Loxhd1 Mutations Cause Mechanotransduction Defects in Cochlear Hair Cells.

Sound detection happens in the inner ear via the mechanical deflection of the hair bundle of cochlear hair cells. The hair bundle is an apical specialization consisting of actin-filled membrane protrusions (called stereocilia) connected by tip links (TLs) that transfer the deflection force to gate the mechanotransduction channels. Here, we identified the hearing loss-associated Loxhd1/DFNB77 gene as being required for the mechanotransduction process. LOXHD1 consists of 15 polycystin lipoxygenase α-toxin (PLAT) repeats, which in other proteins can bind lipids and proteins. LOXHD1 was distributed along the length of the stereocilia. Two LOXHD1 mouse models with mutations in the 10th PLAT repeat exhibited mechanotransduction defects (in both sexes). While mechanotransduction currents in mutant inner hair cells (IHCs) were similar to wild-type levels in the first postnatal week, they were severely affected by postnatal day 11. The onset of the mechanotransduction phenotype was consistent with the temporal progression of postnatal LOXHD1 expression/localization in the hair bundle. The mechanotransduction defect observed in Loxhd1-mutant IHCs was not accompanied by a morphologic defect of the hair bundle or a reduction in TL number. Using immunolocalization, we found that two proteins of the upper and lower TL protein complexes (Harmonin and LHFPL5) were maintained in the mutants, suggesting that the mechanotransduction machinery was present but not activatable. This work identified a novel LOXHD1-dependent step in hair bundle development that is critical for mechanotransduction in mature hair cells as well as for normal hearing function in mice and humans.SIGNIFICANCE STATEMENT Hair cells detect sound-induced forces via the hair bundle, which consists of membrane protrusions connected by tip links. The mechanotransduction machinery forms protein complexes at the tip-link ends. The current study showed that LOXHD1, a multirepeat protein responsible for hearing loss in humans and mice when mutated, was required for hair-cell mechanotransduction, but only after the first postnatal week. Using immunochemistry, we demonstrated that this defect was not caused by the mislocalization of the tip-link complex proteins Harmonin or LHFPL5, suggesting that the mechanotransduction protein complexes were maintained. This work identified a new step in hair bundle development, which is critical for both hair-cell mechanotransduction and hearing.

Alu retrotransposons and COVID-19 susceptibility and morbidity.

SARS-CoV-2 has spread rapidly across the world and is negatively impacting the global human population. COVID-19 patients display a wide variety of symptoms and clinical outcomes, including those attributed to genetic ancestry. Alu retrotransposons have played an important role in human evolution, and their variants influence host response to viral infection. Intronic Alus regulate gene expression through several mechanisms, including both genetic and epigenetic pathways. With respect to SARS-CoV-2, an intronic Alu within the ACE gene is hypothesized to be associated with COVID-19 susceptibility and morbidity. Here, we review specific Alu polymorphisms that are of particular interest when considering host response to SARS-CoV-2 infection, especially polymorphic Alu insertions in genes associated with immune response and coagulation/fibrinolysis cascade. We posit that additional research focused on Alu-related pathways could yield novel biomarkers capable of predicting clinical outcomes as well as patient-specific treatment strategies for COVID-19 and related infectious diseases.

Seroprevalence of Brucella antibodies in Donkeys (Equus asinus) in Yobe south senatorial zone, Northeastern Nigeria.

A cross-sectional survey was conducted to determine the seroprevalence and risk factors influencing the presence of Brucella spp. antibodies in donkeys in Yobe south senatorial zone, Nigeria. The study was aimed at determining the importance of Brucella spp. infection in donkeys (Equus asinus). A total of 200 sera samples from of 105 males and 95 female donkeys were collected and screened for brucellosis using the rose bengal plate test (RBPT) and the indirect enzyme-linked immunosorbent assay (iELISA). Data obtained were analyzed to determine associations and risk factors. The analysis revealed that 21.5% and 18.5% were seropositive by RBPT and iELISA respectively, with 22.0% and 20.0% of the male and female donkeys being seropositive by RBPT, and 19.0% and 17.9% of the male and female donkeys being seropositive by iELISA, respectively. There was a statistically significant association between donkey age and positive rate of iELISA for detecting Brucella infection. Though the positive rate was higher for males than females, there was no statistically significant association between sex and location of donkeys and the sensitivities of RBPT and iELISA for detecting Brucella infection. In conclusion, this study indicates that brucellosis exists with high seroprevalence particularly among male and adult donkeys and is of public health significance and economic importance because it can lead to infertility and abortion in the stock.

Single cell sequencing reveals gene expression signatures associated with bone marrow stromal cell subpopulations and time in culture.

BACKGROUND: Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. METHODS: Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). For some passages, single BMSCs were separated using microfluidics and their transcriptomes were analyzed by RNA-Seq. RESULTS: Transcriptome analysis by microarray and RNA-Seq of unseparated BMSCs from passages 2, 4, 6, 8, 9 and 10 yielded similar results; both data sets grouped passages 4 and 6 and passages 9 and 10 together and genes differentially expressed among these early and late passage BMSCs were similar. 3D Diffusion map visualization of single BMSCs from passages 3, 4, 6, 8 and 9 clustered passages 3 and 9 into two distinct groups, but there was considerable overlap for passages 4, 6 and 8 cells. Markers for early passage, FGFR2, and late passage BMSCs, PLAT, were able to identify three subpopulations within passage 3 BMSCs; one that expressed high levels of FGFR2 and low levels of PLAT; one that expressed low levels of FGFR2 and high levels of PLAT and one that expressed intermediate levels of FGFR2 and low levels of PLAT. CONCLUSIONS: Single BMSCs can be separated by microfluidics and their transcriptome analyzed by next generation sequencing. Single cell analysis of early passage BMSCs identified a subpopulation of cells expressing high levels of FGFR2 that might include skeletal stem cells.

Nodule-specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation.

Symbiotic nitrogen fixation in legumes is mediated by an interplay of signaling processes between plant hosts and rhizobial symbionts. In legumes, several secreted protein families have undergone expansions and play key roles in nodulation. Thus, identifying lineage-specific expansions (LSEs) of nodulation-associated genes can be a strategy to discover candidate gene families. Using bioinformatic tools, we identified 13 LSEs of nodulation-related secreted protein families, each unique to either Glycine, Arachis or Medicago lineages. In the Medicago lineage, nodule-specific Polycystin-1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members. We examined NPD function using CRISPR/Cas9 multiplex genome editing to create Medicago truncatula NPD knockout lines, targeting one to five NPD genes. Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control. Double- and triple-knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of a DHHC-type zinc finger and an aspartyl protease gene, possible candidates for the observed disturbance of proper nodule function. By postulating that gene family expansions can be used to detect candidate genes, we identified a family of nodule-specific PLAT domain proteins and confirmed that they play a role in successful nodule formation.

A conserved π-cation and an electrostatic bridge are essential for 11R-lipoxygenase catalysis and structural stability.

Lipoxygenases (LOXs) are lipid-peroxidizing enzymes that consist of a regulatory calcium- and membrane-binding PLAT (polycystin-1, lipoxygenase, α-toxin) domain and a catalytic domain. In a previous study, the crystal structure of an 11R-LOX revealed a conserved π-cation bridge connecting these two domains which could mediate the regulatory effect of the PLAT domain to the active site. Here we analyzed the role of residues Trp107 and Lys172 that constitute the π-cation bridge in 11R-LOX along with Arg106 and Asp173-a potential salt bridge, which could also contribute to the inter-domain communication. According to our kinetic assays and protein unfolding experiments conducted using differential scanning fluorimetry and circular dichroism spectroscopy, mutants with a disrupted link display diminished catalytic activity alongside reduced stability of the protein fold. The results demonstrate that both these bridges contribute to the two-domain interface, and are important for proper enzyme activation.

PRRX2 as a novel TGF-ß-induced factor enhances invasion and migration in mammary epithelial cell and correlates with poor prognosis in breast cancer.

TGF-ß and cancer progression share a multifaceted relationship. Despite the knowledge of TGF-ß biology in the development of cancer, several factors that mediate the cancer-promoting role of TGF-ß continue to be identified. This study aimed to identify and characterise novel factors potentially related to TGF-ß-mediated tumour aggression in breast cells. We treated the human mammary epithelial cell line MCF10A with TGF-ß and identified TGF-ß-dependent upregulation of PRRX2, the gene encoding paired-related homeobox 2 transcription factor. Overexpression of PRRX2 enhanced migration, invasion and anchorage-independent growth of MCF10A cells and induced partial epithelial mesenchymal transition (EMT), as determined by partial fibroblastoid morphology of cells, upregulation of EMT markers and partially disrupted acinar structure in a three-dimensional culture. We further identified PLAT, the gene encoding tissue-type plasminogen activator (tPA), as the highest differentially expressed gene in PRRX2-overexpressing MCF10A cells, and demonstrated direct binding and transactivation of the PLAT promoter by PRRX2. Furthermore, PLAT knockdown inhibited PRRX2-mediated enhanced migration and invasion, suggesting that tPA may mediate PRRX2-induced migration and invasion. Finally, the significant correlation of PRRX2 expression with poor survival in 118 primary breast tumour samples (P = 0.027) and the increased PRRX2 expression in metaplastic breast carcinoma samples, which is pathogenetically related to EMT, validated the biological importance of PRRX2-enhanced migration and invasion and PRRX2-induced EMT. Thus, our data suggest that upregulation of PRRX2 may be a mechanism contributing to TGF-ß-induced invasion and EMT in breast cancer. © 2016 Wiley Periodicals, Inc.

[Role of PLAT, PKHD1L1, STK38L and TEAD1 genes Alu-polymorphism for longevity].

The distribution of allele and genotype frequencies of Alu(I/D)-polymorphic sites in PLAT (TPA25), PKHD1L1 (Yb8AC702), STK38L (Ya5ac2145) и TEAD1 (Ya5ac2013) genes was first characterized in the ethnically homogeneous group (Tatars from the Republic of Bashkortostan, Russia), and was established (found) the association of each gene polymorphism with age. The study group consisted of 1580 unrelated individuals aged between 21 and 109 years, including 204 long-livers. It was found that STK38L*I/D genotype had positive association with longevity in the total group (OR=1,016, p=0,034). Long-lived women had a high probability of detection of PKHD1L1*I/I (OR=1,289, p=0,009), PLAT*D/D (OR=1,175, p=0,016) and TEAD1*I/I (OR=1,047, p=0,042) genotypes. PKHD1L1*I/D genotype was a significant factor in providing of male longevity (OR=1,713, p=0,030). Therefore, age-dependent changes in genotype frequencies are specific for each studied gene.

Stabilisation and characterisation of the isolated regulatory domain of human 5-lipoxygenase.

5-Lipoxygenase (5-LOX) is the key player of pro-inflammatory leukotriene biosynthesis. Its regulatory or so-called PLAT (polycystin-1, lipoxygenase, α-toxin) domain binds allosteric modulators like calcium, membranes, coactosin-like protein and Dicer, thereby influencing 5-LOX activity at the nuclear membrane by mediating translocation. The PLAT domain may also regulate cytosolic 5-LOX activity and possibly influence microRNA metabolism. Hence, it has also evolved as a promising target for anti-inflammatory therapy. Research focusing on this substructure of 5-LOX requires an assay system based on the isolated domain. However, we found that the isolated PLAT domain was highly prone to aggregation and therefore unsuitable for interaction studies. Substitution of the single, membrane-binding tryptophan 75 with glycine reduced aggregation and substantially increased its thermal stability. Calcium interaction of the single mutant was confirmed by differential scanning fluorimetry. Moreover, crosslinking experiments demonstrated the ability of the isolated PLAT domain to bind Dicer C-terminus whereas the interaction with coactosin-like protein required the interplay of the catalytic and the PLAT domain.

Fasting reduces liver fibrosis in a mouse model for chronic cholangiopathies.

Chronic cholangiopathies often lead to fibrosis, as a result of a perpetuated wound healing response, characterized by increased inflammation and excessive deposition of proteins of the extracellular matrix. Our previous studies have shown that food deprivation suppresses the immune response, which led us to postulate its beneficial effects on pathology in liver fibrosis driven by portal inflammation. We investigated the consequences of fasting on liver fibrosis in Abcb4(-/-) mice that spontaneously develop it due to a lack of phospholipids in bile. The effect of up to 48h of food deprivation was studied by gene expression profiling, (immuno)histochemistry, and biochemical assessments of biliary output, and hepatic and plasma lipid composition. In contrast to increased biliary output in the wild type counterparts, bile composition in Abcb4(-/-) mice remained unchanged with fasting and did not influence the attenuation of fibrosis. Markers of inflammation, however, dramatically decreased in livers of Abcb4(-/-) mice already after 12h of fasting. Reduced presence of activated hepatic stellate cells and actively increased tissue remodeling further propelled a decrease in parenchymal fibrosis in fasting. This study is the first to show that food deprivation positively influences liver pathology in a fibrotic mouse model for chronic cholangiopathies, opening a door for new strategies to improve liver regeneration in chronic disease.

Transcriptomic profiling of progesterone in the male fathead minnow (Pimephales promelas) testis.

P4 is a hormone with diverse functions that include roles in reproduction, growth, and development. The objectives of this study were to examine the effects of P4 on androgen production in the mature teleost testis and to identify molecular signaling cascades regulated by P4 to improve understanding of its role in male reproduction. Fathead minnow (FHM) testis explants were treated in vitro with two concentrations of P4 (10(-8) and 10(-6) M) for 6 and 12 h. P4 significantly increased testosterone (T) production in the FHM testis but did not affect 11-ketotestosterone. Gene network analysis revealed that insulin growth factor (Igf1) and tumor necrosis factor receptor (Tnfr) signaling was significantly depressed with P4 treatment after 12h. There was also a 20% increase in a gene network for follicle-stimulating hormone secretion and an 18% decrease in genes involved in vasopressin signaling. Genes in steroid metabolism (e.g. star, cyp19a, 11bhsd) were not significantly affected by P4 treatments in this study, and it is hypothesized that pre-existing molecular machinery may be more involved in the increased production of T rather than the de novo expression of steroid-related transcripts and receptors. There was a significant decrease in prostaglandin E synthase 3b (cytosolic) (ptges3b) after treatment with P4, suggesting that there is cross talk between P4 and prostaglandin pathways in the reproductive testis. P4 has a role in regulating steroid production in the male testis and may do so by modulating gene networks related to endocrine pathways, such as Igf1, Tnfr, and vasopressin.

Foliar architecture differentially restrains metal sequestration capacity in wheat grains (Triticum aestivum L.) grown in hyper-chloride-contaminated soils.

Anthropogenic activities, such as industrial wastewater and use of water softeners, cause hyper-accumulation of Cl- in water sources and soils. Currently, industries have no sustainable method to remove these Cl- ions from wastewater. This study was conducted to evaluate the integrative responses of wheat cultivated in five industrial effluent-affected areas (S2-S6) by investigating soil characters and bioaccumulation of metals in wheat plants and grains. The S4 site (near the second chloride outlet) exhibited a higher concentration of CO2, SO2, NO2, Cl-, Cd, Mn, Ni, Cr, and Zn. Soil from S6 (sewage wastewater downstream getting mixed with chloride-contaminated water) had a minimum level of nutrients (Na, K, and Ca), maximum metals (Cd, Fe, Pb, Mn), and reduction in plant biomass. In site S2 (sewage wastewater upstream of the chloride factory), a higher level of minerals and metals was noted in the roots. Maximum metals in grains occurred in S6 with higher organic osmolytes. The sequestration capacity of metals in leaves was also increased by alterations in anatomical traits. Results indicated that metals and hyper-Cl- concentration employed a negative influence on the plants because of poor soil quality, extremely damaged microstructures leading to reduced yield, poor grain quality, and excessive translocation from roots to wheat grains. These findings revealed that contaminated plants used as either green forage or hay are noxious to animals and if used as grain for feed or humans can lead to serious health hazards.

YO2 Induces Melanoma Cell Apoptosis through p53-Mediated LRP1 Downregulation.

The multifunctional endocytic receptor low-density lipoprotein receptor-related protein 1 (LRP1) has been implicated in melanoma growth. However, the mechanism of LRP1 expression in melanoma cells remains only partially understood. In most melanomas, the TP53 tumor suppressor is retained as a non-mutated, inactive form that fails to suppress tumors. We identify TP53 as a regulator of LRP1-mediated tumor growth. TP53 enhances the expression of miRNA miR-103/107. These miRNAs target LRP1 expression on melanoma cells. TP53 overexpression in human and murine melanoma cells was achieved using lentivirus or treatment with the small molecule YO-2, a plasmin inhibitor known to induce apoptosis in various cancer cell lines. TP53 restoration enhanced the expression of the tumor suppressor miR-103/107, resulting in the downregulation of LRP1 and suppression of tumor growth in vivo and in vitro. Furthermore, LRP1 overexpression or p53 downregulation prevented YO-2-mediated melanoma growth inhibition. We identified YO-2 as a novel p53 inducer in melanoma cells. Cotreatment of YO-2 with doxorubicin blocked tumor growth in vivo and in a murine melanoma model, suggesting that YO-2 exerts anti-melanoma effects alone or in combination with conventional myelosuppressive drugs.

A Coagulation-Related Gene-Based Prognostic Model for Invasive Ductal Carcinoma.

Background: Invasive ductal carcinoma (IDC) is the most common type of metastatic breast cancer. Due to the lack of valuable molecular biomarkers, the diagnosis and prognosis of IDC remain a challenge. A large number of studies have confirmed that coagulation is positively correlated with angiogenesis-related factors in metastatic breast cancer. Therefore, the purpose of this study was to construct a COAGULATION-related genes signature for IDC using the bioinformatics approaches. Methods: The 50 hallmark gene sets were obtained from the molecular signature database (MsigDB) to conduct Gene Set Variation Analysis (GSVA). Gene Set Enrichment Analysis (GSEA) was applied to analyze the enrichment of HALLMARK_COAGULATION. The COAGULATION-related genes were extracted from the gene set. Then, Limma Package was used to identify the differentially expressed COAGULATION-related genes (DECGs) between ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) samples in GSE26340 data set. A total of 740 IDC samples from The Cancer Genome Atlas (TCGA) database were divided into a training set and a validation set (7:3). The univariate and multivariate Cox regression analyses were performed to construct a risk signature, which divided the IDC samples into the high- and low-risk groups. The overall survival (OS) curve and receiver operating characteristic (ROC) curve were drawn in both training set and validation set. Finally, a nomogram was constructed to predict the 1-, 2-, 3-, 4-, and 5-year survival rates of IDC patients. Quantitative real-time fluorescence PCR (qRT-PCR) was performed to verify the expression levels of the prognostic genes. Results: The "HALLMARK_COAGULATION" was significantly activated in IDC. There was a significant difference in the clinicopathological parameters between the DCIS and IDC patients. Twenty-four DECGs were identified, of which five genes (SERPINA1, CAPN2, HMGCS2, MMP7, and PLAT) were screened to construct the prognostic model. The high-risk group showed a significantly lower survival rate than the low-risk group both in the training set and validation set (p=3.5943e-06 and p=0.014243). The risk score was demonstrated to be an independent predictor of IDC prognosis. A nomogram including risk score, pathological_stage, and pathological_N provided a quantitative method to predict the survival probability of 1-, 2-, 3-, 4-, and 5-year in IDC patients. The results of decision curve analysis (DCA) further demonstrated that the nomogram had a high potential for clinical utility. Conclusion: This study established a COAGULATION-related gene signature and showed its prognostic value in IDC through a comprehensive bioinformatics analysis, which may provide a potential new prognostic mean for patients with IDC.

Bottom up proteomics identifies neuronal differentiation pathway networks activated by cathepsin inhibition treatment in neuroblastoma cells that are enhanced by concurrent 13-cis retinoic acid treatment.

Neuroblastoma is the second most common pediatric cancer involving the peripheral nervous system in which stage IVS metastatic tumors regress due to spontaneous differentiation. 13-cis retinoic acid (13-cis RA) is currently used in the clinic for its differentiation effects and although it improves outcomes, relapse is seen in half of high-risk patients. Combinatorial therapies have been shown to be more effective in oncotherapy and since cathepsin inhibition reduces tumor growth, we explored the potential of coupling 13-cis RA with a cathepsin inhibitor (K777) to enhance therapeutic efficacy against neuroblastoma. Shotgun proteomics was used to identify proteins affected by K777 and dual (13-cis RA/K777) treatment in neuroblastoma SK-N-SH cells. Cathepsin inhibition was more effective in increasing proteins involved in neuronal differentiation and neurite outgrowth than 13-cis RA alone, but the combination of both treatments enhanced the neuronal differentiation effect. SIGNIFICANCE: As neuroblastoma can spontaneously differentiate, determining which proteins are involved in differentiation can guide development of more accurate diagnostic markers and more effective treatments. In this study, we established a differentiation proteomic map of SK-N-SH cells treated with a cathepsin inhibitor (K777) and K777/13-cis RA (dual). Bioinformatic analysis revealed these treatments enhanced neuronal differentiation and axonogenesis pathways. The most affected proteins in these pathways may become valuable biomarkers of efficacy of drugs designed to enhance differentiation of neuroblastoma [1].

Knockdown of PLAT enhances the anticancer effect of gefitinib in non-small cell lung cancer.

BACKGROUND: Tyrosine kinase inhibitors (TKIs), such as gefitinib, are widely used as standard treatments for non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations. However, the subsequent inevitable drug resistance has become a major challenge in clinical treatment. The aim of this study was to investigate the role of tissue-type plasminogen activator (PLAT) in gefitinib resistance in NSCLC. METHODS: The function of PLAT was determined using gefitinib-resistant cells and a nude mouse model. The gene knockdown was achieved by Lentivirus based RNA silence technique. Expression of relevant genes and proteins, cell viability, proliferation, apoptosis, cell cycle, reactive oxygen species levels, mitochondrial membrane potential and differential gene expression was detected by RT-qPCR, western blot, cell counting kit-8 assay, EdU incorporation, flow cytometry, JC-1 dye assay and complementary DNA arrays. The effects of PLAT knockdown on tumorigenesis was analyzed in vivo. RESULTS: Gefitinib-resistant cells expressed higher levels of PLAT and that knockdown of PLAT in resistant cells restored gefitinib sensitivity. Tumor proliferation was limited in vivo following PLAT knockdown. Moreover, PLAT knockdown affected mitochondrial function, caused caspase activation and cell cycle arrest, and activated TNF-α signaling, leading to apoptosis of gefitinib-resistant PC9 cells. CONCLUSIONS: Our results suggest that PLAT reduces apoptosis of NSCLC cells and knockdown of PLAT enhances anticancer effect of gefitinib by upregulating TNF-α signaling.

CeRNA Expression Profiling Identifies KIT-Related circRNA-miRNA-mRNA Networks in Gastrointestinal Stromal Tumour.

Gastrointestinal stromal tumours (GISTs) are the most common human sarcomas and are typically located in the stomach or small intestine. Although circular RNAs (circRNAs) reportedly play vital roles in tumour oncogenesis and progression, the molecular basis of the aggressive tumour biology of these circRNAs in GISTs remains unclear. In this study, we applied SBC ceRNA microarrays to screen for tumour-specific circRNA profiles in GISTs and identified that a total of 5,770 circRNAs and 1,815 mRNAs were differentially expressed in GISTs. Three significantly differential circRNAs (circ_0069765, circ_0084097, and circ_0079471) and their host genes (KIT, PLAT, and ETV1) were also verified in 68 pairs of GISTs and adjacent normal gastrointestinal tissues by qRT-PCR. A GIST-specific circRNA-miRNA-mRNA regulatory network analysis demonstrated that the specific KIT-related regulatory networks involved the three circRNAs, the circRNA host genes and three miRNAs (miR-142-5p, miR-144-3p and miR-485-3p), which may be key regulators of GISTs that could serve as molecular biomarkers and potential therapeutic targets for this malignant disease.

An MRI comparative image evaluation under diagnostic and radiotherapy planning set-ups using a carbon fibre tabletop for pelvic radiotherapy.

PURPOSE: To quantitatively and qualitatively evaluate and compare MR images acquired from the usual diagnostic set-up with images acquired in a radiotherapy set-up. MATERIALS AND METHODS: MR images of a phantom and 18 prostate cancer patients imaging using the usual diagnostic set-up with a curved tabletop (DX-set-up) and using a radiotherapy set-up (RT-set-up) with a flat tabletop, were analysed retrospectively. Quantitative assessments were made by measuring signal-to-noise ratio (SNR) and contrast to noise ratio (CNR). Non-parametric tests were used. Qualitative assessments were made independently by three radiologists. Inter-rater reliability was measured as the percentage of agreement and Gwet's AC2 test. RESULTS: The use of the RT-set-up was linked to 19.3% SNR drop on the phantom image. Up to 24% SNR prostate drop was observed in patients' images. Up to 34% CNR drop was observed in patients' images. Although image quality of the RT-set-up was acceptable, all measured domains were worse than the corresponding DX-set-up. Additionally diagnostic images were linked to a better percentage of agreement among raters. CONCLUSIONS: SNR, CNR and image quality were significantly worse when using the RT-set-up than with the DX-set-up although Image quality in the RT-set-up was acceptable.

Bottom up proteomics reveals novel differentiation proteins in neuroblastoma cells treated with 13-cis retinoic acid.

Neuroblastoma, a cancer of the sympathetic nervous system, is the second most common pediatric cancer. A unique feature of neuroblastoma is remission in some patients due to spontaneous differentiation of metastatic tumors. 13-cis retinoic acid (13-cis RA) is currently used in the clinic to treat neuroblastoma due to its differentiation inducing effects. In this study, we used shotgun proteomics to identify proteins affected by 13-cis RA treatment in neuroblastoma SK-N-SH cells. Our results showed that 13-cis RA reduced proteins involved in extracellular matrix synthesis and organization and increased proteins involved in cell adhesion and neurofilament formation. These changes indicate that 13-cis RA induces tumor cell differentiation by decreasing extracellular matrix rigidity and increasing neurite overgrowth. Differentially-affected proteins identified in this study may be novel biomarkers of drug efficacy in the treatment of neuroblastoma. SIGNIFICANCE: As neuroblastoma can spontaneously differentiate, determining which proteins are involved in differentiation can guide development of novel treatments. 13-cis retinoic acid is currently used in the clinic as a differentiation inducer. Here we have established a proteome map of SK-N-SH cells treated with 13-cis retinoic acid. Bioinformatic analysis revealed the involvement of development, differentiation, extracellular matrix assembly, collagen biosynthesis, and neurofilament bundle association. This proteome map provides information as to which proteins are important for differentiation and identifies networks that can be targeted by drugs to treat neuroblastoma [1].

Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants.

The two-spotted spider mite Tetranychus urticae is an important pest with an exceptionally broad host plant range. This generalist rapidly acclimatizes and adapts to a new host, hereby overcoming nutritional challenges and a novel pallet of constitutive and induced plant defenses. Although recent studies reveal that a broad transcriptomic response upon host plant transfer is associated with a generalist life style in arthropod herbivores, it remains uncertain to what extent these transcriptional changes are general stress responses or host-specific. In the present study, we analyzed and compared the transcriptomic changes that occur in a single T. urticae population upon long-term transfer from Phaseolus vulgaris to a similar, but chemically defended, host (cyanogenic Phaseolus lunatus) and to multiple economically important crops (Glycine max, Gossypium hirsutum, Solanum lycopersicum and Zea mays). These long-term host plant transfers were associated with distinct transcriptomic responses with only a limited overlap in both specificity and directionality, suggestive of a fine-tuned transcriptional plasticity. Nonetheless, analysis at the gene family level uncovered overlapping functional processes, recruiting genes from both well-known and newly discovered detoxification families. Of note, our analyses highlighted a possible detoxification role for Tetranychus-specific short-chain dehydrogenases and single PLAT domain proteins, and manual genome annotation showed that both families are expanded in T. urticae Our results shed new light on the molecular mechanisms underlying the remarkable adaptive potential for host plant use of generalist arthropods and set the stage for functional validation of important players in T. urticae detoxification of plant secondary metabolites.