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1.
Cell ; 177(7): 1933-1947.e25, 2019 06 13.
Article in English | MEDLINE | ID: mdl-31160049

ABSTRACT

Heterotrimetic G proteins consist of four subfamilies (Gs, Gi/o, Gq/11, and G12/13) that mediate signaling via G-protein-coupled receptors (GPCRs), principally by receptors binding Gα C termini. G-protein-coupling profiles govern GPCR-induced cellular responses, yet receptor sequence selectivity determinants remain elusive. Here, we systematically quantified ligand-induced interactions between 148 GPCRs and all 11 unique Gα subunit C termini. For each receptor, we probed chimeric Gα subunit activation via a transforming growth factor-α (TGF-α) shedding response in HEK293 cells lacking endogenous Gq/11 and G12/13 proteins, and complemented G-protein-coupling profiles through a NanoBiT-G-protein dissociation assay. Interrogation of the dataset identified sequence-based coupling specificity features, inside and outside the transmembrane domain, which we used to develop a coupling predictor that outperforms previous methods. We used the predictor to engineer designer GPCRs selectively coupled to G12. This dataset of fine-tuned signaling mechanisms for diverse GPCRs is a valuable resource for research in GPCR signaling.


Subject(s)
Heterotrimeric GTP-Binding Proteins/metabolism , Models, Biological , Receptors, G-Protein-Coupled/metabolism , Signal Transduction , Female , HEK293 Cells , Heterotrimeric GTP-Binding Proteins/genetics , Humans , Male , PC-3 Cells , Receptors, G-Protein-Coupled/genetics
2.
Genome Res ; 31(4): 564-575, 2021 04.
Article in English | MEDLINE | ID: mdl-33712417

ABSTRACT

Transcriptional enhancers are critical for development and phenotype evolution and are often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. To examine the enhancer regulatory code for pluripotent stem cells, we identified genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs). Examination of these regions revealed that they contain on average 12.6 conserved transcription factor binding site (TFBS) sequences. Enriched TFBSs are a diverse repertoire of 70 different sequences representing the binding sequences of both known and novel ESC regulators. Using a diverse set of TFBSs from this repertoire was sufficient to construct short synthetic enhancers with activity comparable to native enhancers. Site-directed mutagenesis of conserved TFBSs in endogenous enhancers or TFBS deletion from synthetic sequences revealed a requirement for 10 or more different TFBSs. Furthermore, specific TFBSs, including the POU5F1:SOX2 comotif, are dispensable, despite cobinding the POU5F1 (also known as OCT4), SOX2, and NANOG master regulators of pluripotency. These findings reveal that a TFBS sequence diversity threshold overrides the need for optimized regulatory grammar and individual TFBSs that recruit specific master regulators.


Subject(s)
Embryonic Stem Cells/metabolism , Enhancer Elements, Genetic , Transcription Factors/metabolism , Animals , Binding Sites , Humans , Mice , Pluripotent Stem Cells/metabolism
3.
Am J Gastroenterol ; 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38912697

ABSTRACT

BACKGROUND: Hybrid endoscopic submucosal dissection (H-ESD) which utilizes ESD knife along with snare-based resection, has been developed to overcome the technical complexity of conventional ESD (C-ESD). This study aimed to compare the therapeutic outcomes of H-ESD vs. C-ESD for non-pedunculated colorectal lesions ≥20 mm in size. METHODS: We conducted a multicenter randomized controlled trial to compare H-ESD and C-ESD (Short-ESD trial). Patients with colorectal lesions between 20-50 mm in size were randomly assigned (1:1) to H-ESD or C-ESD. Primary outcome was procedure time/speed. Secondary outcomes were en-bloc and complete (R0) resection rates and adverse event rates. RESULTS: A total of 89 patients (median age 63 years; 49.3% women) with median polyp size 30 mm underwent H-ESD (n=40) and C-ESD (n=49). The mean procedure time of H-ESD was significantly shorter than that of C-ESD (41.1±16.3 vs. 54.3±28.2 minutes; p=0.007). The en-bloc and R0 resection rates trended lower in the H-ESD vs C-ESD groups (77.5% vs. 87.8%; p=0.26 and 72.5% vs. 79.6%; p=0.46) without reaching statistical significance. Adverse event rate was similar between H-ESD and C-ESD (10% vs 8.2%; p=1.00). CONCLUSION: Both H-ESD and C-ESD were safe and effective for resection of large colorectal lesions. H-ESD was associated with a shorter procedure time. H-ESD may represent a viable alternative to C-ESD, with the main advantage being easy applicability of a snare-based technique for colorectal lesions. Future studies are needed to further define the most suitable lesions for H-ESD, as to optimize efficiency and safety without compromising resection outcomes. ClinicaTrials.gov NCT NCT05347446.

4.
PLoS Pathog ; 18(6): e1010588, 2022 06.
Article in English | MEDLINE | ID: mdl-35709296

ABSTRACT

As intracellular parasites, viruses exploit cellular proteins at every stage of infection. Adenovirus outbreaks are associated with severe acute respiratory illnesses and conjunctivitis, with no specific antiviral therapy available. An adenoviral vaccine based on human adenovirus species D (HAdV-D) is currently in use for COVID-19. Herein, we investigate host interactions of HAdV-D type 37 (HAdV-D37) protein IIIa (pIIIa), identified by affinity purification and mass spectrometry (AP-MS) screens. We demonstrate that viral pIIIa interacts with ubiquitin-specific protease 9x (USP9x) and Ran-binding protein 2 (RANBP2). USP9x binding did not invoke its signature deubiquitination function but rather deregulated pIIIa-RANBP2 interactions. In USP9x-knockout cells, viral genome replication and viral protein expression increased compared to wild type cells, supporting a host-favored mechanism for USP9x. Conversely, RANBP2-knock down reduced pIIIa transport to the nucleus, viral genome replication, and viral protein expression. Also, RANBP2-siRNA pretreated cells appeared to contain fewer mature viral particles. Transmission electron microscopy of USP9x-siRNA pretreated, virus-infected cells revealed larger than typical paracrystalline viral arrays. RANBP2-siRNA pretreatment led to the accumulation of defective assembly products at an early maturation stage. CRM1 nuclear export blockade by leptomycin B led to the retention of pIIIa within cell nuclei and hindered pIIIa-RANBP2 interactions. In-vitro binding analyses indicated that USP9x and RANBP2 bind to C-terminus of pIIIa amino acids 386-563 and 386-510, respectively. Surface plasmon resonance testing showed direct pIIIa interaction with recombinant USP9x and RANBP2 proteins, without competition. Using an alternative and genetically disparate adenovirus type (HAdV-C5), we show that the demonstrated pIIIa interaction is also important for a severe respiratory pathogen. Together, our results suggest that pIIIa hijacks RANBP2 for nuclear import and subsequent virion assembly. USP9x counteracts this interaction and negatively regulates virion synthesis. This analysis extends the scope of known adenovirus-host interactions and has potential implications in designing new antiviral therapeutics.


Subject(s)
Adenoviridae Infections , Adenoviruses, Human , COVID-19 , Active Transport, Cell Nucleus , Adenoviridae/genetics , Adenoviruses, Human/genetics , Humans , Molecular Chaperones , Nuclear Pore Complex Proteins , RNA, Small Interfering , Ubiquitin Thiolesterase/genetics , Ubiquitin-Specific Proteases , Viral Proteins/genetics
5.
J Fluoresc ; 2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38592594

ABSTRACT

A photoluminescent terbium (III)-based Metal Organic Framework (MOF) was synthesized at room temperature by layer diffusion method utilizing mixed carboxylate linkers (4,4'-oxybis(benzoic acid) and benzene-1,3,5 tricarboxylic acid). Synthesized MOF has crystalline nature and rod-shaped morphology and is thermally stable up to 455 °C. The fluorescence emission spectra and theoretical results revealed that carboxylate linkers functioned as sensitizers for Tb(III) photoluminescence which resulted in four distinct emission peaks at 495, 547, 584, and 621 nm corresponding to the transitions 5D4 → 7F6, 5D4 → 7F5, 5D4 → 7F4, and 5D4 → 7F3. Using synthesized MOF as fluorescent probe, hydroquinone was detected in aqueous medium with a detection limit of 0.048 µM, remarkable recovery (95.6-101.1%), and relative standard deviation less than 2.25%. The quenching phenomenon may be ascribed to electron transfer from synthesized probe to oxidized hydroquinone via carboxylic groups on the surface of MOF, which is further supported by photo-induced electron transfer mechanism. This study introduces a cheaper, faster, and more accurate method for hydroquinone detection.

6.
J Fluoresc ; 34(1): 449-463, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37294382

ABSTRACT

Luminescent antimony doped tin oxide nanoparticles have drawn tremendous attention from researchers due to its low cost, chemical inertness and stability. Herein, a quick, facile and economic hydrothermal/solvothermal method was utilized for the preparation of antimony doped (1%, 3%, 5%, 7% and 10%) tin oxide nanoparticles. The antimony doping in a reasonable range can change the properties of SnO2. As such, a lattice distortion increases with increase in doping, which is evidenced through crystallographic studies. It was found that the highest photocatalytic degradation efficiency of malachite green (MG) dye of about 80.86% was achieved with 10% Sb-doped SnO2 in aqueous media due to small particle size. Moreover, 10% Sb-doped SnO2 also showed the highest fluorescence quenching efficiency of about 27% for Cd2+ of concentration 0.11 µg/ml in the drinking water. The limit of detection (LOD) comes out as 0.0152 µg/ml. This sample selectively detected the cadmium ion even in the presence of other heavy metal ions. Notably, 10% Sb-doped SnO2 could appeared as a promising sensor for fast analysis of Cd2+ ions in real samples.

7.
Nucleic Acids Res ; 50(W1): W598-W610, 2022 07 05.
Article in English | MEDLINE | ID: mdl-35639758

ABSTRACT

In this study we show that protein language models can encode structural and functional information of GPCR sequences that can be used to predict their signaling and functional repertoire. We used the ESM1b protein embeddings as features and the binding information known from publicly available studies to develop PRECOGx, a machine learning predictor to explore GPCR interactions with G protein and ß-arrestin, which we made available through a new webserver (https://precogx.bioinfolab.sns.it/). PRECOGx outperformed its predecessor (e.g. PRECOG) in predicting GPCR-transducer couplings, being also able to consider all GPCR classes. The webserver also provides new functionalities, such as the projection of input sequences on a low-dimensional space describing essential features of the human GPCRome, which is used as a reference to track GPCR variants. Additionally, it allows inspection of the sequence and structural determinants responsible for coupling via the analysis of the most important attention maps used by the models as well as through predicted intramolecular contacts. We demonstrate applications of PRECOGx by predicting the impact of disease variants (ClinVar) and alternative splice forms from healthy tissues (GTEX) of human GPCRs, revealing the power to dissect system biasing mechanisms in both health and disease.


Subject(s)
Machine Learning , Receptors, G-Protein-Coupled , Signal Transduction , Software , Humans , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Internet , beta-Arrestins/chemistry , beta-Arrestins/metabolism , Heterotrimeric GTP-Binding Proteins/chemistry , Heterotrimeric GTP-Binding Proteins/metabolism , Computers , Genetic Predisposition to Disease/genetics , Alternative Splicing/genetics
8.
Angew Chem Int Ed Engl ; 63(16): e202401545, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38386517

ABSTRACT

We report the triply selective and sequential diversification of a single Csp 3 carbon carrying Cl, Bpin and GeEt3 for the modular and programmable construction of sp3-rich molecules. Various functionalizations of Csp 3-Cl and Csp 3-BPin (e.g. alkylation, arylation, homologation, amination, hydroxylation) were tolerated by the Csp 3-GeEt3 group. Moreover, the methodological repertoire of alkyl germane functionalization was significantly expanded beyond the hitherto known Giese addition and arylation to alkynylation, alkenylation, cyanation, halogenation, azidation, C-S bond formation as well as the first demonstration of stereo-selective functionalization of a Csp 3-[Ge] bond.

9.
Org Biomol Chem ; 21(12): 2493-2498, 2023 Mar 22.
Article in English | MEDLINE | ID: mdl-36880335

ABSTRACT

A metal-free approach for the synthesis of tetrahydroindolo[2,3-b]carbazoles has been developed through an acid-mediated one-pot [3 + 3]-annulation of 2-indolylmethanols and 3-indolyl-substituted para-quinone methides. This operationally simple protocol allowed us to prepare many unsymmetrical tetrahydroindolo[2,3-b]carbazoles in good to excellent yields with a broad substrate scope. This concept was also elaborated to the synthesis of tetrahydrothieno[2,3-b]carbazoles and tetrahydrothieno[3,2-b]carbazoles.

10.
Org Biomol Chem ; 21(24): 5072-5078, 2023 Jun 21.
Article in English | MEDLINE | ID: mdl-37273009

ABSTRACT

We describe here an acid-mediated one-pot approach to access substituted xanthene and thioxanthane derivatives from ortho-heteroaryl phenyl-substituted para-quinone methides via 1,6 intramolecular arylation. The scope of this work was further elaborated to the synthesis of 10H-indolo[1,2-a]indole-based heterocyclic systems using indole based para-quinone methides.

11.
J Fluoresc ; 2023 Aug 14.
Article in English | MEDLINE | ID: mdl-37578675

ABSTRACT

Metal organic framework, UiO-67 was synthesized by coordinating Zr(IV) with 4,4'-biphenyldicarboxylic acid (BPDC) ligand. Morphology and crystallinity of MOF was confirmed with FE-SEM and PXRD procedure. Danofloxacin (DANO), a veterinary fluoroquinolone antibiotic, was detected in milk by employing UiO-67 as "turn-on" fluorescent sensor. Original photoluminescent (PL) efficiency of UiO-67 sensor was enhanced on its electronic interaction with DANO molecule. Significant PL efficiency enhancement, lower detection limit 0.49 ng/mL (1.37 nM), swift detection (time < 1 min), and excellent linear correlation (R2 = 0.9988) indicated extraordinary sensitivity of developed UiO-67 sensor for DANO. Selectivity and performance of sensor was unaltered in presence of interfering species and detection results were obtained under permissible variation limits. Method applied successfully for ultra-trace detection of DANO residues in milk samples.

12.
Arch Pharm (Weinheim) ; 356(8): e2200579, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37276367

ABSTRACT

The objective of the present investigation was to prepare and optimize lyophilized mixed micelles (Lyp-EXE-MMs) of exemestane (EXE) with improved solubility, bioavailability, in vivo anticancer activity, and physical stability, by using various cryoprotectants. The prepared lyophilized mixed micelles were characterized by various techniques, including dynamic light scattering, zeta potential, powdered X-ray diffraction, differential scanning calorimetry (DSC), nuclear magnetic resonance (1 H NMR), transmission electron microscopy (TEM), and so on. Thereafter, the lyophilized micelles were evaluated for ex vivo permeation, in vitro drug release and gene/protein expression (RT-PCR and Western blot analysis) in MCF-7 breast cancer cells. The developed formulation was also investigated for its in vivo anticancer study in BALB/c mice with induced breast cancer. The use of trehalose (10% w/w) was proven to be a suitable cryoprotectant for these micelles. Lyp-EXE-MMs were spherical, with a particle size of 42.9 ± 3.8 nm and a polydispersity index of 0.307 ± 0.122. Furthermore, % drug loading and % entrapment efficiency were found to be 5.8 ± 1.4 and 89.1 ± 1.1, respectively. Lyp-EXE-MMs showed sustained release behavior as compared to EXE-suspensions in SGF/SIF (pH 1.2 and 6.8) and phosphate buffer saline (pH 7.4). The micelles induced apoptosis through the regulation of BAX, BCL2, Caspase-3, p53, and CYP19A1 in MCF-7 cells, which was correlated to enhanced ex vivo drug permeation. Animals receiving EXE micelle formulations showed reduced tumor volume and improved survivability and pharmacokinetic parameters as compared to pure EXE. Lyp-EXE-MMs were found to withstand simulated harsh conditions of SGF/SIF during stability studies. The fabricated EXE micellar preparations hold a promising approach for breast cancer treatment.


Subject(s)
Androstadienes , Micelles , Animals , Mice , Structure-Activity Relationship , Solubility , Androstadienes/chemistry , Androstadienes/pharmacokinetics , Drug Carriers/chemistry
13.
Chem Rec ; 21(12): 4150-4173, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34369640

ABSTRACT

In the last few years, there has been an explosive growth in the area of para-quinone methide (p-QM) chemistry. This boom is actually due to the unique reactivity pattern of p-QMs, and also their remarkable synthetic applications. In fact, p-QMs serve as synthons for unsymmetrical diaryl- and triarylmethanes, and also for the construction of diverse range of carbocycles and heterocycles. In the last few years, a wide range of structurally complex heterocyclic frameworks could be accessed through the synthetic transformations of structurally modified stable p-QMs. Therefore, the main focus of this review article is to cover the recent advancements in the transition-metal, Lewis acid and base-catalyzed/mediated synthetic transformations of the stable p-quinone methides (p-QMs) to oxygen- and nitrogen-containing heterocycles.


Subject(s)
Indolequinones , Oxygen , Nitrogen , Nucleotides
14.
Org Biomol Chem ; 19(44): 9541-9564, 2021 11 18.
Article in English | MEDLINE | ID: mdl-34704583

ABSTRACT

The development of novel small molecule-based catalysts for organic transformations has increased noticeably in the last two decades. A very recent addition to this particular research area is cyclopropene- and cyclopropenium-based catalysts. At one point in time, particularly in the mid-20th century, much attention was focused on the structural aspects and physical properties of cyclopropene-based compounds. However, a paradigm shift was observed in the late 20th century, and the focus shifted to the synthetic utility of these compounds. In fact, a wide range of cyclopropene derivatives have been found serving as valuable synthons for the construction of carbocycles, heterocycles and other useful organic compounds. In the last few years, the catalytic applications of cyclopropene/cyclopropenium-based compounds have been uncovered and many synthetic protocols have been developed using cyclopropene-based compounds as organocatalysts. Therefore, the main objective of this review is to highlight recent developments in the catalytic applications of cyclopropene-based small molecules in different areas of organocatalysis such as phase-transfer catalysis (PTC), Brønsted base catalysis, hydrogen-bond donor catalysis, nucleophilic carbene catalysis, and electrophotocatalysis developed within the past two decades.

15.
Nucleic Acids Res ; 47(W1): W395-W401, 2019 07 02.
Article in English | MEDLINE | ID: mdl-31143927

ABSTRACT

G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.


Subject(s)
GTP-Binding Proteins/chemistry , Receptors, G-Protein-Coupled/chemistry , Recombinant Fusion Proteins/chemistry , Software , Amino Acid Sequence , Animals , Binding Sites , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Humans , Internet , Models, Molecular , Mutation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Engineering , Protein Interaction Domains and Motifs , Receptors, G-Protein-Coupled/genetics , Receptors, G-Protein-Coupled/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Signal Transduction
16.
Environ Geochem Health ; 43(5): 2081-2103, 2021 May.
Article in English | MEDLINE | ID: mdl-33389370

ABSTRACT

Dust samples were collected from roads of five distinct types of land use zones (National Highway, residential areas, sensitive areas, mining areas, and busy traffic areas) of Dhanbad to determine the pollution characteristics, health risk, and identifying the source of trace elements. The dust samples were segregated into ≤ 60 µm and trace elements like Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn were analysed. Concentrations of Cd, Cr, Cu, Fe, and Mn were observed highest in the mining areas, whereas Ni, Pb, and Zn presented higher concentration values at National Highway and busy traffic zones. Cd showed highest geo-accumulation index (Igeo), contamination factor (Cf), and ecological risk (ER) among all the trace elements. The health risk assessment model was performed to assess the health effects of carcinogenic and non-carcinogenic pollutants caused due to multi-elemental exposure on adults and children. The significantly higher HQ (Hazard Quotient) and HI (Hazard Index) values posed by Cr, Fe, and Mn indicated potential non-carcinogenic risks to the people of Dhanbad. Similarly, values of CR (Cancer Risk) for Cd, Cr and Ni were within the range of 10-6-10-4, which indicated to cause carcinogenic risk to the population by the exposure of road dust. Principal Component Analysis (PCA) and Pearson correlation showed that coal mining activities in Jharia coalfield, coal-based industries like coke-oven plants, coal washeries and heavy vehicular load in the roads of Dhanbad were the major causes of emission of these trace elements.


Subject(s)
Dust/analysis , Environmental Exposure/analysis , Environmental Pollution/analysis , Metals, Heavy/analysis , Adult , Carcinogens/analysis , Carcinogens/toxicity , Child , Cities , Coal/analysis , Coal Mining , Environmental Exposure/adverse effects , Environmental Monitoring , Environmental Pollutants/analysis , Humans , India , Industry , Metals, Heavy/toxicity , Risk Assessment , Spatio-Temporal Analysis , Trace Elements/analysis
17.
AAPS PharmSciTech ; 22(1): 24, 2021 Jan 05.
Article in English | MEDLINE | ID: mdl-33400035

ABSTRACT

The present study pursued the systematic development of a stable solid self-emulsifying drug delivery system (SMEDDS) of an atypical antipsychotic drug, aripiprazole (APZ), which exhibits poor aqueous solubility and undergoes extensive p-glycoprotein efflux and hepatic metabolism. Liquid SMEDDS excipients were selected on the basis of solubility studies, and the optimum ratio of surfactant/co-surfactant was determined using pseudo-ternary phase diagrams. The prepared formulations were subjected to in vitro characterization studies to facilitate the selection of optimum liquid SMEDD formulation containing 30% Labrafil® M 1944 CS, 46.7% Cremophor® EL and 23.3% PEG 400 which were further subjected to solidification using maltodextrin as a hydrophilic carrier. The optimized solid SMEDDS was extensively evaluated for stability under accelerated conditions, dissolution at various pH and pharmacokinetic profile. Solid-state attributes of the optimized solid SMEDDS indicated a marked reduction in crystallinity of APZ and uniform adsorption of liquid SMEDDS. Stability study of the solid SMEDDS demonstrated that the developed formulation retained its stability during the accelerated storage conditions. Both the optimized liquid and solid SMEDDS exhibited enhanced dissolution rate which was furthermore independent of the pH of the dissolution medium. Oral bioavailability studies in Sprague-Dawley rats confirmed quicker and greater extent of absorption with solid SMEDDS as evident from the significant reduction in Tmax in case of solid SMEDDS (0.83 ± 0.12 h) as compared with commercial tablet (3.33 ± 0.94 h). The results of the present investigation indicated the development of a stable solid SMEDDS formulation of APZ with enhanced dissolution and absorption attributes.


Subject(s)
Aripiprazole/administration & dosage , Drug Delivery Systems , Administration, Oral , Animals , Aripiprazole/chemistry , Aripiprazole/pharmacokinetics , Biological Availability , Drug Delivery Systems/methods , Drug Liberation , Emulsions/chemistry , Female , Hydrogen-Ion Concentration , Rats , Rats, Sprague-Dawley
18.
Genome Res ; 27(2): 246-258, 2017 02.
Article in English | MEDLINE | ID: mdl-27895109

ABSTRACT

Transcriptional enhancers are critical for maintaining cell-type-specific gene expression and driving cell fate changes during development. Highly transcribed genes are often associated with a cluster of individual enhancers such as those found in locus control regions. Recently, these have been termed stretch enhancers or super-enhancers, which have been predicted to regulate critical cell identity genes. We employed a CRISPR/Cas9-mediated deletion approach to study the function of several enhancer clusters (ECs) and isolated enhancers in mouse embryonic stem (ES) cells. Our results reveal that the effect of deleting ECs, also classified as ES cell super-enhancers, is highly variable, resulting in target gene expression reductions ranging from 12% to as much as 92%. Partial deletions of these ECs which removed only one enhancer or a subcluster of enhancers revealed partially redundant control of the regulated gene by multiple enhancers within the larger cluster. Many highly transcribed genes in ES cells are not associated with a super-enhancer; furthermore, super-enhancer predictions ignore 81% of the potentially active regulatory elements predicted by cobinding of five or more pluripotency-associated transcription factors. Deletion of these additional enhancer regions revealed their robust regulatory role in gene transcription. In addition, select super-enhancers and enhancers were identified that regulated clusters of paralogous genes. We conclude that, whereas robust transcriptional output can be achieved by an isolated enhancer, clusters of enhancers acting on a common target gene act in a partially redundant manner to fine tune transcriptional output of their target genes.


Subject(s)
Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Developmental/genetics , Mouse Embryonic Stem Cells/metabolism , Transcription, Genetic , Animals , CRISPR-Cas Systems , Cell Differentiation/genetics , Gene Deletion , Mice
19.
Bioinformatics ; 35(18): 3232-3239, 2019 09 15.
Article in English | MEDLINE | ID: mdl-30753279

ABSTRACT

MOTIVATION: Mammalian genomes can contain thousands of enhancers but only a subset are actively driving gene expression in a given cellular context. Integrated genomic datasets can be harnessed to predict active enhancers. One challenge in integration of large genomic datasets is the increasing heterogeneity: continuous, binary and discrete features may all be relevant. Coupled with the typically small numbers of training examples, semi-supervised approaches for heterogeneous data are needed; however, current enhancer prediction methods are not designed to handle heterogeneous data in the semi-supervised paradigm. RESULTS: We implemented a Dirichlet Process Heterogeneous Mixture model that infers Gaussian, Bernoulli and Poisson distributions over features. We derived a novel variational inference algorithm to handle semi-supervised learning tasks where certain observations are forced to cluster together. We applied this model to enhancer candidates in mouse heart tissues based on heterogeneous features. We constrained a small number of known active enhancers to appear in the same cluster, and 47 additional regions clustered with them. Many of these are located near heart-specific genes. The model also predicted 1176 active promoters, suggesting that it can discover new enhancers and promoters. AVAILABILITY AND IMPLEMENTATION: We created the 'dphmix' Python package: https://pypi.org/project/dphmix/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Genome , Genomics , Heart , Animals , Cluster Analysis , Humans , Mice , Software , Supervised Machine Learning
20.
Metab Eng ; 57: 203-216, 2020 01.
Article in English | MEDLINE | ID: mdl-31805379

ABSTRACT

Chinese hamster ovary (CHO) cell expression systems have been exquisitely developed for the production of recombinant biotherapeutics (e.g. standard monoclonal antibodies, mAbs) and are able to generate efficacious, multi-domain proteins with human-like post translational modifications at high concentration with appropriate product quality attributes. However, there remains a need for development of new CHO cell expression systems able to produce more challenging secretory recombinant biotherapeutics at higher yield with improved product quality attributes. Amazingly, the engineering of lipid metabolism to enhance such properties has not been investigated even though the biosynthesis of recombinant proteins is at least partially controlled by cellular processes that are highly dependent on lipid metabolism. Here we show that the global transcriptional activator of genes involved in lipid biosynthesis, sterol regulatory element binding factor 1 (SREBF1), and stearoyl CoA desaturase 1 (SCD1), an enzyme which catalyzes the conversion of saturated fatty acids into monounsaturated fatty acids, can be overexpressed in CHO cells to different degrees. The amount of overexpression obtained of each of these lipid metabolism modifying (LMM) genes was related to the subsequent phenotypes observed. Expression of a number of model secretory biopharmaceuticals was enhanced between 1.5-9 fold in either SREBF1 or SCD1 engineered CHO host cells as assessed under batch and fed-batch culture. The SCD1 overexpressing polyclonal pool consistently showed increased concentration of a range of products. For the SREBF1 engineered cells, the level of SREBF1 expression that gave the greatest enhancement in yield was dependent upon the model protein tested. Overexpression of both SCD1 and SREBF1 modified the lipid profile of CHO cells and the cellular structure. Mechanistically, overexpression of SCD1 and SREBF1 resulted in an expanded endoplasmic reticulum (ER) that was dependent upon the level of LMM overexpression. We conclude that manipulation of lipid metabolism in CHO cells via genetic engineering is an exciting new approach to enhance the ability of CHO cells to produce a range of different types of secretory recombinant protein products via modulation of the cellular lipid profile and expansion of the ER.


Subject(s)
Batch Cell Culture Techniques , Biological Products/metabolism , Endoplasmic Reticulum , Lipid Metabolism/genetics , Metabolic Engineering , Animals , CHO Cells , Cricetulus , Endoplasmic Reticulum/enzymology , Endoplasmic Reticulum/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Stearoyl-CoA Desaturase/biosynthesis , Stearoyl-CoA Desaturase/genetics , Sterol Regulatory Element Binding Protein 1/biosynthesis , Sterol Regulatory Element Binding Protein 1/genetics
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