BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of Biomedical and Biofilm Image Datasets.

Micrograph comparison remains useful in bioscience. This technology provides researchers with a quick snapshot of experimental conditions. But sometimes a two- condition comparison relies on researchers' eyes to draw conclusions. Our Bioimage Analysis, Statistic, and Comparison (BASIN) software provides an objective and reproducible comparison leveraging inferential statistics to bridge image data with other modalities. Users have access to machine learning-based object segmentation. BASIN provides several data points such as images' object counts, intensities, and areas. Hypothesis testing may also be performed. To improve BASIN's accessibility, we implemented it using R Shiny and provided both an online and offline version. We used BASIN to process 498 image pairs involving five bioscience topics. Our framework supported either direct claims or extrapolations 57% of the time. Analysis results were manually curated to determine BASIN's accuracy which was shown to be 78%. Additionally, each BASIN version's initial release shows an average 82% FAIR compliance score.

Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC).

This study investigates the effects of a dual selective Class I histone deacetylase (HDAC)/lysine-specific histone demethylase 1A (LSD1) inhibitor known as 4SC-202 (Domatinostat) on tumor growth and metastasis in a highly metastatic murine model of Triple Negative Breast Cancer (TNBC). 4SC-202 is cytotoxic and cytostatic to the TNBC murine cell line 4T1 and the human TNBC cell line MDA-MB-231; the drug does not kill the normal breast epithelial cell line MCF10A. Furthermore, 4SC-202 reduces cancer cell migration. In vivo studies conducted in the syngeneic 4T1 model, which closely mimics human TNBC in terms of sites of metastasis, reveal reduced tumor burden and lung metastasis. The mechanism of action of 4SC-202 may involve effects on cancer stem cells (CSC) which can self-renew and form metastatic lesions. Approximately 5% of the total 4T1 cell population grown in three-dimensional scaffolds had a distinct CD44high/CD24low CSC profile which decreased after treatment. Bulk transcriptome (RNA) sequencing analyses of 4T1 tumors reveal changes in metastasis-related pathways in 4SC-202-treated tumors, including changes to expression levels of genes implicated in cell migration and cell motility. In summary, 4SC-202 treatment of tumors from a highly metastatic murine model of TNBC reduces metastasis and warrants further preclinical studies.

Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid.

Central nervous system atypical teratoid/rhabdoid tumors (ATRTs) are rare and aggressive tumors with a very poor prognosis. Current treatments for ATRT include resection of the tumor, followed by systemic chemotherapy and radiation therapy, which have toxic side effects for young children. Gene expression analyses of human ATRTs and normal brain samples indicate that ATRTs have aberrant expression of epigenetic markers including class I histone deacetylases (HDAC's) and lysine demethylase (LSD1). Here, we investigate the effect of a small molecule epigenetic modulator known as Domatinostat (4SC-202), which inhibits both class I HDAC's and Lysine Demethylase (LSD1), on ATRT cell survival and single cell heterogeneity. Our findings suggest that 4SC-202 is both cytotoxic and cytostatic to ATRT in 2D and 3D scaffold cell culture models and may target cancer stem cells. Single-cell RNA sequencing data from ATRT-06 spheroids treated with 4SC-202 have a reduced population of cells overexpressing stem cell-related genes, including SOX2. Flow cytometry and immunofluorescence on 3D ATRT-06 scaffold models support these results suggesting that 4SC-202 reduces expression of cancer stem cell markers SOX2, CD133, and FOXM1. Drug-induced changes to the systems biology landscape are also explored by multi-omics enrichment analyses. In summary, our data indicate that 4SC-202 has both cytotoxic and cytostatic effects on ATRT, targets specific cell sub-populations, including those with cancer stem-like features, and is an important potential cancer therapeutic to be investigated in vivo.

4SC-202 as a Potential Treatment for the Pediatric Brain Tumor Medulloblastoma.

This project involves an examination of the effect of the small molecule inhibitor 4SC-202 on the growth of the pediatric brain cancer medulloblastoma. The small molecule inhibitor 4SC-202 significantly inhibits the viability of the pediatric desmoplastic cerebellar human medulloblastoma cell line DAOY, with an IC50 = 58.1 nM, but does not affect the viability of noncancerous neural stem cells (NSC). 4SC-202 exposure inhibits hedgehog expression in the DAOY cell line. Furthermore, microarray analysis of human medulloblastoma patient tumors indicate significant upregulation of key targets in the Hedgehog signaling pathway and Protein Tyrosine Kinase (PTK7).

A Case of Fulminant Meningococcemia: It Is All in the Complement.

Eculizumab is a novel monoclonal antibody that inhibits complement-mediated hemolysis in patients with paroxysmal nocturnal hemoglobinuria (PNH). Complement deficiency is a well-known risk factor for meningococcal infection. We describe a case of a young patient with PNH treated with eculizumab who presented with a life-threatening case of nongroupable meningococcemia. As this new biologic agent becomes more widely prescribed, providers should be aware of the increased risk of meningococcemia. In addition to vaccination, providers may consider the use of oral penicillin for antibiotic prophylaxis against Neisseria meningitidis in these cases of functional complement deficiency.

Therapeutic Targeting of PTK7 is Cytotoxic in Atypical Teratoid Rhabdoid Tumors.

Novel discoveries involving the evaluation of potential therapeutics are based on newly identified molecular targets for atypical teratoid rhabdoid tumors (ATRT), which are the most common form of infantile brain tumors. Central nervous system ATRTs are rare, aggressive, and fast growing tumors of the brain and spinal cord and carry a very poor prognosis. Currently, the standard of care for ATRT patients is based on surgical resection followed by systemic chemotherapy and radiotherapy, which result in severe side effects. As protein tyrosine kinases have proven to be actionable targets that reduce tumor growth in a number of cancers, we examined how inhibiting tyrosine kinases affected ATRT tumor growth. Here, we examine the therapeutic efficacy of the broad-spectrum tyrosine kinase inhibitor vatalanib in the treatment of ATRT. Vatalanib significantly reduced the growth of ATRT tumor cell lines, both in two-dimensional cell culture and in three-dimensional cell culture using a spheroid model. As vatalanib had a remarkable effect on the growth of ATRT, we decided to use a transcriptomic approach to therapy by examining new actionable targets, such as tyrosine kinases. Next-generation RNA-sequencing and NanoString data analysis showed a significant increase in PTK7 RNA expression levels in ATRT tumors. Inhibition of PTK7 by siRNA treatment significantly decreases the viability of ATRT patient-derived tumor cell lines.Implications: These studies provide the groundwork for future preclinical in vivo studies aiming to investigate the efficacy of PTK7 inhibition on ATRT tumor growth. Mol Cancer Res; 15(8); 973-83. ©2017 AACR.

Improved selectivity for Pb(II) by sulfur, selenium and tellurium analogues of 1,8-anthraquinone-18-crown-5: synthesis, spectroscopy, X-ray crystallography and computational studies.

We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene-9,10-dione in a 1 : 1 ratio. The optical properties of the new compounds are examined and the sulfur and selenium analogues produce an intense green emission enhancement upon association with Pb(II) in acetonitrile. Selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was also competitive for Ca(II) ion. UV-Visible and luminescence titrations reveal that 2 and 3 form 1 : 1 complexes with Pb(II), confirmed by single-crystal X-ray studies where Pb(II) is complexed within the macrocycle through coordinate covalent bonds to neighboring carbonyl, ether and heteroether donor atoms. Cyclic voltammetry of 2-8 showed classical, irreversible oxidation potentials for sulfur, selenium and tellurium heteroethers in addition to two one-electron reductions for the anthraquinone carbonyl groups. DFT calculations were also conducted on 1, 2, 3, 6, 6 + Pb(II) and 6 + Mg(II) to determine the trend in energies of the HOMO and the LUMO levels along the series.

Selective fluorescence sensing of copper(II) and water via competing imine hydrolysis and alcohol oxidation pathways sensitive to water content in aqueous acetonitrile mixtures.

Addition of hydrazines to a 1,8-disubstituted anthraquinone macrocycle containing a polyether ring produces site-selective imination, where hydrazone formation produces the more sterically hindered adduct. Reduction of the remaining carbonyl group to a secondary alcohol followed by addition of copper(II) ion causes intense yellow fluorescence to occur, which is selective for this metal cation and allows this system to be used as a fluorescence sensor. In the presence of water, a green-fluorescent intermediate appears, which slowly decomposes to produce the original starting anthraquinone. The addition of a large amount of water radically changes the reaction pathway. In this case, oxidation of the secondary alcohol is kinetically faster than hydrolysis of the hydrazone, although the same anthraquinone product is ultimately produced. Stern-Volmer data suggest that dioxygen quenches the green emission through both dynamic and static mechanisms; the static ground-state effect is most likely due to association of oxygen with the copper-bound fluorescent intermediate.

Viral response to chemotherapy in endemic burkitt lymphoma.

PURPOSE: Some EBV-directed therapies are predicted to be effective only when lytic viral replication occurs. We studied whether cyclophosphamide chemotherapy induces EBV to switch from latent to lytic phases of infection in a series of EBV-associated Burkitt lymphomas. EXPERIMENTAL DESIGN: Children with first presentation of an expanding, solid maxillary or mandibular mass consistent with Burkitt lymphoma underwent fine-needle aspiration just prior to the initiation of cyclophosphamide therapy and again 1 to 5 days later. Aspirated cells were examined for latent and lytic EBV infection using in situ hybridization to EBV-encoded RNA (EBER), immunohistochemical analysis of the lytic EBV proteins BZLF1 and BMRF1, reverse transcription PCR targeting BZLF1 transcripts, and EBV viral load measurement by quantitative PCR. RESULTS: Among 21 lymphomas expressing EBER prior to chemotherapy, 9 of 10 still expressed EBER on day 1 after therapy whereas only 2 of 11 (18%) specimens still expressed EBER at days 3 to 5, implying that chemotherapy was fairly effective at eliminating latently infected cells. Neither of the lytic products, BZLF1 or BMRF1, were significantly upregulated at the posttherapy time points examined. However, EBV genomic copy number increased in 5 of 10 samples 1 day after treatment began, suggesting that viral replication occurs within the first 24 hours. CONCLUSION: Cyclophosphamide may induce the lytic phase of EBV infection and is fairly effective in diminishing EBER-expressing tumor cells within 5 days. These findings provide the rationale for a trial testing synergistic tumor cell killing using cyclophosphamide with a drug like ganciclovir targeting lytically infected cells.

Neisseria gonorrhoeae antimicrobial susceptibility in Lilongwe, Malawi, 2007.

BACKGROUND: Malawi adopted syndromic management of sexually transmitted infections in 1993. Based on clinical efficacy and cost, gentamicin 240 mg intramuscularly, and doxycycline 100 mg twice daily x 7 days was selected as the first line regimen to treat urethritis. We sought to establish current laboratory-based Neisseria gonorrhoeae antibiotic susceptibility patterns for Malawi and describe the pattern of susceptibility since syndromic management began. METHODS: Between May 15 and August 10, 2007, 126 men with urethritis attending the STD clinic at Kamuzu Central Hospital in Lilongwe had history, genital exam, and urethral swabs taken. All were treated with gentamicin and doxycycline in accordance with Malawi guidelines. Gonorrhea was diagnosed by Gram stain and culture. Antimicrobial susceptibility patterns in gonococcal isolates were determined by disk diffusion and E-test minimum inhibitory concentration (MIC) determination and agar dilution MIC determination. RESULTS: One hundred six isolates were cultured, and MICs were determined for 100. High levels of resistance to tetracycline and penicillin were observed, but isolates were uniformly susceptible to both gentamicin and ciprofloxacin. Susceptibility patterns identified by the agar dilution MIC and E-test MIC agreed. CONCLUSIONS: The most recent study continues the trend of high susceptibility of gonococcal isolates to gentamicin in Malawi after 14 years of use and suggests agar dilution MICs may be substituted with the simpler E-test methods in future susceptibility testing. However because of the lack of susceptibility criteria for aminoglycosides for N. gonorrhoeae and the difficulty obtaining clinical/in vitro correlates in this setting, caution should be exercised in using these data for modifying treatment regimens.

Epidemiology of injuries at a tertiary care center in Malawi.

BACKGROUND: Injury surveillance is an ongoing process required for primary, secondary, and tertiary injury prevention. In Malawi, hospital-based injury data are not available. METHODS: From February to June 2008 we collected data on injured patients presenting to Kamuzu Central Hospital in Lilongwe, Malawi. The sample (n = 1,474) was predominantly male (75.7%), and age distribution was bimodal (peak age groups <5 years and 26-30 years). Road-traffic injury (RTI) was the most common reason for treatment (43.4%), followed by assault (24.0%), which was more common than expected. The most common injuries were lacerations, contusions, and abrasions. We observed both gender- and age-specific patterns in injury mechanism: Injured females were more likely than injured males to have suffered an injury as a passenger in a car or on a bicycle, or to have suffered from falls, foreign bodies, and burns; injured males were more likely than injured females to have suffered an injury as an automobile driver or bicyclist, or from an assault. Falls, burns, and foreign bodies affected younger victims, whereas bicyclists, automobile drivers, and motorcycle operators were generally older persons. RESULTS: The hospital admission rate was 26.8%. Most patients arrived by private vehicle (43.8%), which was also the fastest means of transportation. There were 25 mass casualties leading to 102 admissions; all but one were due to RTIs, and seven were associated with at least one fatality. CONCLUSIONS: This study elucidated injury epidemiology in Malawi and identified questions for future research. Other developing countries should conduct such prospective data collection to identify region-specific injury patterns and to promote injury prevention.