Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but a high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells are sufficient to induce a luminal-to-basal phenotypic switch, implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and we identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of the luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

Bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola, is an important disease of rice. Transposon-mediated mutational analysis of the pathogen with a quantitative assay revealed candidate virulence factors including genes involved in the pathogenesis of other phytopathogenic bacteria, virulence factors of animal pathogens, and genes not previously associated with virulence.Bacterial leaf streak is an important disease of rice (Oryza sativa) for which control measures are limited (22). In particular, no simply inherited gene for resistance to the disease has been reported. The disease is caused by Xanthomonas oryzae pv. oryzicola, a member of the gamma subdivision of the class Proteobacteria. The pathogen enters through leaf stomata or wounds and colonizes the parenchyma apoplast, causing interveinal lesions that appear water soaked initially and then develop into translucent, yellow-to-white streaks. Leaf streak is prevalent in Asia and parts of Africa, where it can decrease yield by as much as 30%. In the United States, the pathogen is quarantined and has been designated a select agent under the Agricultural Bioterrorism Act of 2002. To lay the groundwork for disease prevention and control strategies based on interference with bacterial virulence, transposon-mediated mutational analysis of X. oryzae pv. oryzicola was carried out to identify candidate virulence factors.Identification and characterization of reduced-virulence mutants. Strain BLS303 of X. oryzae pv. oryzicola (C. VeraCruz, International Rice Research Institute) was mutagenized by using the EZ::TN ϽR6K␥ori/KAN-2Ͼ Tn5 insertion kit (Epicentre Biotechnologies), which generates random, stable insertions. BLS303 cells were transformed by electroporation as described previously (30). Insertion mutants were selected on glucose yeast extract agar (18) containing 25 g/ml kanamycin and then cultured overnight in liquid glucose yeast extract with kanamycin. Cells were washed twice and resuspended in sterile water to an optical density at 600 nm of 0.5 and used to spot infiltrate, in duplicate, leaves of 4-week-old rice plants of Indica variety IRBB10 with a needleless syringe. Plants were grown and maintained in a PGC-105 growth chamber (1,000 mol/m 2 /s; Percival Scientific, Inc., Perry, IA) under a cycle of 12 h of light at 28°C and 12 h of dark at 25°C with relative humidity at 75 to 80%. Symptoms were observed after 4 days. Ten thousand mutants were screened. For 153 mutants, symptoms appeared reduced relative to the wild type or were absent. These were characterized further with a more stringent quantitative assay (Fig. 1). In this assay, leaves of 8-week-old rice plants were inoculated with a mutant on one side of the midrib and the wild type directly opposite on the other. For each mutant, five replicate, paired inoculations on each of two leaves were made. After 10 days, lesion lengths were measured for each paired inoculation, and a paired, two-tailed Student t test was performed across all replicates. By this test, 21 mutants were conf...

To define transcriptional dependencies of triple-negative breast cancer (TNBC), we identified transcription factors highly and specifically expressed in primary TNBCs and tested their requirement for cell growth in a panel of breast cancer cell lines. We found that EN1 (engrailed 1) is overexpressed in TNBCs and its downregulation preferentially and significantly reduced viability and tumorigenicity in TNBC cell lines. By integrating gene expression changes after EN1 downregulation with EN1 chromatin binding patterns, we identified genes involved in WNT and Hedgehog signaling, neurogenesis, and axonal guidance as direct EN1 transcriptional targets. Quan-titative proteomic analyses of EN1-bound chromatin complexes revealed association with transcriptional repressors and coactivators including TLE3, TRIM24, TRIM28, and TRIM33. High expression of EN1 correlated with short overall survival and increased risk of developing brain metastases in patients with TNBC. Thus, EN1 is a prognostic marker and a potential therapeutic target in TNBC.Significance: These findings show that the EN1 transcription factor regulates neurogenesis-related genes and is associated with brain metastasis in triple-negative breast cancer.

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The National Cancer Institute's Small Business Innovation Research Development Center (NCI SBIR) provides federal research and development funding and commercialization resources to more than 400 small businesses each year developing novel technologies to prevent, diagnose, and treat cancer. Although federal funding is vital for life science startups at the early stage of development, it is often insufficient to translate the technology from discovery to commercial product. Early-stage startups must connect to follow-on capital and resources to bring NCI-funded technologies to patients. Most startups face challenges in securing additional funding due to lack of access to investors and strategic partners and the ability to effectively pitch their technology. In 2015, the NCI SBIR started the Investor Initiatives program to connect funded small businesses with targeted investors and strategic partners to address the aforementioned obstacles. This program leverages an extensive network of investors and partners to conduct business-focused reviews and provide pitch coaching. The program incentivizes earlier collaborations between NCI-funded companies and private investors through various channels. The program has supported 117 companies from years 2016-2019 to attend 27 investor showcase events. Follow-up surveys show that the program and the assistance offered by NCI SBIR have contributed to a total of 32 completed deals as of April 29, 2020. This paper will discuss the Investor Initiatives program and its outcomes from 2016 to 2019 and demonstrate the effectiveness of a federal program that leverages public-private partnerships to assist portfolio companies with raising follow-on funding to accelerate the translation of research into clinical practice.

<p>FOXA1 peaks in MCF7 cells expressing lacZ or EN1-V5.</p>

<p>List of genes differentially expressed in SUM159 cells expressing shNLGN4X.</p>

<p>FOXA1 peaks in MCF7 cells expressing lacZ or EN1-V5.</p>