Defective monocyte plasticity and altered cAMP pathway characterize USB1-mutated poikiloderma with neutropenia Clericuzio type.

Poikiloderma with neutropenia (PN) Clericuzio type (OMIM #604173) is a rare disease with areas of skin hyper- and hypopigmentation caused by biallelic USB1 variants. The current study was spurred by poor healing of a perianal tear wound in one affected child homozygous for c.266-1G>A (p.E90Sfster8) mutation, from a family reported previously. Treatment with G-CSF/CSF3 or GM-CSF/CSF2 transiently increased neutrophil/monocytes count with no effect on wound healing. Analysis of peripheral blood revealed a lack of non-classical (CD14+/- CD16+ ) monocytes, associated with a systemic inflammatory cytokine profile, in the two affected brothers. Importantly, despite normal expression of cognate receptors, monocytes from PN patients did not respond to M-CSF or IL-34 in vitro, as determined by cytokine secretion or CD16 expression. RNAseq of monocytes showed 293 differentially expressed genes, including significant downregulation of GATA2, AKAP6 and PDE4DIP that are associated with leucocyte differentiation and cyclic adenosine monophosphate (cAMP) signalling. Notably, the plasma cAMP was significantly low in the PN patients. Our study revealed a novel association of PN with a lack of non-classical monocyte population. The defects in monocyte plasticity may contribute to disease manifestations in PN and a defective cAMP signalling may be the primary effect of the splicing errors caused by USB1 mutation.

A novel approach for predicting upstream regulators (PURE) that affect gene expression.

External factors such as exposure to a chemical, drug, or toxicant (CDT), or conversely, the lack of certain chemicals can cause many diseases. The ability to identify such causal CDTs based on changes in the gene expression profile is extremely important in many studies. Furthermore, the ability to correctly infer CDTs that can revert the gene expression changes induced by a given disease phenotype is a crucial step in drug repurposing. We present an approach for Predicting Upstream REgulators (PURE) designed to tackle this challenge. PURE can correctly infer a CDT from the measured expression changes in a given phenotype, as well as correctly identify drugs that could revert disease-induced gene expression changes. We compared the proposed approach with four classical approaches as well as with the causal analysis used in Ingenuity Pathway Analysis (IPA) on 16 data sets (1 rat, 5 mouse, and 10 human data sets), involving 8 chemicals or drugs. We assessed the results based on the ability to correctly identify the CDT as indicated by its rank. We also considered the number of false positives, i.e. CDTs other than the correct CDT that were reported to be significant by each method. The proposed approach performed best in 11 out of the 16 experiments, reporting the correct CDT at the very top 7 times. IPA was the second best, reporting the correct CDT at the top 5 times, but was unable to identify the correct CDT at all in 5 out of the 16 experiments. The validation results showed that our approach, PURE, outperformed some of the most popular methods in the field. PURE could effectively infer the true CDTs responsible for the observed gene expression changes and could also be useful in drug repurposing applications.

Immunological modifications following chemotherapy are associated with delayed recurrence of ovarian cancer.

Introduction: Ovarian cancer recurs in most High Grade Serous Ovarian Cancer (HGSOC) patients, including initial responders, after standard of care. To improve patient survival, we need to identify and understand the factors contributing to early or late recurrence and therapeutically target these mechanisms. We hypothesized that in HGSOC, the response to chemotherapy is associated with a specific gene expression signature determined by the tumor microenvironment. In this study, we sought to determine the differences in gene expression and the tumor immune microenvironment between patients who show early recurrence (within 6 months) compared to those who show late recurrence following chemotherapy. Methods: Paired tumor samples were obtained before and after Carboplatin and Taxol chemotherapy from 24 patients with HGSOC. Bioinformatic transcriptomic analysis was performed on the tumor samples to determine the gene expression signature associated with differences in recurrence pattern. Gene Ontology and Pathway analysis was performed using AdvaitaBio's iPathwayGuide software. Tumor immune cell fractions were imputed using CIBERSORTx. Results were compared between late recurrence and early recurrence patients, and between paired pre-chemotherapy and post-chemotherapy samples. Results: There was no statistically significant difference between early recurrence or late recurrence ovarian tumors pre-chemotherapy. However, chemotherapy induced significant immunological changes in tumors from late recurrence patients but had no impact on tumors from early recurrence patients. The key immunological change induced by chemotherapy in late recurrence patients was the reversal of pro-tumor immune signature. Discussion: We report for the first time, the association between immunological modifications in response to chemotherapy and the time of recurrence. Our findings provide novel opportunities to ultimately improve ovarian cancer patient survival.

Epidemic intelligence studies: A research agenda for political scientists.

This research letter introduces readers to health intelligence by conceptualizing critical components and providing a primer for research within political science broadly considered. Accordingly, a brief review of the literature is provided, concluding with possible future research agendas. The aim is to elaborate on the importance of public health intelligence to national security studies, and to political science more generally.

FOXQ1 recruits the MLL complex to activate transcription of EMT and promote breast cancer metastasis.

Aberrant expression of the Forkhead box transcription factor, FOXQ1, is a prevalent mechanism of epithelial-mesenchymal transition (EMT) and metastasis in multiple carcinoma types. However, it remains unknown how FOXQ1 regulates gene expression. Here, we report that FOXQ1 initiates EMT by recruiting the MLL/KMT2 histone methyltransferase complex as a transcriptional coactivator. We first establish that FOXQ1 promoter recognition precedes MLL complex assembly and histone-3 lysine-4 trimethylation within the promoter regions of critical genes in the EMT program. Mechanistically, we identify that the Forkhead box in FOXQ1 functions as a transactivation domain directly binding the MLL core complex subunit RbBP5 without interrupting FOXQ1 DNA binding activity. Moreover, genetic disruption of the FOXQ1-RbBP5 interaction or pharmacologic targeting of KMT2/MLL recruitment inhibits FOXQ1-dependent gene expression, EMT, and in vivo tumor progression. Our study suggests that targeting the FOXQ1-MLL epigenetic axis could be a promising strategy to combat triple-negative breast cancer metastatic progression.

Electrophoretic mobility of individual molecules of alkaline phosphatase.

The electrophoretic mobilities and catalytic rates of individual molecules of bovine intestinal alkaline phosphatase were determined in CHES and borate buffers of identical pH using a capillary electrophoresis based method. Both properties were found to be heterogeneous. In the presence of CHES, the mobility and rate were found to be -1.9 ± 0.2 × 10-9 m2 V-1 s-1 and 9.8 ± 7.4 × 104 min-1 (N = 38), respectively. In the presence of borate, the mobility and rate were found to be -6.9 ± 0.5 × 10-9 m2 V-1 s-1 and 2.0 ± 1.3 × 104 min-1 (N = 41), respectively. The means and variances for both properties were found to differ significantly between the two buffers. The difference in average mobility was attributed to an increase in negative charge caused by borate complexing with the carbohydrate moieties attached to the enzyme. The difference in variance was attributed to heterogeneous complexation with borate due to heterogeneity in the glycosylation. The differences in mean values for the catalytic rate were attributed to the inhibitory effect of borate and the difference in variance may suggest that the KI of this binding may also be heterogeneous.

Analysis of cyanide using fluorogenic derivatization and capillary electrophoresis.

Samples containing cyanide were incubated at 85 °C in the presence of the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ) and glutamic acid, and analyzed by capillary electrophoresis utilizing post-separation laser-induced fluorescence detection in a sheath flow cuvette. The separation time on a 25 cm long capillary at 800 Vcm-1 was 3 min with the fluorescent product eluting at 107 s. Flushing of the capillary was not required between runs. Signal was proportional with cyanide concentration from 50 nM to 1.5 µM. LOD and LOQ were determined to be 26 and 87 nM respectively. As an application, free cyanide in five individual apple seeds was measured and found to range from 12 to 86 ng/mg, with a mean of 55 ± 32 ng/mg. As a means for the detection of amygdalin, cyanide was enzymatically produced from amygdalin using the enzymes ß-glucosidase and mandelonitrile lyase. The cyanide was then reacted with FQ and injected onto the capillary. Amygdalin was detected at a concentration of 1 µM.

RNA binding protein RBMS3 is a common EMT effector that modulates triple-negative breast cancer progression via stabilizing PRRX1 mRNA.

The epithelial-to-mesenchymal transition (EMT) has been recognized as a driving force for tumor progression in breast cancer. Recently, our group identified the RNA Binding Motif Single Stranded Interacting Protein 3 (RBMS3) to be significantly associated with an EMT transcriptional program in breast cancer. Additional expression profiling demonstrated that RBMS3 was consistently upregulated by multiple EMT transcription factors and correlated with mesenchymal gene expression in breast cancer cell lines. Functionally, RBMS3 was sufficient to induce EMT in two immortalized mammary epithelial cell lines. In triple-negative breast cancer (TNBC) models, RBMS3 was necessary for maintaining the mesenchymal phenotype and invasion and migration in vitro. Loss of RBMS3 significantly impaired both tumor progression and spontaneous metastasis in vivo. Using a genome-wide approach to interrogate mRNA stability, we found that ectopic expression of RBMS3 upregulates many genes that are resistant to degradation following transcriptional blockade by actinomycin D (ACTD). Specifically, RBMS3 was shown to interact with the mRNA of EMT transcription factor PRRX1 and promote PRRX1 mRNA stability. PRRX1 is required for RBMS3-mediated EMT and is partially sufficient to rescue the effect of RBMS3 knockdown in TNBC cell lines. Together, this study identifies RBMS3 as a novel and common effector of EMT, which could be a promising therapeutic target for TNBC treatment.

Discovery of primary prostate cancer biomarkers using cross cancer learning.

Prostate cancer (PCa), the second leading cause of cancer death in American men, is a relatively slow-growing malignancy with multiple early treatment options. Yet, a significant number of low-risk PCa patients are over-diagnosed and over-treated with significant and long-term quality of life effects. Further, there is ever increasing evidence of metastasis and higher mortality when hormone-sensitive or castration-resistant PCa tumors are treated indistinctively. Hence, the critical need is to discover clinically-relevant and actionable PCa biomarkers by better understanding the biology of PCa. In this paper, we have discovered novel biomarkers of PCa tumors through cross-cancer learning by leveraging the pathological and molecular similarities in the DNA repair pathways of ovarian, prostate, and breast cancer tumors. Cross-cancer disease learning enriches the study population and identifies genetic/phenotypic commonalities that are important across diseases with pathological and molecular similarities. Our results show that ADIRF, SLC2A5, C3orf86, HSPA1B are among the most significant PCa biomarkers, while MTRNR2L1, EEPD1, TEPP and VN1R2 are jointly important biomarkers across prostate, breast and ovarian cancers. Our validation results have further shown that the discovered biomarkers can predict the disease state better than any randomly selected subset of differentially expressed prostate cancer genes.

Heritable Susceptibility to Breast Cancer among African-American Women in the Detroit Research on Cancer Survivors Study.

BACKGROUND: African-American women have high rates of breast cancer associated with hereditary features. However, no studies have reported the prevalence of inherited variation across all genes known to be breast cancer risk factors among African-American patients with breast cancer not selected for high-risk characteristics. METHODS: We evaluated 182 African-American women diagnosed with invasive breast cancer in metropolitan Detroit via targeted capture and multiplex sequencing of 13 well-established breast cancer risk genes and five suggested breast cancer risk genes. RESULTS: We identified 24 pathogenic variants in 23 women [12.6%; 95% confidence interval (CI), 8.2%-18.4%] and five genes (BRCA2, BRCA1, ATM, RAD50, CDH1). BRCA1 and BRCA2 accounted for 58.3% of all pathogenic variants. An additional six pathogenic variants were found in suggested breast cancer risk genes (MSH6, MUTYH, NF1, BRIP1). CONCLUSIONS: The prevalence of germline pathogenic variants is relatively high among African-American patients with breast cancer unselected for high-risk characteristics across a broad spectrum of genes. IMPACT: This study helps to define the genomic landscape of breast cancer susceptibility in African-American women who could benefit from enhanced surveillance and screening.

Austrocnephia, new genus, for five species of 'Paracnephia' (Diptera: Simuliidae), with a key to Australian black fly genera.

A segregate of the so-called Australian 'Paracnephia' (Diptera: Simuliidae) is assigned to a new genus, Austrocnephia. The taxon is fully diagnosed and a key to constituent species presented. Two species-groups are recognized: the aurantiaca species-group, comprised of A. aurantiaca (Tonnoir 1925) and A. strenua (Mackerras Mackerras 1950), and the tonnoiri species-group, comprised of A. fuscoflava (Mackerras Mackerras 1948), A. orientalis (Mackerras Mackerras 1950) and A. tonnoiri (Drummond 1931). Both species-groups are diagnosed and the included species fully redescribed. Detailed locality data is given, as is information about biology, when known. Brief comments are offered about the historical biogeography of Austrocnephia. A key to Australian simuliid genera is also provided.

Profiling the Mutational Landscape in Known Driver Genes and Novel Genes in African American Non-Small Cell Lung Cancer Patients.

PURPOSE: Identifying novel driver genes and mutations in African American non-small cell lung cancer (NSCLC) cases can inform targeted therapy and improve outcomes for this traditionally underrepresented population. EXPERIMENTAL DESIGN: Tumor DNA, RNA, and germline DNA were collected from African American NSCLC patients who participated in research conducted at the Karmanos Cancer Institute (KCI) in Detroit, Michigan. Known mutations were ascertained through the Sequenom LungCarta panel of 214 mutations in 26 genes, RET/ROS1 fusions, amplification of FGFR1, and expression of ALK. Paired tumor and normal DNA was whole-exome sequenced for a subset of cases without known driver mutations. RESULTS: Of the 193 tumors tested, 77 known driver mutations were identified in 66 patients (34.2%). Sixty-seven of the 127 patients without a known driver mutation were sequenced. In 54 of these patients, 50 nonsynonymous mutations were predicted to have damaging effects among the 26 panel genes, 47 of which are not found in The Cancer Genome Atlas NSCLC white or African American samples. Analyzing the whole-exome sequence data using MutSig2CV identified a total of 88 genes significantly mutated at FDR q < 0.1. Only 5 of these genes were previously reported as oncogenic. CONCLUSIONS: These findings suggest that broader mutation profiling including both known and novel driver genes in African Americans with NSCLC will identify additional mutations that may be useful in treatment decision-making.

Redescription of Austrosimulium bancrofti (Taylor) (Diptera: Simuliidae): Australia's second-worst problem black fly.

Though the taxonomic establishment of Austrosimulium bancrofti (Taylor) was muddled, the species, because of its pest status, has been the most highly researched black fly in Australia. The literature is, however, widely spread. This current work consolidates much of that and provides redescription of all stages.

A new genus, Protaustrosimulium, for four species of Australian black flies (Diptera: Simuliidae).

Protaustrosimulium n. gen. is described for four species: two previously named species from southeastern Australia-Paracnephia pilfreyi (Davies Györkös 1988) and Paracnephia terebrans (Tonnoir 1925)-plus two newly described ones from the southwestern-most corner of Western Australia-Prot. amphorum n. sp. and Prot. opscurum n. sp. Molecular and morphological data suggest a close relationship between members of the new genus and Austrosimulium Tonnoir 1925. Monophyly of Protaustrosimulium is supported mainly by characters of adult females, as two of the four species are known only in that life stage. Two species groups are recognized: the pilfreyi-group for Prot. pilfreyi and Prot. amphorum, and the terebrans-group for Prot. terebrans and Prot. opscurum. The constituent species in each group are distributed vicariously in southeastern and southwestern Australia-a common biogeographical pattern in Australian simuliids.

The extrema of circulating miR-17 are identified as biomarkers for aggressive prostate cancer.

MicroRNAs (miRNAs) constitute short non-coding RNAs that can post-transcriptionally modulate the expression of many oncogenes and tumor suppressor genes engaged in key cellular processes. Deregulated serum miRNA signatures have been detected in various solid cancers including prostate cancer, suggesting that circulating miRNAs could function as non-invasive biomarkers of tumor emergence and progression. To determine whether serum miRNA expression levels are different between patients with aggressive and non-aggressive prostate cancer, we analyzed a panel of miRNAs from the blood of African American (AA) prostate cancer patients using a new recursive partitioning method that allows hypothesis testing of each split. We observed that both extrema of circulating miR-17, i.e. upregulation and downregulation, are associated with aggressive prostate cancer. A similar effect was observed in tumor samples from a separate dataset representing a different population of prostate cancer patients and in AA prostate cancer samples from the TCGA. The dual effect is consistent with the contradictory findings on the role of miR-17 in prostate cancer progression, whereby it controls important oncogenic and tumor-suppressive genes.

Citrate analysis using capillary electrophoresis and complexation with Eu3+-tetracycline.

A sensitive assay for citrate was developed. Citrate was incubated with 50 µM Eu3+-tetracycline and the complex separated using capillary electrophoresis utilizing post-column laser-induced luminescence detection in a sheath flow cuvette. Signal was linear with citrate concentration from 10 µM to 200 nM. Injection volumes were 320 pL. For the 200 nM sample, this corresponds to the injection of 64 amoles of citrate. Separation time was < 90 s with a total run time of 5 min. As an application the method was used to analyze citrate in agricultural and medicinal products. The method was also used to develop an assay for the enzyme citrate synthase.

Nothogreniera new genus, for two species of Australian "Paracnephia" (Diptera: Simuliidae).

Two species of Australian Simuliidae known only from adult females and currently assigned to "Paracnephia" are re-described, as are their now-known males and immature stages. Morphological character states of "Paracnephia" fergusoni (Tonnoir) and "P." fergusoni var. (Mackerras Mackerras) reveal that they are markedly distinct from all other Australian species, and are here assigned to the new genus-Nothogreniera-the most plesiomorphic Gondwanan Australian simuliid. Structural variation among populations of N. fergusoni suggests that this entity comprises a species complex.

Reassignment of Western Australia Paracnephia gladiator Moulton Adler to a new genus, Bunyipellum (Diptera: Simuliidae).

With new material available of most stages of many known Australian Paracnephia, including new species, it is now clear that certain segregates warrant assignment to new genera. This applies to Paracnephia gladiator Moulton Adler, a Western Australia simuliid with numerous unique character states. The species is fully redescribed and assigned to Bunyipellum nov. gen. A diagnosis is provided and relationships discussed, as is historical biogeography. Bunyipellum appears to be more closely related to elements of the South American simuliid fauna than to any other Gondwanan Australian species.