Abstract 3413: A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway

The TGF-β pathway is a multifunctional signaling cascade with context-dependent roles in diverse biologic processes, including tumor promotion or suppression, metastasis, stem cell homeostasis, and immune suppression. Due to its highly context-dependent nature, decoding functional outcomes of the TGF-β pathway in specific tissues is highly challenging. Here, we present comprehensive genomic, transcriptomic and epigenomic analyses of the TGF-β pathway identified by 44 core pathway genes across 33 TCGA tumor types and 9125 samples. The core pathway genes involve TGF-β like ligands, receptors, intracellular SMAD molecules and adaptors. Although individual core pathway genes were rarely mutated or copy number altered in different cancer types, 41% of all samples have at least one genomic alteration in the TGF-β pathway, predominantly in the form of mutations. We identified a highly conserved TGF-β downstream gene expression signature associated with alterations in core pathway genes, suggesting that the alterations in the pathway have shared functional consequences. We observed a significant enrichment of the genomic alterations in gastrointestinal cancers (GI) with a distinct gene expression signature. The newly identified gene expression signature (over- or downregulation of key TGF-β downstream genes) in pan-cancer cohort was associated with significantly poor prognosis, particularly when it co-occurred with genomic alterations in the core pathway. Analysis of mutational hotspot sites revealed 6 genes with hotspots recurring in at least 9 (up to 78) mutational incidences. The hotspot mutations were also highly enriched in GI cancers. We identified previously characterized cancer mutation sites on SMAD4 and SMAD2 as hotspots mainly in GI cancers. We hypothesized novel functions to two of the newly identified hotpot sites through structural and trancriptomic analyses, and two other novel hotspot sites in the pathway await functional characterization. miRNA and epigenomic analyses revealed that TGF-β pathway activity is limited by epigenetic silencing or miRNA expression, especially in cancers with very low pathway gene expression levels. This multidimensional study provides the multifacefed landscape of TGF-β signaling in both individual disease and pan-cancer settings to guide future functional and therapeutic studies of this key cancer pathway.

Citation Format: Anil Korkut, Sobia Zaidi, Rupa Kanchi, Ashton C. Berger, Gordon Robertson, Lawrence N. Kwong, Mike Datto, Jason Roszik, Shiyun Ling, Andre Schultz, Visweswaran Ravikumar, Ganiraju Manyam, Arvind Rao, Simon Shelley, Yuexin Liu, Zhenlin Ju, Donna Hansel, Guillermo de Velasco, Arjun Pennathur, Jesper B. Andersen, Colm J. O'Rourke, Kazufumi Ohshiro, Wilma Jogunoori, Nancy Gough, Shulin Li, Hatice Osmanbeyoglu, Andres Houseman, Shuyun Rao, Maciej Wiznerowicz, Jian Chen, Shoujun Gu, Wencai Ma, Jiexin Zhang, Pan Tong, Andrew D. Cherniack, Chuxia Deng, Linda Resar-Smith, Jaffer Ajani, The Cancer Genome Atlas Research Network, John N. Weinstein, Lopa Mishra, Rehan Akbani. A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3413.

Breast cancer Ki67 expression prediction by DCE-MRI radiomics features

AIM

To investigate whether quantitative radiomics features extracted from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) are associated with Ki67 expression of breast cancer.

MATERIALS AND METHODS

This institutional review board-approved retrospective study comprised 377 Chinese women who were diagnosed with invasive breast cancer in 2015. This cohort included 53 low-Ki67 expression (Ki67 proliferation index less than 14%) and 324 cases with high-Ki67 expression (Ki67 proliferation index more than 14%). A binary-classification of low-versus high- Ki67 expression was performed. A set of 56 quantitative radiomics features, including morphological, greyscale statistic, and texture features, were extracted from the segmented lesion area. Three machine learning classification methods, including naive Bayes, k-nearest neighbour and support vector machine, were employed for the classification and the least absolute shrink age and selection operator (LASSO) method was used to select most predictive features set for the classifiers. Classification performance was evaluated by the area under receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity.

RESULES

The model that used naive Bayes classification method achieved the best performance than the other two methods, yielding 0.773 AUC, 0.757 accuracy, 0.777 sensitivity and 0.769 specificity. Three most predictive features, i.e., contrast, entropy and line likeness, were selected by the LASSO method and showed a statistical significance (p<0.05) in the classification.

CONCLUSION

The present study showed that quantitative radiomics imaging features of breast tumour extracted from DCE-MRI are associated with breast cancer Ki67 expression. Future larger studies are needed in order to further evaluate the findings.

[Dynamic variation trend and prognostic value of bronchial wall thickness in severely burned patients combined with inhalation injury]

Objective: To explore the dynamic variation trend of bronchial wall thickness (BWT) in severely burned patients combined with inhalation injury, and to determine the value of BWT to prognosis of patients. Methods: Forty-three severely burned patients with inhalation injury hospitalized in Intensive Burn Department of the Affiliated Hospital of Nankai University (Tianjin No.4 Hospital) from July to November 2016, conforming to the study criteria, were divided into survival group (n=27) and death group (n=16) according to the prognosis of patients within 14 days after admission. All patients underwent fiberoptic bronchoscopy and inhalation injury rating based on abbreviated injury scale at admission. High resolution CT examination was performed in patients of two groups at admission and 24 h post admission, 3, 7, and 14 d post admission to measure the BWT of right superior lobar bronchus trunk opening. Receiver operating characteristic curves of rating of inhalation damage at admission and BWT at admission were drawn to evaluate the predictive value for death of 43 patients. Data were processed with chi-square test, independent sample t test, Wilcoxon rank sum test, analysis of variance for repeated measurement and least-significant difference-t test. Results: (1) The numbers of patients rated as 0, 1, 2, 3, and 4 grade for inhalation injury in survival group and death group were 0, 19, 6, 2, and 0, and 0, 2, 7, 7, and 0, respectively. There were statistically significant differences between the two groups (Z=-3.79, P<0.01). (2) BWT of patients in death group at admission and 24 h post admission, 3, 7, and 14 d post admission was respectively (2.72±0.26), (3.18±0.22), (2.98±0.18), (2.29±0.17), and (1.45±0.21) mm, which was significantly larger than (2.24±0.15), (2.49±0.15), (1.51±0.17), (1.04±0.16), and (1.01±0.13) mm in survival group (t=7.55, 12.14, 27.11, 19.99, 7.11, P<0.01). BWT of patients in survival group and death group at 24 h post admission, 3, 7, and 14 d post admission showed statistically significant difference when compared with that at admission within the corresponding group (t=5.97, 16.63, 28.21, 38.57, 5.34, 3.31, 4.39, 6.48, P<0.01). BWT of patients in survival group and death group on 3, 7, and 14 d post admission was significantly smaller than that at 24 h post admission within the corresponding group (t=22.27, 34.02, 45.03, 2.77, 10.53, 10.59, P<0.01). BWT of patients in survival group and death group on 7 and 14 d post admission was significantly smaller than that on 3 d post admission within the corresponding group (t=10.49, 18.26, 9.57, 11.44, P<0.01). BWT of patients in survival group and death group on 14 d post admission was significantly smaller than that on 7 d post admission within the corresponding group (t=6.97, 6.15, P<0.01). (3) The total areas under ROC curves of inhalation injury rating at admission and BWT at admission for predicting death of 43 patients were 0.880 and 0.956, respectively (with 95% confidence intervals 0.768-0.991, 0.882-1.000, P<0.05). Grade 1.5 and 2.75 mm were respectively chosen as the optimal threshold values of inhalation injury rating at admission and BWT at admission, with sensitivity of 87.50%, 83.33% and specificity of 77.78%, 96.00%, respectively. Conclusions: The BWT of survived and dead patients with severe burn and inhalation injury increases significantly post burn, while the BWT of survived patients restores to normal level faster. BWT can be used to assess the severity of inhalation injury and to predict death in severely burned patients combined with inhalation injury.

Predicting high-risk endometrioid carcinomas using proteins

Background

The lethality of endometrioid endometrial cancer (EEC) is primarily attributable to advanced-stage diseases. We sought to develop a biomarker model that predicts EEC surgical stage at the time of clinical diagnosis.

Results

PSES was significantly correlated with surgical stage in the TCGA cohort (P < 0.0001) and in the validation cohort (P = 0.0003). Even among grade 1 or 2 tumors, PSES was significantly higher in advanced than in early stage tumors in both the TCGA (P = 0.005) and MD Anderson Cancer Center (MDACC) (P = 0.006) cohorts. Patients with positive PSES score had significantly shorter progression-free survival than those with negative PSES in the TCGA (hazard ratio [HR], 2.033; 95% CI, 1.031 to 3.809; P = 0.04) and validation (HR, 3.306; 95% CI, 1.836 to 9.436; P = 0.0007) cohorts. The ErbB signaling pathway was most significantly enriched in the PSES proteins and downregulated in advanced stage tumors.

Methods

Using reverse-phase protein array expression profiles of 170 antibodies for 210 EEC cases from TCGA, we constructed a Protein Scoring of EEC Staging (PSES) scheme comprising 6 proteins (3 of them phosphorylated) for surgical stage prediction. We validated and evaluated its diagnostic potential in an independent cohort of 184 EEC cases obtained at MDACC using receiver operating characteristic curve analyses. Kaplan-Meier survival analysis was used to examine the association of PSES score with patient outcome, and Ingenuity pathway analysis was used to identify relevant signaling pathways. Two-sided statistical tests were used.

Conclusions

PSES may provide clinically useful prediction of high-risk tumors and offer new insights into tumor biology in EEC.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Geniposide prevents H2 O2 -induced oxidative damage in melanocytes by activating the PI3K-Akt signalling pathway

BACKGROUND

Oxidative stress is one possible pathogenic event in vitiligo that induces melanocyte destruction. Geniposide exerts certain antioxidant effects on various cells by activating the phosphoinositol 3-kinase (PI3K)-Akt signalling pathway. However, researchers have not clearly determined whether geniposide protects human melanocytes from oxidative stress or identified the underlying mechanism of such protection.

AIM

To determine whether geniposide protects melanocytes from H₂ O₂ -induced oxidative damage and to explore the role of the PI3K-Akt signalling pathway in this protective effect.

METHODS

The antioxidant effects of geniposide on human melanocytes were examined by measuring cell viability, apoptosis rates, reactive oxygen species (ROS) production and activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT). We examined expression of Akt, phosphorylated Akt (p-Akt), Bcl-2, Bax, and cleaved caspase 3 and cleaved caspase 9 proteins to determine the involvement of the PI3K-Akt pathway.

RESULTS

Pretreatment with geniposide 5, 25, 125 or 625 μmol/L increased cell viability and decreased the apoptosis rate of H₂ O₂ -treated melanocytes. In addition, geniposide enhanced the antioxidant activity of SOD and CAT, and decreased intracellular ROS accumulation. Furthermore, geniposide increased the levels of p-Akt and regulated the expression of downstream proteins in the PI3K-Akt pathway, such as Bcl-2, Bax, and cleaved caspase 3 and 9, in H₂ O₂ -treated melanocytes. Notably, these effects were largely blocked by treatment with LY294002 prior to H₂ O₂ treatment.

CONCLUSIONS

Based on these results, geniposide protects human melanocytes from H₂ O₂ -induced oxidative damage, and the PI3K-Akt signalling pathway is involved in its antioxidant effect.

DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations

Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations (www.cs.hmc.edu/dtlrnb).

Predictive Gene Signatures Determine Tumor Sensitivity to MDM2 Inhibition

Early clinical trials using murine double minute 2 (MDM2) inhibitors demonstrated proof-of-concept of p53-induced apoptosis by MDM2 inhibition in cancer cells; however, not all wild-type TP53 tumors are sensitive to MDM2 inhibition. Therefore, more potent inhibitors and biomarkers predictive of tumor sensitivity are needed. The novel MDM2 inhibitor DS-3032b is 10-fold more potent than the first-generation inhibitor nutlin-3a. TP53 mutations were predictive of resistance to DS-3032b, and allele frequencies of TP53 mutations were negatively correlated with sensitivity to DS-3032b. However, sensitivity to DS-3032b of TP53 wild-type tumors varied greatly. We thus used two methods to create predictive gene signatures. First, by comparing sensitivity to MDM2 inhibition with basal mRNA expression profiles in 240 cancer cell lines, a 175-gene signature was defined and validated in patient-derived tumor xenograft models and ex vivo human acute myeloid leukemia (AML) cells. Second, an AML-specific 1,532-gene signature was defined by performing random forest analysis with cross-validation using gene expression profiles of 41 primary AML samples. The combination of TP53 mutation status with the two gene signatures provided the best positive predictive values (81% and 82%, compared with 62% for TP53 mutation status alone). In addition, the top-ranked 50 genes selected from the AML-specific 1,532-gene signature conserved high predictive performance, suggesting that a more feasible size of gene signature can be generated through this method for clinical implementation. Our model is being tested in ongoing clinical trials of MDM2 inhibitors.Significance: This study demonstrates that gene expression profiling combined with TP53 mutational status predicts antitumor effects of MDM2 inhibitors in vitro and in vivoCancer Res; 78(10); 2721-31. ©2018 AACR.

The SET protein promotes androgen production in testicular Leydig cells

Approximately 40% of middle‐aged men exhibit symptoms of late‐onset hypogonadism (LOH). However, the mechanism of androgen deficiency is still currently unclear. As shown in our previous studies, the SET protein is expressed in testicular Leydig cells and ovarian granule cells. This study was designed to investigate the effect of the SET protein on androgen production in Leydig cells. The AdCMV/SET and AdH1siRNA/SET adenoviruses were individually transduced into a cultured mouse Leydig cell line (mLTC‐1) with or without human chorionic gonadotropin (HCG) stimulation in vitro. The primary mouse Leydig cells were used to confirm the main data from mLTC‐1 cells. The SET protein was expressed in the cytoplasm and nucleus of mLTC‐1 cells. Testosterone production was significantly increased in mLTC‐1 cells overexpressing the SET protein compared with the control group (p < 0.05), whereas testosterone production was significantly decreased in the SET knockdown mLTC‐1 cells (p < 0.05). Consistent with the testosterone levels, the expression levels of the steroidogenic acute regulatory (StAR) and cytochrome P450c17α‐hydroxylase (CYP17a1) mRNAs and proteins synchronously changed according to the expression level of the SET protein. Interestingly, the expression of the SET protein was significantly increased in the mLTC‐1 cells stimulated with 0.04 and 0.1 U/mL hCG. In the mLTC‐1 cells transfected with AdH1siRNA/SET and concurrently stimulated with 0.1 U/mL hCG, both testosterone production and StAR expression were significantly lower than in the cells without SET knockdown (p < 0.05). In conclusion, the SET protein participates in regulating testosterone production by increasing the expression of StAR and CYP17a1, and it may be a downstream factor of the classic luteinizing hormone (LH)/luteinizing hormone receptor (LHR) signaling pathway. This study improves our understanding of the intracellular mechanism of testicular steroidogenesis and the pathophysiological mechanism of LOH in the aging male.

Morphological analysis and quantitative evaluation of myopic maculopathy by three-dimensional magnetic resonance imaging

PurposeTo study the characteristic morphology and quantitatively evaluate the eye shape in different types of myopic maculopathy.MethodsA total of 103 eyes from 65 patients with high myopic maculopathy were examined by spectral-domain optical coherence tomography (SD-OCT) and three-dimensional magnetic resonance imaging (3D MRI). The participants were classified into two groups, namely myopic traction maculopathy (MTM) eyes and non-MTM eyes, with SD-OCT imaging. Volume renderings and morphology analysis of the 3D MRI of the eyeball were obtained. Quantitative analysis was achieved in the calculation of vitreous volume and the three-dimensional diameters of the eyeball in three cardinal axes. The eye shape distribution and the diameters of the eyeball were compared between the two groups. Eye shape distribution, vitreous volume, and eyeball diameter were compared between MTM and non-MTM eyes.ResultsThe MTM and non-MTM groups had a total of 68 and 35 eyes, respectively. A significant difference was found in the eye shape distribution (P<0.0001) between MTM and non-MTM eyes. Most of the MTM eyes had undergone a non-uniform expansion of the eyeball, whereas the non-MTM eyes had expanded uniformly. There was no significant difference (P>0.05) in either vitreous volume or other diameters between the two groups.ConclusionsNon-uniform globe expansion and staphyloma formation might play an important role in the pathogenesis of MTM.

Effects of coexisting BDE-47 on the migration and biodegradation of BDE-99 in river-based aquifer media recharged with reclaimed water

Two prominent polybrominated diphenyl ether (PBDE) congeners have been included in the persistent organic pollutant list, 2,2',4,4',5-tetrabromodiphenyl ether (BDE-99) and 2,2,4,4'-tetrabromodiphenyl ether (BDE-47), which have been detected in treated municipal wastewater, river water, and sediments in China. A lab-scale column experiment was established to investigate the effects of the competitive sorption of BDE-47 on BDE-99 biodegradation and migration in two types of river-based aquifer soils during groundwater recharge with reclaimed water. Two types of recharge columns were used, filled with either silty clay (SC) or black carbon-amended silty clay (BCA). The decay rate constants of BDE-99 in the BCA and SC systems were 0.186 and 0.13 m^-1 in the single-solute system and 0.128 and 0.071 m^-1 in the binary-solute system, respectively, showing that the decay of BDE-99 was inhibited by the coexistence of BDE-47. This was particularly evident in the SC system because the higher hydrophobicity of BDE-99 determined the higher affinity and competition for sorption sites onto black carbon. The biodegradation of BDE-99 was suppressed by the coexistence of BDE-47, especially in the SC system. Lesser-brominated congeners (BDE-47 and BDE-28) and higher-brominated congeners (BDE-100, BDE-153, BDE-154, and BDE-183) were generated in the four recharge systems, albeit at different ratios. Bacterial biodiversity was influenced by the presence of BDE-47 in the SC system, while it had no significant effect on the BCA system, because the high sorption capacity of black carbon on the hydrophobic PBDEs effectively reduced their toxicity. The ranking order of the most abundant classes changed markedly due to the coexistence of BDE-47 in both the SC and BCA systems. The ranking order of the most abundant genera changed from Azospira, Methylotenera, Desulfovibrio, Methylibium, and Bradyrhizobium to Halomonas, Hyphomicrobium, Pseudomonas, Methylophaga, and Shewanella, which could be involved in PBDE degradation.

Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines

Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis are highly toxic to lepidopteran pests. Strains of transgenic rice expressing cry genes have been developed that are resistant to rice pests. Understanding the mode of action of Cry toxins in rice pests will improve our ability to use them effectively as insecticides. In this study, we tested the hypothesis that alkaline phosphatases (ALPs) are involved in Cry1A, Cry2Aa and Cry1Ca toxicity in Chilo suppressalis, an important insect pest of rice crops in China. We first cloned three novel C. suppressalis alps (Csalps) from the larval midgut of C. suppressalis. RNA interference knockdown of six different Csalp genes (Csalp1, Csalp2, Csalp3, Csalp4, Csalp5 and Csalp6) showed that knockdown of three of these, Csalp1, Csalp2 and Csalp4, reduced larval mortality to the transgenic rice strain TT51, which expresses a fusion protein of Cry1Ab and Cry1Ac, whereas suppression of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp6 transcripts decreased the susceptibility of larvae to the transgenic rice strain T2A-1, which expresses cry2Aa. Moreover, downregulation of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp5 transcripts conferred significant tolerance to the transgenic rice strain T1C-19, which expresses cry1Ca. These results suggest that these ALPs play a key role in the toxicity of Cry1A, Cry2A and Cry1C to C. suppressalis.

Signalling transduction events involved in agonist-induced PGE2/EP4 receptor externalization in cultured rat dorsal root ganglion neurons

BACKGROUND

Prostaglandin E2 (PGE2) enriched in inflamed tissues contributes to chronic pain by sensitizing nociceptive dorsal root ganglion (DRG) neurons (nociceptors). Of four PGE2 receptors (EP1-4), EP4 plays a major role in PGE2-induced nociceptor sensitization. We have previously reported that PGE2 or EP4 agonists stimulated EP4 externalization in cultured DRG neurons and this event contributes to nociceptor sensitization. However, the signalling transduction events governing this event remain unknown.

METHODS

In this study, using antibody-based externalization assay, we examined EP subtypes and multiple signalling transduction events involved in PGE2-induced EP4 externalization in cultured DRG neurons.

RESULTS

In addition to EP4 agonist, EP2 agonist, to a lesser extent, also induced EP4 externalization while EP1 and EP3 agonists had no effect. The extracellular and intracellular calcium chelators, the inhibitors of CaMKII, cAMP, PKA, PKC, PKCε, PLC, MAPKs, PI3K and Akt suppressed agonist-induced EP4 externalization. The activator of AC, two PKA-specific cAMP analogues and one Epac-specific cAMP analogue also induced EP4 externalization. ELISA showed that double sequential exposures to EP4 agonists induced a greater release of pain peptide CGRP from cultured DRG neurons than a single exposure, an event blocked by the inhibitor of anterograde transport from ER/Golgi complex to cell surface.

CONCLUSIONS

Taken together, these data suggest that mobilization of extracellular and intracellular calcium as well as the activation of CaMKII, cAMP/PKA, cAMP/Epac, PKC/PKCε, MAPKs, PI3K-Akt and PLC signalling transduction pathways are involved in agonist-induced EP4 externalization. Agonist-enhanced EP4 externalization increases EP4 cell surface abundance and activity, thus enhancing nociceptor sensitization.

SIGNIFICANCE

This study adds mechanistic information regarding signalling transduction events involved in agonist-induced EP4 cell surface trafficking. EP4 and EP2 (to lesser extent) receptors, extra- and intracellular Ca⁺⁺ , CaKMII, cAMP, PKA, PKC, PKCε, PLC, MAPK, PI3K and Akt are involved in this event. Agonist-induced EP4 externalization contributes to enhanced nociceptor sensitization.

Overcoming drug-resistant lung cancer by paclitaxel loaded tetrahedral DNA nanostructures

Drug-loaded tetrahedron DNA nanostructures and their cytotoxic effect on drug-resistant cells have been studied.

Expression pattern of high-affinity tyrosine kinase Aduring the development of human fetal spinal cord

High-affinity tyrosine kinase A (TrkA) is responsible for the biological activities of nerve growth factor. Most studies of the molecular mechanisms of TrkA that underlie the development of the spinal cord have been conducted in animals and the expression pattern of TrkA during the development of the human fetal spinal cord is not well characterized. We investigated 45 3-28-week-old (G3W-G28W) human fetuses. We assessed the expression pattern of TrkA in the human fetal spinal cord using immunohistochemistry, western blot and reverse transcription polymerase chain reaction to clarify the spatiotemporal developmental changes and to determine the role TrkA plays in development. TrkA immunoreactive products were detected widely in the alar and basal plates, ependyma, glial cells, gray and white matter, internal limiting membrane, mantle layer, marginal layer, neuroepithelium and neurons during this period of development. Expression levels of TrkA mRNA and protein peaked at G12W and G16W, respectively. The strong expression of TrkA was closely related to the formation of the dorsal and ventral horns, and the differentiation of somatic motor neurons during late embryonic development. Our findings suggest that TrkA receptors play crucial roles during the development of human fetal spinal cord. The characteristic expression patterns may clarify the developmental characteristics of the human spinal cord.

C-reactive protein promotes bone destruction in human myeloma through the CD32-p38 MAPK-Twist axis

Bone destruction is a hallmark of myeloma and affects 80% of patients. Myeloma cells promote bone destruction by activating osteoclasts. In investigating the underlying mechanism, we found that C-reactive protein (CRP), a protein secreted in increased amounts by hepatocytes in response to myeloma-derived cytokines, activated myeloma cells to promote osteoclastogenesis and bone destruction in vivo. In mice bearing human bone grafts and injected with multiple myeloma cells, CRP bound to surface CD32 (also known as FcγRII) on myeloma cells, which activated a pathway mediated by the kinase p38 MAPK and the transcription factor Twist that enhanced the cells' secretion of osteolytic cytokines. Furthermore, analysis of clinical samples from newly diagnosed myeloma patients revealed a positive correlation between the amount of serum CRP and the number of osteolytic bone lesions. These findings establish a mechanism by which myeloma cells are activated to promote bone destruction and suggest that CRP may be targeted to prevent or treat myeloma-associated bone disease in patients.

Tumor Trp53 status and genotype affect the bone marrow microenvironment in acute myeloid leukemia

The genetic heterogeneity of acute myeloid leukemia (AML) and the variable responses of individual patients to therapy suggest that different AML genotypes may influence the bone marrow (BM) microenvironment in different ways. We performed gene expression profiling of bone marrow mesenchymal stromal cells (BM-MSC) isolated from normal C57BL/6 mice or mice inoculated with syngeneic murine leukemia cells carrying different human AML genotypes, developed in mice with Trp53 wild-type or nullgenetic backgrounds. We identified a set of genes whose expression in BM-MSC was modulated by all four AML genotypes tested. In addition, there were sets of differentially-expressed genes in AML-exposed BM-MSC that were unique to the particular AML genotype or Trp53 status. Our findings support the hypothesis that leukemia cells alter the transcriptome of surrounding BM stromal cells, in both common and genotype-specific ways. These changes are likely to be advantageous to AML cells, affecting disease progression and response to chemotherapy, and suggest opportunities for stroma-targeting therapy, including those based on AML genotype.

Inverse incoherent engineering

We propose a protocol to construct shortcuts of adiabaticity for open quantum systems in unitary evolution. Using the dynamical invariants of open quantum systems, we design a convenient form of the driver Hamiltonian to accelerate the adiabatic decoherence free subspaces scheme (TDFs) and engineer a quantum state from the initial state into the target state. Since the trajectory of TDFSs is determined by the incoherent control process, we would like to call it as the inverse incoherent engineering protocol. We apply the method to a two-qubits system which interacts with a time-dependent vacuum squeezed field to prepare some maximally entangled states of it. The results illustrate that our protocol can be used both in the adiabatic and nonadiabatic regime with perfect fidelity.

Fluorescent markers of various organelles in the wheat pathogen Zymoseptoria tritici

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17 vectors are described that allow labelling of 7 subcellular structures.

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The fluorescent markers target the plasma membrane, endoplasmic reticulum, nucleus.

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Markers also target the actin cytoskeleton, peroxisomes and autophagosomes.

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These markers complete are toolkit of fluorescent reporters.

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Reporters allow cell biological studies in the Septoria tritici blotch fungus.

Development of novel strategies to control fungal plant pathogens requires understanding of their cellular organisation and biology. Live cell imaging of fluorescent organelle markers has provided valuable insight into various aspects of their cell biology, including invasion strategies in plant pathogenic fungi. Here, we introduce a set of 17 vectors that encode fluorescent markers to visualize the plasma membrane, endoplasmic reticulum (ER), chromosomes, the actin cytoskeleton, peroxisomes and autophagosomes in the wheat pathogen Zymoseptoria tritici. We fused either enhanced green-fluorescent protein (eGFP) or a codon-optimised version of GFP (ZtGFP) to homologues of a plasma membrane-located Sso1-like syntaxin, an ER signalling and retention peptide, a histone H1 homologue, the LifeAct actin-binding peptide, a mitochondrial acetyl-CoA dehydrogenase, a peroxisomal import signal and a homologue of the ubiquitin-like autophagosomal protein Atg8. We expressed these markers in wildtype strain IPO323 and confirmed the specificity of these markers by counterstaining or physiological experiments. This new set of molecular tools will help understanding the cell biology of the wheat pathogen Z. tritici.