ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97.

The t(X,17) chromosomal translocation, generating the ASPSCR1::TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCCs), frustrating efforts to identify therapeutic targets for these rare cancers. Here, proteomic analysis identifies VCP/p97, an AAA+ ATPase with known segregase function, as strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1::TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1::TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributes with ASPSCR1::TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrate the oncogenic transcriptional signature of ASPSCR1::TFE3, by facilitating assembly of higher-order chromatin conformation structures demonstrated by HiChIP. Finally, ASPSCR1::TFE3 and VCP demonstrate co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.

Humidity-Induced Protein-Based Artificial Synaptic Devices for Neuroprosthetic Applications.

Neuroprosthetics and brain-machine interfaces are immensely beneficial for people with neurological disabilities, and the future generation of neural repair systems will utilize neuromorphic devices for the advantages of energy efficiency and real-time performance abilities. Conventional synaptic devices are not compatible to work in such conditions. The cerebrospinal fluid (CSF) in the central part of the nervous system is composed of 99% water. Therefore, artificial synaptic devices, which are the fundamental component of neuromorphic devices, should resemble biological nerves while being biocompatible, and functional in high-humidity environments with higher functional stability for real-time applications in the human body. In this work, artificial synaptic devices are fabricated based on gelatin-PEDOT: PSS composite as an active material to work more effectively in a highly humid environment (≈90% relative humidity). These devices successfully mimic various synaptic properties by the continuous variation of conductance, like, excitatory/inhibitory post-synaptic current(EPSC/IPSC), paired-pulse facilitation/depression(PPF/PPD), spike-voltage dependent plasticity (SVDP), spike-duration dependent plasticity (SDDP), and spike-rate dependent plasticity (SRDP) in environments at a relative humidity levels of ≈90%.

ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97.

The t(X,17) chromosomal translocation, generating the ASPSCR1-TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCC), frustrating efforts to identify therapeutic targets for these rare cancers. Proteomic analysis showed that VCP/p97, an AAA+ ATPase with known segregase function, was strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1-TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1-TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributed with ASPSCR1-TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrated the oncogenic transcriptional signature of ASPSCR1-TFE3, by facilitating assembly of higher-order chromatin conformation structures as demonstrated by HiChIP. Finally, ASPSCR1-TFE3 and VCP demonstrated co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCP's potential as a novel therapeutic target.

MOF-Assimilated High-Sensitive Organic Field-Effect Transistors for Rapid Detection of a Chemical Warfare Agent.

The selective and rapid detection of trace amounts of highly toxic chemical warfare agents has become imperative for efficiently using military and civilian defense. Metal-organic frameworks (MOFs) are a class of inorganic-organic hybrid porous material that could be potential next-generation toxic gas sensors. However, the growth of a MOF thin film for efficiently utilizing the material properties for fabricating electronic devices has been challenging. Herein, we report a new approach to efficiently integrate MOF as a receptor through diffusion-induced ingress into the grain boundaries of the pentacene semiconducting film in the place of the most adaptive chemical functionalization method for sensor fabrication. We used bilayer conducting channel-based organic field-effect transistors (OFETs) as a sensing platform comprising CPO-27-Ni as the sensing layer, coated on the pentacene layer, showed a strong response toward sensing of diethyl sulfide, which is one of the stimulants of bis (2-chloroethyl) sulfide, a highly toxic sulfur mustard (HD). Using OFET as a sensing platform, these sensors can be a potential candidate for trace amounts of sulfur mustard detection below 10 ppm in real time as wearable devices for onsite uses.

Interface engineering of moisture-induced ionic albumen dielectric layers through self-crosslinking of cysteine amino acids for low voltage, high-performance organic field-effect transistors.

The interface roughness between the semiconducting and dielectric layers of organic field-effect transistors (OFETs) plays a crucial role in the charge transport mechanism through the device. Here we report the interface engineering of a moisture induced ionic albumen material through systematic control of the temperature-dependent self-crosslinking of cysteine amino acids in the dielectric layer. The evolution of the surface morphologies of albumen and pentacene semiconducting films has been studied to achieve a smooth interface for enhanced charge transport. A structural transition of pentacene films from crystalline dendrite to amorphous was induced by the higher surface roughness of the albumen film. The devices showed a high transconductance of 11.68 µS at a lower threshold voltage of -0.9 V.

Dual role of G-quadruplex in translocation renal cell carcinoma: Exploring plausible Cancer therapeutic innovation.

BACKGROUND: Renal Cell Carcinoma (RCC) is the ninth leading cause of death among kidney cancer. Xp11.2 translocation harboring TFE3 fusion proteins, act as an oncogene in translocation cancers that constitute the hallmark of translocation renal cell carcinoma (tRCC). G-quadruplex (G4), an alternative nucleic acid structure is an emerging and promising factor in cancer. The presence of G4 within the genome plays a pioneering role in cancer as it contributes to genomic aberration as well as inhibition in cell proliferation. SCOPE OF REVIEW: Here we discuss the link between G4 and tRCC. We compile the available information of G-quadruplex & propose their dual role in tRCC, suggesting both stabilization and destabilization of G-quadruplex could be considered targets for tRCC. MAJOR CONCLUSIONS: Our in Silico analysis of TFE3 and their three fusions partner's PRCC, SFPQ, and ASPSCR1 discloses a few putative G4 forming sequences (PQS) in their corresponding fusion gene or fusion transcript. Stabilization of G4 structure within fusion gene/transcript can be of great use towards potential therapeutics targeting fusion protein derived oncogenesis, as G4 is a serious menace for DNA polymerization, transcription & translation. G-quadruplex at intron-2 of the TFE3 has been reported to mediate its translocation also. Both stabilization and destabilization of the G4 structure would be a promising approach in the suppression of cancerous cell proliferation. GENERAL SIGNIFICANCE: Pioneering studies discovered the relevance of G4 in cancer therapy and explore our approaches towards therapeutic innovation against oncogenic fusion protein and tRCC. Selectively targeting G4 in oncogenic fusion transcript will emerge as potential druggable structures.

Identification & characterization of leucine-rich repeat kinase 2 & parkin RBR E3 ubiquitin protein ligase variants in patients with Parkinson's disease.

BACKGROUND & OBJECTIVES: Parkinson's disease (PD) is a motor disorder that affects movement. More than 24 loci and 28 associated genes have been identified to be associated with this disease. The present study accounts for the contribution of two candidates, leucine-rich repeat kinase 2 ( LRRK2) and parkin RBR E3 ubiquitin protein ligase ( PRKN) in the PD patients, and their characterization in silico and in vitro. METHODS: A total of 145 sporadic PD cases and 120 ethnically matched healthy controls were enrolled with their informed consent. Mutation screening was performed by direct DNA sequencing of the targeted exons of LRRK2 and all exons flanking introns of PRKN. The effect of the pathogenic PRKN variants on a drug (MG-132) induced loss of mitochondrial membrane potential (△ΨM) was measured by a fluorescent dye tetramethylrhodamine methyl ester (TMRM). RESULTS: Twelve and 20 genetic variants were identified in LRRK2 and PRKN, respectively. Interestingly, five out of seven exonic LRRK2 variants were synonymous. Further assessment in controls confirmed the rarity of two such p.Y1527 and p.V1615. Among the pathogenic missense variations (as predicted in silico) in PRKN, two were selected (p.R42H and p.A82E) for their functional study in vitro, which revealed the reduced fluorescence intensity of TMRM as compared to wild type, in case of p.R42H but not the other. INTERPRETATION & CONCLUSIONS: About 6.2 per cent of the cases (9/145) in the studied patient cohort were found to carry pathogenic (as predicted in silico) missense variations in PRKN in heterozygous condition but not in case of LRRK2 which was rare. The presence of two rare synonymous variants of LRRK2 (p.Y1527 and p.V1615) may support the phenomenon of codon bias. Functional characterization of selected PRKN variations revealed p.R42H to cause disruption of mitochondrial membrane potential (△ΨM) rendering cells more susceptible to cellular stress.

Monensin induces cell death by autophagy and inhibits matrix metalloproteinase 7 (MMP7) in UOK146 renal cell carcinoma cell line.

Monensin is a metal ionophore used as anticancer agent in many types of cancer cells. In this study, therapeutic potential of monensin was evaluated in TFE3 translocated renal cell carcinoma (RCC) cell line UOK146. UOK146 cells were treated with different concentrations of monensin, and cell death was induced as shown by MTT assay. Autophagy was studied by LC3 western, FACS and LC3 puncta formation after monensin treatment. Mitochondrial potential was studied by staining with TMRM and FACS. Antimetastatic potential of monensin was checked by inhibition of wound closure and MMP7 expression at RNA level. Dead and floating cells after the 10 µM monensin treatment were observed under phase contrast microscope. FACS analysis following TMRM staining showed that mitochondrial membrane gets depolarized after monensin treatment. FACS analysis after acridine orange staining showed increased double positive (green and red) cells, and LC3 upregulation and increased LC3 punta displayed autophagy activation in UOK146 cell line after monensin treatment. These findings showed that monensin acts as antiproliferative agent, activating autophagy and downregulates PRCC-TFE3 fusion transcript in Xp11.2 translocated tumor cell line.

Novel splicing in IGFN1 intron 15 and role of stable G-quadruplex in the regulation of splicing in renal cell carcinoma.

The IGFN1 (Immunoglobulin-Like And Fibronectin Type III Domain Containing 1) gene has a role in skeletal muscle function and is also involved in metastatic breast cancer, and the isoforms with three N-terminal globular domains are sufficient for its function in skeletal muscle. Two novel splicing isoforms of IGFN1 have been identified in renal cell carcinoma (RCC), one with 5'exon extension and an isoform with a novel exon. The role of G-quadruplex, a non-B DNA, was explored for the splicing alteration of IGFN1 in RCC. G-quadruplexes are the secondary structures acquired by stacking of G-quartets by Hoogsteen hydrogen bonding in DNA and RNA. IGFN1 has intronic potential G-quadruplex forming sequence (PQS) folding into G-quadruplex and is studied for its involvement in aberrant splicing. A PQS in the intron 15 of IGFN1 gene was observed in our in silico analysis by QGRS mapper and non BdB web servers. We observed PQS folds into stable G-quadruplex structure in gel shift assay and circular dichroism (CD) spectroscopy in the presence of G-quadruplex stabilizing agents Pyridostatin (PDS) and KCl, respectively. G-quadruplex formation site with single base resolution was mapped by Sanger sequencing of the plasmid constructs harbouring the cloned PQS and its mutant. This stable G-quadruplex inhibits reverse transcriptase and taq polymerase in reverse transcriptase & PCR stop assays. PDS changes the different splicing isoforms of IGFN1 in UOK146 cell line, displaying involvement of intronic G-quadruplex in IGFN1 splicing. These results lead us to propose that a stable G-quadruplex structure is formed in IGFN1 intron and a reason behind IGFN1 aberrant splicing which could be targeted for therapeutic intervention.

Sodium butyrate induces cell death by autophagy and reactivates a tumor suppressor gene DIRAS1 in renal cell carcinoma cell line UOK146.

Sodium butyrate (SB), a histone deacetylase inhibitor, is emerging as a potent anti-cancer drug for different types of cancers. In the present study, anti-cancer activity of SB in Xp11.2 (TFE3) translocated renal cell carcinoma cell line UOK146 was studied. Anti-proliferative effect of SB in renal cell carcinoma (RCC) cell line UOK146 was evaluated by MTT assay and morphological characteristics were observed by phase contrast microscopy which displayed the cell death after SB treatment. SB induces DNA fragmentation and change in nuclear morphology observed by increased sub-G1 region cell population and nuclear blebbings. Cell cycle arrest at G2/M phase was found after SB treatment. UOK146 cell line shows autophagy mode of cell death as displayed by acridine orange staining and flow cytometry analysis. LC3-II, a protein marker of autophagy, was also found to be upregulated after SB treatment. A tumor suppressor gene DIRAS1 was upregulated after SB treatment, displaying its anti-cancer potential at molecular level. These findings suggest that SB could serve as a novel regulator of tumor suppressors and lead to the discovery of novel therapeutics with better and enhanced anti-cancer activity.

G-quadruplex structure at intron 2 of TFE3 and its role in Xp11.2 translocation and splicing.

Transcription Factor E3 (TFE3) translocation is found in a group of different type of cancers and most of the translocations are located in the 5' region of TFE3 which may be considered as Breakpoint Region (BR). In our In silico study by QGRS mapper and non BdB web servers we found a Potential G-quadruplex forming Sequence (PQS) in the intron 2 of TFE3 gene. In vitro G-quadruplex formation was shown by native PAGE in presence of Pyridostatin(PDS), which with inter molecular secondary structure caused reduced mobility to migrate slower. G-quadruplex formation was mapped at single base resolution by Sanger sequencing and Circular Dichroism showed the formation of parallel G-quadruplex. FRET analysis revealed increased and decreased formation of G-quadruplex in presence of PDS and antisense oligonucleotide respectively. PCR stop assay, transcriptional and translational inhibition by PQS showed stable G-quadruplex formation affecting the biological processes. TFE3 minigene splicing study showed the involvement of this G-quadruplex in TFE3 splicing too. Therefore, G-quadruplex is evident to be the reason behind TFE3 induced oncogenesis executed by translocation and also involved in the mRNA splicing.

Heteroleptic arene Ru(II) dipyrrinato complexes: DNA, protein binding and anti-cancer activity against the ACHN cancer cell line.

Four organometallic complexes [(η(6)-C6H6)RuCl(pmpzdpm)], 1; [(η(6)-C6H6)RuCl(pypzdpm)], 2; [(η(6)-C10H14)RuCl(pmpzdpm)], 3 and [(η(6)-C10H14)RuCl(pypzdpm)], 4 containing 5-(2-pyrimidyl-piperazine)phenyldipyrromethene (pmpzdpm) and 5-(2-pyridylpiperazine)phenyldipyrromethene (pypzdpm) have been designed and synthesized. The complexes 1-4 have been fully characterized by elemental analyses and spectroscopic studies (ESI-MS, IR, (1)H, (13)C NMR, UV-vis). Their electrostatic/intercalative interaction with CT DNA has been investigated by UV-vis and competitive ethidium bromide displacement studies while their protein binding affinity toward bovine serum albumin (BSA) was realized by UV-vis, fluorescence, synchronous and three dimensional (3D) fluorescence studies. The interaction with DNA and protein has further been validated by in silico studies. Cellular uptake, in vitro cytotoxicity and flow cytometric analyses have been performed to determine the mode of cell death against the kidney cancer cell line ACHN. Cell cycle analysis suggested that the complexes cause cell cycle arrest in the subG1 phase and overall results indicated that the in vitro antitumor activity of 1-4 lies in the order of 3 >4 >1 >2 (IC50, 7.0 1; 8.0 2; 2.0 3; 4.0 µM,4 ).

Layered double hydroxides as effective carrier for anticancer drugs and tailoring of release rate through interlayer anions.

Hydrophobic anticancer drug, raloxifene hydrochloride (RH) is intercalated into a series of magnesium aluminum layered double hydroxides (LDHs) with various charge density anions through ion exchange technique for controlled drug delivery. The particle nature of the LDH in presence of drug is determined through electron microscopy and surface morphology. The release of drug from the RH intercalated LDHs was made very fast or sustained by altering the exchangeable anions followed by the modified Freundlich and parabolic diffusion models. The drug release rate is explained from the interactions between the drug and LDHs along with order-disorder structure of drug intercalated LDHs. Nitrate bound LDH exhibits greater interaction with drug and sustained drug delivery against the loosely interacted phosphate bound LDH-drug, which shows fast release. Cell viability through MTT assay suggests drug intercalated LDHs as better drug delivery vehicle for cancer cell line against poor bioavailability of the pure drug. In vivo study with mice indicates the differential tumor healing which becomes fast for greater drug release system but the body weight index clearly hints at damaged organ in the case of fast release system. Histopathological experiment confirms the damaged liver of the mice treated either with pure drug or phosphate bound LDH-drug, fast release system, vis-à-vis normal liver cell morphology for sluggish drug release system with steady healing rate of tumor. These observations clearly demonstrate that nitrate bound LDH nanoparticle is a potential drug delivery vehicle for anticancer drugs without any side effect.

Aqueous Extract of Anticancer Drug CRUEL Herbomineral Formulation Capsules Exerts Anti-proliferative Effects in Renal Cell Carcinoma Cell Lines.

PURPOSE: Anti-cancer activity evaluation of aqueous extract of CRUEL (herbomineral formulation) capsules on renal cell carcinoma cell lines, and exploration of mechanisms of cell death. MATERIALS AND METHODS: To detect the cytotoxic dose concentration in renal cell carcinoma (RCC) cells, MTT assays were performed and morphological changes after treatment were observed by inverted microscopy. Drug effects against RCC cell lines were assessed with reference to cell cycle distribution (flow cytometry), anti-metastatic potential (wound healing assay) and autophagy(RT-PCR). RESULTS: CRUEL showed anti-proliferative effects against RCC tumor cell lines with an IC50 value of approximately 4mg/mL in vitro, while inducing cell cycle arrest at S-phase of the cell cycle and inhibiting wound healing. LC3 was found to be up-regulated after drug treatment by RT-PCR resulting in an autophagy mode of cell death. CONCLUSIONS: This study provides experimental validation for antitumor activity of CRUEL.

Asparagus racemosus leaf extract inhibits growth of UOK 146 renal cell carcinoma cell line: simultaneous oncogenic PRCCTFE3 fusion transcript inhibition and apoptosis independent cell death.

AIMS: To evaluate anti-cancer activity of Asparagus racemosus (AR) leaf extract on UOK146, a renal cell carcinoma cell line, and explore its mechanism of action. MATERIALS AND METHODS: Dried AR leaves were extracted with chloroform and dissolved in DMSO. This extract was applied to UOK146 and cell death was estimated by MTT assay. In addition PRCC-TFE3 fusion transcripts were detected by real time PCR. RESULTS: Extract was found to be cytotoxic with an IC50 of 0.9 mg/ml as estimated by dose response curve. Antitumor activity of the permissible doses of the extract was assessed by the down regulation of PRCC-TFE3 fusion transcript (38%) responsible for oncogenicity of the UOK146 cell line. No increment in the BAX, a proapoptotic marker level was observed. CONCLUSIONS: Evidence of antiproliferative effect, PRCC-TFE3 fusion transcript inhibition and static BAX level clearly indicate that AR extract provides or elicits an apoptosis independent anticancer effect on RCC cells by some specific mechanism of regulation.