerability differential varied with place, time of hunting season, vear, and species. Age ratios obtained from bagged ducks and corrected for the greater vulnerability of juveniles offered the best means of determining the adult-juvenile composition of duck populations.