Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis of osteosarcoma identifies suppression of wnt pathway and up-regulation of adiponectin as potential biomarker

Osteosarcoma (OS) is primary malignant bone tumour with complicated early diagnosis. There are no specific markers currently available for predicting the prognosis and chemosensitivity of OS. In present study we performed transcriptome profiling of single patient tumour tissue with RNA-seq technology. We analysed surgically removed sarcoma sample from single 16 years old male patient. Transciptome analysis was done with RNA-seq technology, bioinformatics with Lifescope and R Bioconductor. Validation experiments were done with quantitative real-time PCR (QRTPCR). After quality and coverage filtering, RNA-seq experiment resulted 29,311,899 mapped reads for sarcoma and 22,099,159 mapped reads for normal bone tissue. 65 genes were differentially expressed with FDR corrected statistical significance below 0.05. Seven genes were down-regulated and 58 genes were up-regulated in sarcoma. The most highly up-regulated gene in sarcoma was adiponectin, ADIPOQ (with adjusted p-value 5.5E-07, log2 fold change was 7.9). Many of the genes we found are related to the adipose tissue metabolism (ADIPOQ, PLIN1, FABP4) and to the Wnt signalling suppression (WIF1, SOST). We also found novel fusion transcript between the genes LMTK2 and ZSWIM5. LMTK2 is lemur tyrosine kinase 2, and it has been shown to be involved in NGF-TrkA signalling. Interestingly, studies support the involvement of LMTK2 in development of prostate cancer. ZSWIM5 is zinc finger SWIM domain protein 5 and its function is not known. Immunohistochemical analysis confirmed positive staining for adiponectin in osteosarcoma. This paper is a good illustration how transcriptome analysis can find new biomarkers and targets for complex diseases.
Pancreatic β‐cell Na+ channels control global Ca2+ signaling and oxidative metabolism by inducing Na+ and Ca2+ responses that are propagated into mitochondria

Communication between the plasma membrane and mitochondria is essential for initiating the Ca2+ and metabolic signals required for secretion in β cells. Although voltage‐dependent Na+ channels are abundantly expressed in β cells and activated by glucose, their role in communicating with mitochondria is unresolved. Here, we combined fluorescent Na+, Ca2+, and ATP imaging, electrophysiological analysis with tetrodotoxin (TTX)‐dependent block of the Na+ channel, and molecular manipulation of mitochondrial Ca2+ transporters to study the communication between Na+ channels and mitochondria. We show that TTX inhibits glucose‐dependent depolarization and blocks cytosolic Na+ and Ca2+ responses and their propagation into mitochondria. TTX‐sensitive mitochondrial Ca2+ influx was largely blocked by knockdown of the mitochondrial Ca2+ uniporter (MCU) expression. Knockdown of the mitochondrial Na+/Ca2+ exchanger (NCLX) and Na+ dose response analysis demonstrated that NCLX mediates the mitochondrial Na+ influx and is tuned to sense the TTX‐sensitive cytosolic Na+ responses. Finally, TTX blocked glucose‐dependent mitochondrial Ca2+ rise, mitochondrial metabolic activity, and ATP production. Our results show that communication of the Na+ channels with mitochondria shape both global Ca2+ and metabolism signals linked to insulin secretion in β cells. —Nita, I. I. , Hershfinkel, M. , Kantor, C. , Rutter, G. A. , Lewis, E. C. , Sekler, I. Pancreatic β‐cell Na+ channels control global Ca2+ signaling and oxidative metabolism by inducing Na+ and Ca2+ responses that are propagated into mitochondria. FASEB J. 28, 3301–3312 (2014). www.fasebj. org
Autonomous CaMKII requires further stimulation by Ca2+/calmodulin for enhancing synaptic strength

A hallmark feature of Ca2+/calmodulin (CaM)‐dependent protein kinase II (CaMKII) is generation of autonomous (Ca2+‐independent) activity by T286 autophosphorylation. Biochemical studies have shown that “autonomous” CaMKII is ~5‐fold further stimulated by Ca2+/CaM, but demonstration of a physiological function for such regulation within cells has remained elusive. In this study, CaMKII‐induced enhancement of synaptic strength in rat hippocampal neurons required both autonomous activity and further stimulation. Synaptic strength was decreased by CaMKIIα knockdown and rescued by reexpression, but not by mutants impaired for autonomy (T286A) or binding to NMDA‐type glutamate receptor subunit 2B (GluN2B; formerly NR2B; I205K). Full rescue was seen with constitutively autonomous mutants (T286D), but only if they could be further stimulated (additional T305/306A mutation), and not with two other mutations that additionally impair Ca2+/CaM binding. Compared to rescue with wild‐type CaMKII, the CaM‐binding‐impaired mutants even had reduced synaptic strength. One of these mutants (T305/306D) mimicked an inhibitory autophosphorylation of CaMKII, whereas the other one (Δstim) abolished CaM binding without introducing charged residues. Inhibitory T305/306 autophosphorylation also reduced GluN2B binding, but this effect was independent of reduced Ca2+/CaM binding and was not mimicked by T305/306D mutation. Thus, even autonomous CaMKII activity must be further stimulated by Ca2+/CaM for enhancement of synaptic strength. —Barcomb, K. , Buard, I. , Coultrap, S. J., Kulbe, J. R. , O'Leary, H. , Benke, T. A. , Bayer, K. U. Autonomous CaMKII requires further stimulation by Ca2+/calmodulin for enhancing synaptic strength. FASEB J. 28, 3810–3819 (2014). www.fasebj. org
A Novel Mechanism by Which Thiazolidinediones Facilitate the Proteasomal Degradation of Cyclin D1 in Cancer Cells*

This study identifies a novel mechanism by which thiazolidinediones mediate cyclin D1 repression in prostate cancer cells. Based on the finding that the thiazolidinedione family of peroxisome proliferator-activated receptor γ (PPARγ) agonists mediated PPARγ-independent cyclin D1 degradation, we developed a novel PPARγ-inactive troglitazone derivative, STG28, with high potency in cyclin D1 ablation. STG28-mediated cyclin D1 degradation was preceded by Thr-286 phosphorylation and nuclear export, which however, were independent of glycogen synthase kinase 3β. Mutational analysis further confirmed the pivotal role of Thr-286 phosphorylation in STG28-induced nuclear export and proteolysis. Of several kinases examined, inhibition of IκB kinase α blocked STG28-mediated cytoplasmic sequestration and degradation of cyclin D1. Pulldown of ectopically expressed Cul1, the scaffold protein of the Skp-Cullin-F-box E3 ligase, in STG28-treated cells revealed an increased association of cyclin D1 with β-TrCP, whereas no specific binding was noted with other F-box proteins examined, including Skp2, Fbw7, Fbx4, and Fbxw8. This finding represents the first evidence that cyclin D1 is targeted by β-TrCP. Moreover, β-TrCP expression was up-regulated in response to STG28, and ectopic expression and small interfering RNA-mediated knock-down of β-TrCP enhanced and protected against STG28-facilitated cyclin D1 degradation, respectively. Because cyclin D1 lacks the DSG destruction motif, mutational and modeling analyses indicate that cyclin D1 was targeted by β-TrCP through an unconventional recognition site, 279EEVDLACpT286, reminiscent to that of Wee1. Moreover, we obtained evidence that this β-TrCP-dependent degradation takes part in controlling cyclin D1 turnover when cancer cells undergo glucose starvation, which endows physiological relevance to this novel mechanism.
Substrates and Non-transportable Analogues Induce Structural Rearrangements at the Extracellular Entrance of the Glial Glutamate Transporter GLT-1/EAAT2*

To explore rearrangements of the reentrant loop HP2 relative to transmembrane domains (TMs) 7 and 8 during transport by the glial glutamate transporter GLT-1/EAAT2, cysteine pairs were introduced at the extracellular ends of these structural elements. The pairs were introduced around 10–15Å “above” the residues, which make contact with substrate in the related archaeal homologue GltPh. Transport by the double mutants M449C/L466C (HP2/TM 8), L453C/I463C (HP2/TM 8), and I411C/I463C (TM 7/TM 8) was inhibited by copper(II)(1,10-phenanthroline)3 (CuPh) and by Cd2+. Inhibition was only observed when the two cysteines were present in the same construct, but not with the respective single cysteine mutants or when only one cysteine was paired with a mutation to another residue. Glutamate and potassium, both expected to increase the proportion of inward-facing transporters, significantly protected against the inhibition of transport activity of M449C/L466C by CuPh. The non-transportable analogues kainate and d, l-threo-β-benzyloxyaspartate are expected to stabilize an outward-facing conformation, but only the latter potentiated the effect of CuPh on M449C/L466C. However, both analogues increased the aqueous accessibility of the cysteines introduced at positions 449 and 466 to a membrane-impermeant sulfhydryl reagent. Inhibition of L453C/I463C by CuPh was protected not only by glutamate but also by the two analogues. In contrast, these ligands had very little effect on the inhibition of I411C/I463C by CuPh. Our results are consistent with the proposal that HP2 serves as the extracellular gate of the transporter and indicate that glutamate and the two analogues induce distinct conformations of HP2.
Maternal protein-energy malnutrition during early pregnancy in sheep impacts the fetal ornithine cycle to reduce fetal kidney microvascular development

This paper identifies a common nutritional pathway relating maternal through to fetal protein‐energy malnutrition (PEM) and compromised fetal kidney development. Thirty‐one twin‐bearing sheep were fed either a control (n=15) or low‐protein diet (n= 16, 17 vs. 8.7 g crude protein/MJ metabolizable energy) from d 0 to 65 gestation (term, ~ 145 d). Effects on the maternal and fetal nutritional environment were characterized by sampling blood and amniotic fluid. Kidney development was characterized by histology, immunohistochemistry, vascular corrosion casts, and molecular biology. PEM had little measureable effect on maternal and fetal macronutrient balance (glucose, total protein, total amino acids, and lactate were unaffected) or on fetal growth. PEM decreased maternal and fetal urea concentration, which blunted fetal ornithine availability and affected fetal hepatic polyamine production. For the first time in a large animal model, we associated these nutritional effects with reduced micro‐ but not macrovascular development in the fetal kidney. Maternal PEM specifically impacts the fetal ornithine cycle, affecting cellular polyamine metabolism and microvascular development of the fetal kidney, effects that likely underpin programming of kidney development and function by a maternal low protein diet. —Dunford, L. J., Sinclair, K. D. , Kwong, W. Y. , Sturrock, C. , Clifford, B. L. , Giles, T. C. , Gardner, D. S. , Maternal protein‐energy malnutrition during early pregnancy in sheep impacts the fetal ornithine cycle to reduce fetal kidney microvascular development. FASEB J. 28, 4880–4892 (2014). www.fasebj. org
SHP2 regulates osteoclastogenesis by promoting preosteoclast fusion

Genes that regulate osteoclast (OC) development and function in both physiologic and disease conditions remain incompletely understood. Shp2 (the Src homology‐2 domain containing protein tyrosine phosphatase 2), a ubiquitously expressed cytoplasmic protein tyrosine phosphatase, is implicated in regulating M‐CSF and receptor activator of nuclear factor‐κB ligand (RANKL)‐ evoked signaling; its role in osteoclastogenesis and bone homeostasis, however, remains unknown. Using a tissue‐specific gene knockout approach, we inactivated Shp2 expression in murine OCs. Shp2 mutant mice are phenotypically osteopetrotic, featuring a marked increase of bone volume (BV)/total volume (TV) (+42.8%), trabeculae number (Tb.N) (+84.1%), structure model index (+119%), and a decrease of trabecular thickness (Tb.Th) (‐34.1%) and trabecular spacing (Tb.Sp) (‐41.0%). Biochemical analyses demonstrate that Shp2 is required for RANKL‐induced formation of giant multinucleated OCs by up‐regulating the expression of nuclear factor of activated T cells, cytoplasmic 1 (Nfatc1), a master transcription factor that is indispensable for terminal OC differentiation. Shp2 deletion, however, has minimal effect on M‐CSF‐dependent survival and proliferation of OC precursors. Instead, its deficiency aborts the fusion of OC precursors and formation of multinucleated OCs and decreases bone matrix resorption. Moreover, pharmacological intervention of Shp2 is sufficient to prevent preosteoclast fusion in vitro. These findings uncover a novel mechanism through which Shp2 regulates osteoclastogenesis by promoting preosteoclast fusion. Shp2 or its signaling partners could potentially serve as pharmacological targets to regulate the population of OCs locally and/or systematically, and thus treat OC‐related diseases, such as periprosthetic osteolysis and osteoporosis. —Zhou, Y. , Mohan, A. , Moore, D. C. , Lin, L. , Zhou, F. L. , Cao, J., Wu, Q. , Qin, Y. ‐X. , Reginato, A. M. , Ehrlich, M. G. , Yang, W. SHP2 regulates osteoclastogenesis by promoting preosteoclast fusion. FASEB J. 29, 1635‐1645 (2015). www.fasebj. org
Studying 18 MDa virus assemblies with native mass spectrometry.

Following John Fenn's Nobel Laureate lecture (entitled “Electrospray Wings for Molecular Elephants”),[1] native mass spectrometry (MS) has been developed as a powerful analytical technique to study large non-covalent protein complexes. [2] Using soft nano-electrospray ionization (nESI), these protein complexes can be transferred intact into the gas phase without significant loss of quaternary or tertiary structure. Minor modifications of commercially available MS instruments[3] can greatly improve the transmission of large ions, therefore yielding accurate and precise mass analysis of intact protein complexes. As a result, the stoichiometry of protein complexes can be readily determined in a native MS approach. The study of solution-phase and gas-phase dissociation along with the combination of MS with Ion Mobility can also yield valuable information on the stability and topology of a protein complex. [4]
The effect of antireflux treatment on patients with gastroesophageal reflux disease undergoing a mental arithmetic stressor

Background Acute stress exacerbates heartburn in gastroesophageal reflux disease (GERD) patients by enhancing the perceptual responses to intraesophageal acid. The aim of the study was to determine if antireflux treatment can still alter stimulus response functions to acid in patients undergoing acute stress as compared with placebo.
15‐Lipoxygenase‐1 suppression of colitis‐associated colon cancer through inhibition of the IL‐6/STAT3 signaling pathway

The IL‐6/signal transducer and activator of transcription 3 (STAT3) pathway is a critical signaling pathway for colitis‐associated colorectal cancer (CAC). Peroxisome proliferator‐activated receptor (PPAR)‐δ, a lipid nuclear receptor, up‐regulates IL‐6. 15‐Lipoxygenase‐1 (15‐LOX‐1), which is crucial to production of lipid signaling mediators to terminate inflammation, down‐regulates PPAR‐δ. 15‐LOX‐1 effects on IL‐6/STAT3 signaling and CAC tumorigenesis have not been determined. We report that intestinally targeted transgenic 15‐LOX‐1 expression in mice inhibited azoxymethane‐ and dextran sodium sulfate‐induced CAC, IL‐6 expression, STAT3 phosphorylation, and IL‐6/STAT3 downstream target (Notch3 and MUC1) expression. 15‐LOX‐1 down‐regulation was associated with IL‐6 up‐regulation in human colon cancer mucosa. Reexpression of 15‐LOX‐1 in human colon cancer cells suppressed IL‐6 mRNA expression, STAT3 phosphorylation, IL‐6 promoter activity, and PPAR‐δ mRNA and protein expression. PPAR‐δ overexpression in colonic epithelial cells promoted CAC tumorigenesis in mice and increased IL‐6 expression and STAT3 phosphorylation, whereas concomitant 15‐LOX‐1 expression in colonic epithelial cells (15‐LOX‐1‐PPAR‐δ‐Gut mice) suppressed these effects: the number of tumors per mouse (mean ± sem) was 4.22 ± 0.68 in wild‐type littermates, 6.67 ± 0.83 in PPAR‐δ‐Gut mice (P= 0.026), and 2.25 ± 0.25 in 15‐LOX‐1‐PPAR‐δ‐Gut mice (P = 0.0006). Identification of 15‐LOX‐1 suppression of PPAR‐δ to inhibit IL‐6/STAT3 signaling‐driven CAC tumorigenesis provides mechanistic insights that can be used to molecularly target CAC. —Mao, F. , Xu, M. , Zuo, X. , Yu, J., Xu, W. , Moussalli, M. J., Elias, E. , Li, H. S. , Watowich, S. S. , Shureiqi, I. 15‐Lipoxygenase‐1 suppression of colitis‐associated colon cancer through inhibition of the IL‐6/STAT3 signaling pathway. FASEB J. 29, 2359‐2370 (2015). www.fasebj. org
Ca2+ channel subunit α 1D promotes proliferation and migration of endometrial cancer cells mediated by 17β‐estradiol via the G protein‐coupled estrogen receptor

Calcium and calcium channels are closely related to the estrogen‐induced nongenomic effect of endometrial carcinoma, but the specific role of calcium channels is unknown. This study aimed to explore the expression and the biologic effect of the l‐type calcium channel in endometrial carcinoma cells and to clarify the molecular mechanism of the relationship between L‐type calcium channels and estrogen. The immunohistochemical results showed that Ca2+ channel subunit α 1D (Cav1.3) expression was high in atypical hyperplasia (1.90 ± 0.35) and endometrial carcinoma tissues (2.05 ± 0.82) but weak (0.80 ± 0.15) in benign endometrial tissues (P < 0.05). Treatment with 17b‐estradiol rapidly increased Cav1.3 expression in a dose‐ and time‐dependent manner, and 100 nM cell‐impermeable β‐estradiol‐6‐(O‐carboxymethyl) oxime:bovine serum albumin also promoted Cav1.3 expression. Transfection with small interfering RNA against G protein‐coupled estrogen receptor (GPER) suppressed estrogen‐induced up‐regulation of Cav1.3 compared with control cells and markedly reduced the estrogen‐induced phosphorylation of ERK1/2 and CREB. Knocking down the Cav1.3 significantly suppressed estrogen‐stimulated Ca2+ influx, cell proliferation, and migration in endometrial cancer cells. Taken together, Cav1.3 was overexpressed in atypical hyperplasia and endometrial carcinoma, and the estrogen‐induced phosphorylation of downstream molecular ERK1/2 and CREB is the result of activation of the GPER pathway. L‐type channel Cav1.3 is required for estrogen‐stimulated Ca2+ influx and contributes broadly to the development of endometrial cancer. The Cav1.3 channel may be a new target for endometrial carcinoma treatment. —Hao, J., Bao, X. , Jin, B. , Wang, X. , Mao, Z. , Li, X. , Wei, L. , Shen, D. , Wang, J.‐L. Ca + channel subunit a 1D promotes proliferation and migration of endometrial cancer cells mediated by 17β‐estradiol via the G protein‐coupled estrogen receptor FASEB J. 29, 2883‐2893 (2015). www.fasebj. org
Actin polymerization‐enhancing drugs promote ovarian follicle growth mediated by the Hippo signaling effector YAP

Hippo signaling pathway consists of conserved serine/threonine kinases to maintain optimal organ sizes. Studies have demonstrated that fragmentation of murine ovaries increases actin polymerization and disrupts Hippo signaling, leading to nuclear translocation of Hippo signaling effector Yes‐associated protein (YAP) in ovarian follicles and follicle growth. For patients with polycystic ovarian syndrome showing follicle arrest, ovarian wedge resection and laser drilling promote follicle growth. Because these damaging procedures likely involve actin polymerization, we tested whether actin polymerization‐promoting drugs could promote YAP translocation and stimulate follicle growth. Treatment of murine ovaries with μM Jasplakinolide (JASP), an actin polymerization‐promoting cyclic peptide, or sphingosine‐1‐phosphate (S1P), a follicular fluid constituent known to promote actin polymerization, increased the conversion of globular actin to the filamentous form, followed by increased nuclear YAP and expression of downstream connective tissue growth factor (CCN2). After short‐term treatments with JASP or S1P, in vitro cultured and in vivo grafted ovaries showed follicle growth. Furthermore, induction of constitutively active YAP in ovarian grafts of transgenic mice enhanced follicle development, whereas treatment of human ovarian cortices with JASP or S1P increased CCN2 expression. Thus, JASP and S1P stimulate follicle growth and are potential therapeutic agents for treating polycystic ovarian syndrome and other ovarian disorders. —Cheng, Y. , Feng, Y. , Jansson, L. , Sato, Y. , Deguchi, M. , Kawamura, K. , Hsueh, A. J. Actin polymerization‐enhancing drugs promote ovarian follicle growth mediated by the Hippo signaling effector YAP. FASEB J. 29, 2423‐2430 (2015). www.fasebj. org
TPN‐associated intestinal epithelial cell atrophy is modulated by TLR4/EGF signaling pathways

Recent studies suggest a close interaction between epidermal growth factor (EGF) and TLR signaling in the modulation of intestinal epithelial cell (IEC) proliferation; however, how these signaling pathways adjust IEC proliferation is poorly understood. We utilized a model of total parenteral nutrition (TPN), or enteral nutrient deprivation, to study this interaction as TPN results in mucosal atrophy due to decreased IEC proliferation and increased apoptosis. We identified the novel finding of decreased mucosal atrophy in TLR4 knockout (TLR4KO) mice receiving TPN. We hypothesized that EGF signaling is preserved in TLR4KO‐TPN mice and prevents mucosal atrophy. C57B1/6 and strain‐matched TLR4KO mice were provided either enteral feeding or TPN. IEC proliferation and apoptosis were measured. Cytokine and growth factor abundances were detected in both groups. To examine interdependence of these pathways, ErbB1 pharmacologic blockade was used. The marked decline in IEC proliferation with TPN was nearly prevented in TLR4KO mice, and intestinal length was partially preserved. EGF was significantly increased, and TNF‐α decreased in TLR4KO‐TPN versus wild‐type (WT)‐TPN mice. Apoptotic positive crypt cells were 15‐fold higher in WT‐TPN versus TLR4KO‐TPN mice. Bcl‐2 was significantly increased in TLR4KOTPN mice, while Bax decreased 10‐fold. ErbB1 blockade prevented this otherwise protective effect in TLR4KO‐sTPN mice. TLR4 blockade significantly prevented TPN‐associated atrophy by preserving proliferation and preventing apoptosis. This is driven by a reduction in TNF‐α abundance and increased EGF. Potential manipulation of this regulatory pathway may have significant clinical potential to prevent TPN‐associated atrophy. —Freeman, J. J., Feng, Y. , Demehri, F. R. , Dempsey, P. J., Teitelbaum, D. H. TPN‐associated intestinal epithelial cell atrophy is modulated by TLR4/EGF signaling pathways. FASEB J. 29, 2943‐2958 (2015). www.fasebj. org
Gastroesophageal and laryngopharyngeal reflux profiles in patients with obstructive sleep apnea/hypopnea syndrome as determined by combined multichannel intraluminal impedance–pH monitoring

Background The profiles of gastroesophageal reflux (GER) and laryngopharyngeal reflux (LPR) in patients with obstructive sleep apnea/hypopnea syndrome (OSAHS) have never been explored. The aim of the study was to investigate the reflux profile in OSAHS patients.
A Solution-Focused Approach to Case Management and Recovery with Consumers who Have a Severe Mental Disability

Community mental health systems have been increasingly emphasizing providing services and using interventions that support mental health consumers recovering from severe mental disability. It has been noted in the literature that the strengths approach to case management is supportive of mental health consumers experiencing recovery. Although strengths-based case management has been operationalzed by six principles and five functions, it has not been very well operationalized at the micro level of direct interactions between case managers and mental health service recipients. This article describes how the perspective of and techniques from solution-focused therapy can be used to further operationalize the strengths perspective for these direct, one-on-one interactions to facilitate mental health consumer recovery.