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1.
Cancer Biol Med ; 19(11)2022 12 05.
Artículo en Inglés | MEDLINE | ID: mdl-36476337

RESUMEN

Lung cancer remains the leading cause of cancer-associated mortality worldwide, but with the emergence of oncogene targeted therapies, treatment options have tremendously improved. Owing to their biological relevance, members of the ERBB receptor family, including the EGF receptor (EGFR), HER2, HER3 and HER4, are among the best studied oncogenic drivers. Activating EGFR mutations are frequently observed in non-small cell lung cancer (NSCLC), and small molecule tyrosine kinase inhibitors (TKIs) are the established first line treatment option for patients whose tumors bear "typical/classical" EGFR mutations (exon 19 deletions, L858R point mutations). Additionally, new TKIs are rapidly evolving with better efficacy to overcome primary and secondary treatment resistance (e.g., that due to T790M or C797S resistance mutations). Some atypical EGFR mutations, such as the most frequent exon 20 insertions, exhibit relative resistance to earlier generation TKIs through steric hindrance. In this subgroup, newer TKIs, such as mobocertinib and the bi-specific antibody amivantamab have recently been approved, whereas less frequent atypical EGFR mutations remain understudied. In contrast to EGFR, HER2 has long remained a challenging target, but better structural understanding has led to the development of newer generations of TKIs. The recent FDA approval of the antibody-drug conjugate trastuzumab-deruxtecan for pretreated patients with HER2 mutant NSCLC has been an important therapeutic breakthrough. HER3 and HER4 also exert oncogenic potential, and targeted treatment approaches are being developed, particularly for HER3. Overall, strategies to inhibit the oncogenic function of ERBB receptors in NSCLC are currently evolving at an unprecedented pace; therefore, this review summarizes current treatment standards and discusses the outlook for future developments.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas , Neoplasias Pulmonares , Humanos , Receptores ErbB/genética , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Carcinoma de Pulmón de Células no Pequeñas/genética , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Mutación , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico
2.
Molecules ; 27(21)2022 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-36364252

RESUMEN

Natural products are an excellent source of inspiration for the development of new drugs. Among them, betalains have been extensively studied for their antioxidant properties and potential application as natural food dyes. Herein, we describe the seven-step synthesis of new betalamic acid analogs without carboxy groups in the 2- and 6-position with an overall yield of ~70%. The Folin-Ciocalteu assay was used to determine the antioxidant properties of protected intermediate 21. Additionally, the five-step synthesis of betalamic acid analog 35 with three ester moieties was performed. Using NMR techniques, the stability of the obtained compounds towards oxygen was analyzed.


Asunto(s)
Antioxidantes , Pirrolidinas , Antioxidantes/farmacología , Antioxidantes/química , Betalaínas/química , Piridinas/química
3.
Cancer Cell ; 40(10): 1128-1144.e8, 2022 10 10.
Artículo en Inglés | MEDLINE | ID: mdl-36150391

RESUMEN

KRAS-LKB1 (KL) mutant lung cancers silence STING owing to intrinsic mitochondrial dysfunction, resulting in T cell exclusion and resistance to programmed cell death (ligand) 1 (PD-[L]1) blockade. Here we discover that KL cells also minimize intracellular accumulation of 2'3'-cyclic GMP-AMP (2'3'-cGAMP) to further avoid downstream STING and STAT1 activation. An unbiased screen to co-opt this vulnerability reveals that transient MPS1 inhibition (MPS1i) potently re-engages this pathway in KL cells via micronuclei generation. This effect is markedly amplified by epigenetic de-repression of STING and only requires pulse MPS1i treatment, creating a therapeutic window compared with non-dividing cells. A single course of decitabine treatment followed by pulse MPS1i therapy restores T cell infiltration in vivo, enhances anti-PD-1 efficacy, and results in a durable response without evidence of significant toxicity.


Asunto(s)
Neoplasias Pulmonares , Proteínas Proto-Oncogénicas p21(ras) , Decitabina , Genes ras , Humanos , Ligandos , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Proteínas Proto-Oncogénicas p21(ras)/genética , Proteínas Proto-Oncogénicas p21(ras)/metabolismo
4.
Adv Healthc Mater ; 11(24): e2200989, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36100464

RESUMEN

Growing millimeter-scaled functional tissue remains a major challenge in the field of tissue engineering. Therefore, microporous annealed particles (MAPs) are emerging as promising porous biomaterials that are formed by assembly of microgel building blocks. To further vary the pore size and increase overall MAP porosity of mechanically stable scaffolds, rod-shaped microgels with high aspect ratios up to 20 are chemically interlinked into highly porous scaffolds. Polyethylene glycol based microgels (width 10 µm, lengths up to 200 µm) are produced via in-mold polymerization and covalently interlinked into stable 3D scaffolds via epoxy-amine chemistry. For the first time, MAP porosities can be enhanced by increasing the microgel aspect ratio (mean pore sizes ranging from 39 to 82 µm, porosities from 65 to 90%). These porosities are significantly higher compared to constructs made from spherical or lower aspect ratio rod-shaped microgels. Rapid filling of the pores by either murine or primary human fibroblasts is ensured as cells migrate and grow extensively into these scaffolds. Overall, this study demonstrates that highly porous, stable macroporous hydrogels can be achieved with a very low partial volume of synthetic, high aspect ratio microgels, leading to large empty volumes available for cell ingrowth and cell-cell interactions.


Asunto(s)
Microgeles , Humanos , Animales , Ratones , Porosidad , Ingeniería de Tejidos/métodos , Materiales Biocompatibles , Hidrogeles , Movimiento Celular , Andamios del Tejido
5.
Chemistry ; 28(36): e202200883, 2022 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-35388562

RESUMEN

The continuous emergence of antimicrobial resistance is causing a threat to patients infected by multidrug-resistant pathogens. In particular, the clinical use of aminoglycoside antibiotics, broad-spectrum antibacterials of last resort, is limited due to rising bacterial resistance. One of the major resistance mechanisms in Gram-positive and Gram-negative bacteria is phosphorylation of these amino sugars at the 3'-position by O-phosphotransferases [APH(3')s]. Structural alteration of these antibiotics at the 3'-position would be an obvious strategy to tackle this resistance mechanism. However, the access to such derivatives requires cumbersome multi-step synthesis, which is not appealing for pharma industry in this low-return-on-investment market. To overcome this obstacle and combat bacterial resistance mediated by APH(3')s, we introduce a novel regioselective modification of aminoglycosides in the 3'-position via palladium-catalyzed oxidation. To underline the effectiveness of our method for structural modification of aminoglycosides, we have developed two novel antibiotic candidates overcoming APH(3')s-mediated resistance employing only four synthetic steps.


Asunto(s)
Antibacterianos , Farmacorresistencia Bacteriana , Aminoglicósidos/química , Aminoglicósidos/farmacología , Antibacterianos/química , Antibacterianos/farmacología , Bacterias Gramnegativas , Bacterias Grampositivas , Humanos , Fosfotransferasas
6.
Angew Chem Int Ed Engl ; 61(19): e202112959, 2022 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-35146855

RESUMEN

Many life-science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super-resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of 'linker' compounds, that bridge biotarget, fluorophore and a functional moiety via well-established labeling protocols. Linker molecules were synthesized via the Ugi four-component reaction (Ugi-4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation- and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon-rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol-maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self-healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self-healing linker-fluorophore conjugates and demonstrated their applications in super-resolution imaging and single-molecule spectroscopy.


Asunto(s)
Colorantes Fluorescentes , Imagen Individual de Molécula , Colorantes Fluorescentes/química , Ionóforos , Rodaminas/química
7.
Clin Cancer Res ; 28(8): 1640-1650, 2022 04 14.
Artículo en Inglés | MEDLINE | ID: mdl-35091439

RESUMEN

PURPOSE: Activating missense mutations of KRAS are the most frequent oncogenic driver events in lung adenocarcinoma (LUAD). However, KRAS isoforms are highly heterogeneous, and data on the potential isoform-dependent therapeutic vulnerabilities are still lacking. EXPERIMENTAL DESIGN: We developed an isogenic cell-based platform to compare the oncogenic properties and specific therapeutic actionability of KRAS-mutant isoforms. In parallel, we analyzed clinicopathologic and genomic data from 3,560 patients with non-small cell lung cancer (NSCLC) to survey allele-specific features associated with oncogenic KRAS mutations. RESULTS: In isogenic cell lines expressing different mutant KRAS isoforms, we identified isoform-specific biochemical, biological, and oncogenic properties both in vitro and in vivo. These exclusive features correlated with different therapeutic responses to MEK inhibitors, with KRAS G12C and Q61H mutants being more sensitive compared with other isoforms. In vivo, combined KRAS G12C and MEK inhibition was more effective than either drug alone. Among patients with NSCLCs that underwent comprehensive tumor genomic profiling, STK11 and ATM mutations were significantly enriched among tumors harboring KRAS G12C, G12A, and G12V mutations. KEAP1 mutation was significantly enriched among KRAS G12C and KRAS G13X LUADs. KRAS G13X-mutated tumors had the highest frequency of concurrent STK11 and KEAP1 mutations. Transcriptomic profiling revealed unique patterns of gene expression in each KRAS isoform, compared with KRAS wild-type tumors. CONCLUSIONS: This study demonstrates that KRAS isoforms are highly heterogeneous in terms of concurrent genomic alterations and gene-expression profiles, and that stratification based on KRAS alleles should be considered in the design of future clinical trials.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas , Neoplasias Pulmonares , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Carcinoma de Pulmón de Células no Pequeñas/genética , Humanos , Proteína 1 Asociada A ECH Tipo Kelch/genética , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patología , Quinasas de Proteína Quinasa Activadas por Mitógenos/genética , Mutación , Factor 2 Relacionado con NF-E2/genética , Isoformas de Proteínas/genética , Proteínas Proto-Oncogénicas p21(ras)/genética
8.
Cancer Res ; 82(1): 130-141, 2022 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-34548332

RESUMEN

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) are the standard-of-care treatment for EGFR-mutant non-small cell lung cancers (NSCLC). However, most patients develop acquired drug resistance to EGFR TKIs. HER3 is a unique pseudokinase member of the ERBB family that functions by dimerizing with other ERBB family members (EGFR and HER2) and is frequently overexpressed in EGFR-mutant NSCLC. Although EGFR TKI resistance mechanisms do not lead to alterations in HER3, we hypothesized that targeting HER3 might improve efficacy of EGFR TKI. HER3-DXd is an antibody-drug conjugate (ADC) comprised of HER3-targeting antibody linked to a topoisomerase I inhibitor currently in clinical development. In this study, we evaluated the efficacy of HER3-DXd across a series of EGFR inhibitor-resistant, patient-derived xenografts and observed it to be broadly effective in HER3-expressing cancers. We further developed a preclinical strategy to enhance the efficacy of HER3-DXd through osimertinib pretreatment, which increased membrane expression of HER3 and led to enhanced internalization and efficacy of HER3-DXd. The combination of osimertinib and HER3-DXd may be an effective treatment approach and should be evaluated in future clinical trials in EGFR-mutant NSCLC patients. SIGNIFICANCE: EGFR inhibition leads to increased HER3 membrane expression and promotes HER3-DXd ADC internalization and efficacy, supporting the clinical development of the EGFR inhibitor/HER3-DXd combination in EGFR-mutant lung cancer.See related commentary by Lim et al., p. 18.


Asunto(s)
Antineoplásicos/uso terapéutico , Receptores ErbB/antagonistas & inhibidores , Inmunoconjugados/metabolismo , Receptor ErbB-3/metabolismo , Animales , Antineoplásicos/farmacología , Apoptosis , Técnicas de Cultivo de Célula , Línea Celular Tumoral , Humanos , Ratones
9.
Mol Cancer Ther ; 21(2): 322-335, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34789563

RESUMEN

MET-targeted therapies are clinically effective in MET-amplified and MET exon 14 deletion mutant (METex14) non-small cell lung cancers (NSCLCs), but their efficacy is limited by the development of drug resistance. Structurally distinct MET tyrosine kinase inhibitors (TKIs) (type I/II) have been developed or are under clinical evaluation, which may overcome MET-mediated drug resistance mechanisms. In this study, we assess secondary MET mutations likely to emerge in response to treatment with single-agent or combinations of type I/type II MET TKIs using TPR-MET transformed Ba/F3 cell mutagenesis assays. We found that these inhibitors gave rise to distinct secondary MET mutant profiles. However, a combination of type I/II TKI inhibitors (capmatinib and merestinib) yielded no resistant clones in vitro The combination of capmatinib/merestinib was evaluated in vivo and led to a significant reduction in tumor outgrowth compared with either MET inhibitor alone. Our findings demonstrate in vitro and in vivo that a simultaneous treatment with a type I and type II MET TKI may be a clinically viable approach to delay and/or diminish the emergence of on target MET-mediated drug-resistance mutations.


Asunto(s)
Resistencia a Antineoplásicos/efectos de los fármacos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Simulación del Acoplamiento Molecular/métodos , Inhibidores de Proteínas Quinasas/uso terapéutico , Animales , Femenino , Humanos , Ratones , Inhibidores de Proteínas Quinasas/farmacología
10.
Front Cell Dev Biol ; 9: 773101, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34869372

RESUMEN

Cancers that are histologically defined as the same type of cancer often need a distinct therapy based on underlying heterogeneity; likewise, histologically disparate cancers can require similar treatment approaches due to intrinsic similarities. A comprehensive analysis integrated with drug response data and molecular alterations, particularly to reveal therapeutic concordance mechanisms across histologically disparate tumor subtypes, has not yet been fully exploited. In this study, we integrated pharmacological, genomic, and transcriptomic profiling data provided from the Cancer Genome Project (CGP) in a systematic in silico investigation of the pharmacological subtypes of cancers and the intrinsic concordance of molecular mechanisms leading to similar therapeutic responses across histologically disparate tumor subtypes. We further developed a novel approach to redefine cell-to-cell similarity and drug-to-drug similarity from the therapeutic concordance, providing a new point of view to study cancer heterogeneity. This study demonstrates how pharmacological and omics data can be used to systematically classify cancers in terms of response to various compounds and provides us with a purely therapy-oriented perspective to view tumor classifications independent of histology subtypes. The knowledge of pharmacological subtypes of 367 drugs are available via our website (http://www.hywanglab.cn/dtdb/), providing the resources for precision medicine in the perspective of therapeutic response-based re-classification of tumor.

11.
Org Biomol Chem ; 19(38): 8384-8396, 2021 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-34528988

RESUMEN

Conformationally restricted bicyclic KOR agonists 10 with an endo-configured amino moiety were synthesized to analyze the bioactive conformation of conformationally flexible KOR agonists such as 2-5. A seven-step synthesis starting with (S)-configured 4-oxopiperidine-2-carboxylate 13 was developed. cis- and trans-configured diesters 12 were obtained in a 3 : 1 ratio via hydrogenation of the α,ß-unsaturated ester 14. After establishment of the bicyclic scaffold, a diastereoselective reductive amination of ketone 11 provided exclusively the endo-configured bicyclic amines 10a,b. The 3 : 1 mixtures of enantiomers were separated by chiral HPLC, respectively, leading to enantiomerically pure KOR agonists (1S,5S,7R)-10a,b and (1R,5R,7S)-10a,b (ent-10a,b). The KOR affinity was determined in receptor binding studies with the radioligand [3H]U-69 593. The high KOR affinity of endo-configured amines 10a (Ki = 7 nM) and 10b (Ki = 13 nM) indicates that the dihedral angle of the KOR pharmacophoric element N(pyrrolidine)-C-C-N(phenylacetyl) of 42° is close to the bioactive conformation of more flexible KOR agonists. It should be noted that changing the configuration of potent and selective KOR agonists 10a and 10b led to potent and selective σ1 ligands (e.g. ent-10aKi(σ1) = 10 nM).


Asunto(s)
Octanos
12.
J Nat Prod ; 84(10): 2630-2643, 2021 10 22.
Artículo en Inglés | MEDLINE | ID: mdl-34553942

RESUMEN

Claviceps purpurea is an ergot fungus known for its neurotropic alkaloids, which have been identified as the main cause of ergotism, a livestock and human disease triggered by ergot consumption. Tetrahydroxanthone dimers, the so-called ergopigments, presumably also contribute to this toxic effect. Overexpression of the cluster-specific transcription factor responsible for the formation of these pigments in C. purpurea led to the isolation of three new metabolites (8-10). The new pigments were characterized utilizing HRMS, NMR techniques, and CD spectroscopy and shown to be xanthone dimers. Secalonic acid A and its 2,4'- and 4,4'-linked isomers were also isolated, and their absolute configuration was investigated. The contribution of secalonic acid A, its isomers, and new metabolites to the toxicity of C. purpurea was investigated in HepG2 and CCF-STTG1 cells. Along with cytotoxic properties, secalonic acid A was found to inhibit topoisomerase I and II activity.


Asunto(s)
Claviceps/química , Xantenos/química , Células Hep G2 , Humanos , Estructura Molecular , Inhibidores de Topoisomerasa , Xantonas
14.
Org Biomol Chem ; 19(18): 4082-4099, 2021 05 12.
Artículo en Inglés | MEDLINE | ID: mdl-33978027

RESUMEN

In order to analyze the bioactive conformation of flexible KOR agonists the ethylenediamine KOR pharmacophore was conformationally constrained by incorporation into a bicyclic system. For this purpose, 2-azabicyclo[3.2.1.]octan-7-amines were designed, synthesized and pharmacologically evaluated. The primary amine 14 as first key intermediate was prepared in a six-step synthesis starting with methyl cyclopent-3-enecarboxylate 9. Whereas phenylacetamides failed to provide bicyclic compounds, the intramolecular nucleophilic substitution of the sulfonamide 25 was initiated by deprotonation with NaH affording the bicyclic compound 26 in 72% yield. The three-step introduction of the pharmacophoric pyrrolidine ring started with nucleophilic substitution of exo-configured tosylate 26 with NaN3, which unexpectedly occurred under retention of configuration leading to exo-configured azide 31. The final KOR agonists 35 and 36 with exo-configured amino moieties were obtained by removal of the N-tosyl moiety of 33 and introduction of the second pharmacophoric element by acylation with dihalophenylacetyl chlorides. The KOR affinity of the pyrrolidine 35a is in the high nanomolar range (Ki = 862 nM). The low KOR affinity is explained by a non-appropriate dihedral angle of 137°/141° of the N(pyrrolidine)-C-C-N(acyl) system. As observed for stereoisomers of potent KOR agonists, phenylacetamide 35a and more importantly sulfonamides 33a and 33b show moderate affinity at σ1 receptors (Ki = 109-208 nM).

15.
Int J Mol Sci ; 22(6)2021 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-33809660

RESUMEN

Non-small-cell lung cancer (NSCLC) with Kirsten rat sarcoma (KRAS) mutations has notoriously challenged oncologists and researchers for three notable reasons: (1) the historical assumption that KRAS is "undruggable", (2) the disease heterogeneity and (3) the shaping of the tumor microenvironment by KRAS downstream effector functions. Better insights into KRAS structural biochemistry allowed researchers to develop direct KRAS(G12C) inhibitors, which have shown early signs of clinical activity in NSCLC patients and have recently led to an FDA breakthrough designation for AMG-510. Following the approval of immune checkpoint inhibitors for PDL1-positive NSCLC, this could fuel yet another major paradigm shift in the treatment of advanced lung cancer. Here, we review advances in our understanding of the biology of direct KRAS inhibition and project future opportunities and challenges of dual KRAS and immune checkpoint inhibition. This strategy is supported by preclinical models which show that KRAS(G12C) inhibitors can turn some immunologically "cold" tumors into "hot" ones and therefore could benefit patients whose tumors harbor subtype-defining STK11/LKB1 co-mutations. Forty years after the discovery of KRAS as a transforming oncogene, we are on the verge of approval of the first KRAS-targeted drug combinations, thus therapeutically unifying Paul Ehrlich's century-old "magic bullet" vision with Rudolf Virchow's cancer inflammation theory.


Asunto(s)
Neoplasias Pulmonares/genética , Mutación/genética , Proteínas Proto-Oncogénicas p21(ras)/genética , Carcinoma de Pulmón de Células no Pequeñas/genética , Carcinoma de Pulmón de Células no Pequeñas/terapia , Resistencia a Antineoplásicos/genética , Humanos , Neoplasias Pulmonares/terapia , Proteínas Proto-Oncogénicas p21(ras)/antagonistas & inhibidores , Microambiente Tumoral
16.
Mol Cancer Ther ; 20(4): 641-654, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33536188

RESUMEN

RAS gene mutations are the most frequent oncogenic event in lung cancer. They activate multiple RAS-centric signaling networks among them the MAPK, PI3K, and RB pathways. Within the MAPK pathway, ERK1/2 proteins exert a bottleneck function for transmitting mitogenic signals and activating cytoplasmic and nuclear targets. In view of disappointing antitumor activity and toxicity of continuously applied MEK inhibitors in patients with KRAS-mutant lung cancer, research has recently focused on ERK1/2 proteins as therapeutic targets and on ERK inhibitors for their ability to prevent bypass and feedback pathway activation. Here, we show that intermittent application of the novel and selective ATP-competitive ERK1/2 inhibitor LY3214996 exerts single-agent activity in patient-derived xenograft (PDX) models of RAS-mutant lung cancer. Combination treatments were well tolerated and resulted in synergistic (ERKi plus PI3K/mTORi LY3023414) and additive (ERKi plus CDK4/6i abemaciclib) tumor growth inhibition in PDX models. Future clinical trials are required to investigate if intermittent ERK inhibitor-based treatment schedules can overcome toxicities observed with continuous MEK inhibition and-equally important-to identify biomarkers for patient stratification.


Asunto(s)
Genes ras/efectos de los fármacos , Neoplasias Pulmonares/tratamiento farmacológico , Oncogenes/genética , Inhibidores de Proteínas Quinasas/uso terapéutico , Línea Celular Tumoral , Humanos , Neoplasias Pulmonares/patología , Inhibidores de Proteínas Quinasas/farmacología
17.
BMC Genomics ; 22(1): 27, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407103

RESUMEN

BACKGROUND: Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progression of malignancies and are promising candidates as non-invasive diagnostic biomarkers or as targets for therapeutic interventions. Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified. RESULTS: In this study, we performed an unbiased analysis of high-throughput mRNA and miRNA-sequencing data from exosomes of patients with various cancer types and identify candidate reference genes and miRNAs in cancer exosomes. The expression stability of these candidate reference genes was evaluated by the coefficient of variation "CV" and the average expression stability value "M". We subsequently validated these candidate reference genes in exosomes from an independent cohort of ovarian cancer patients and healthy control individuals by qRT-PCR. CONCLUSIONS: Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively. For superior accuracy, we recommend the use of a combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses.


Asunto(s)
Exosomas , MicroARNs , Neoplasias , Exosomas/genética , Humanos , Péptidos y Proteínas de Señalización Intracelular , MicroARNs/genética , Neoplasias/genética , RNA-Seq , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
18.
Gigascience ; 9(6)2020 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-32470133

RESUMEN

BACKGROUND: In cancer cells, fusion genes can produce linear and chimeric fusion-circular RNAs (f-circRNAs), which are functional in gene expression regulation and implicated in malignant transformation, cancer progression, and therapeutic resistance. For specific cancers, proteins encoded by fusion transcripts have been identified as innovative therapeutic targets (e.g., EML4-ALK). Even though RNA sequencing (RNA-Seq) technologies combined with existing bioinformatics approaches have enabled researchers to systematically identify fusion transcripts, specifically detecting f-circRNAs in cells remains challenging owing to their general sparsity and low abundance in cancer cells but also owing to imperfect computational methods. RESULTS: We developed the Python-based workflow "Fcirc" to identify fusion linear and f-circRNAs from RNA-Seq data with high specificity. We applied Fcirc to 3 different types of RNA-Seq data scenarios: (i) actual synthetic spike-in RNA-Seq data, (ii) simulated RNA-Seq data, and (iii) actual cancer cell-derived RNA-Seq data. Fcirc showed significant advantages over existing methods regarding both detection accuracy (i.e., precision, recall, F-measure) and computing performance (i.e., lower runtimes). CONCLUSION: Fcirc is a powerful and comprehensive Python-based pipeline to identify linear and circular RNA transcripts from known fusion events in RNA-Seq datasets with higher accuracy and shorter computing times compared with previously published algorithms. Fcirc empowers the research community to study the biology of fusion RNAs in cancer more effectively.


Asunto(s)
Algoritmos , Biología Computacional/métodos , ARN Circular/genética , ARN/genética , Programas Informáticos , Regulación de la Expresión Génica , Fusión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Neoplasias , Reproducibilidad de los Resultados , Flujo de Trabajo
19.
RSC Adv ; 10(37): 21933-21939, 2020 Jun 08.
Artículo en Inglés | MEDLINE | ID: mdl-35516653

RESUMEN

Physical gels are a versatile class of materials which can find application in sensors, electrochemistry, biomedicine or rheological modifiers. Herein, we present a hydrogen-bonded physical gel which is based on the interaction between phenylcarbonate telechelic poly(ethylene glycol) (PEG-PC) and poly(vinyl amine-co-acetamide) (p(VAm-co-VAA)). The critical gelation concentration was found to be 10 wt% by rheology and NMR. UV-vis spectroscopy and dynamic light scattering reveal the formation of aggregates in the gel. Rheology and differential scanning calorimetry (DSC) was used to show the effect of thermal curing on the mechanical properties of the physical gel.

20.
EBioMedicine ; 49: 106-117, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31668570

RESUMEN

BACKGROUND: KRAS mutations are the most frequent oncogenic aberration in lung adenocarcinoma. KRAS mutant isoforms differentially shape tumour biology and influence drug responses. This heterogeneity challenges the development of effective therapies for patients with KRAS-driven non-small cell lung cancer (NSCLC). METHODS: We developed an integrative pharmacogenomics analysis to identify potential drug targets to overcome MEK/ERK inhibitor resistance in lung cancer cell lines with KRAS(G12C) mutation (n = 12). We validated our predictive in silico results with in vitro models using gene knockdown, pharmacological target inhibition and reporter assays. FINDINGS: Our computational analysis identifies casein kinase 2A1 (CSNK2A1) as a mediator of MEK/ERK inhibitor resistance in KRAS(G12C) mutant lung cancer cells. CSNK2A1 knockdown reduces cell proliferation, inhibits Wnt/ß-catenin signalling and increases the anti-proliferative effect of MEK inhibition selectively in KRAS(G12C) mutant lung cancer cells. The specific CK2-inhibitor silmitasertib phenocopies the CSNK2A1 knockdown effect and sensitizes KRAS(G12C) mutant cells to MEK inhibition. INTERPRETATION: Our study supports the importance of accurate patient stratification and rational drug combinations to gain benefit from MEK inhibition in patients with KRAS mutant NSCLC. We develop a genotype-based strategy that identifies CK2 as a promising co-target in KRAS(G12C) mutant NSCLC by using available pharmacogenomics gene expression datasets. This approach is applicable to other oncogene driven cancers. FUND: This work was supported by grants from the National Natural Science Foundation of China, the National Key Research and Development Program of China, the Lung Cancer Research Foundation and a Mildred-Scheel postdoctoral fellowship from the German Cancer Aid Foundation.


Asunto(s)
Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Terapia Molecular Dirigida , Mutación/genética , Farmacogenética , Proteínas Proto-Oncogénicas p21(ras)/genética , Adenocarcinoma/genética , Adenocarcinoma/patología , Línea Celular Tumoral , Proliferación Celular , Resistencia a Antineoplásicos/efectos de los fármacos , Quinasas MAP Reguladas por Señal Extracelular/antagonistas & inhibidores , Quinasas MAP Reguladas por Señal Extracelular/metabolismo , Genes Dominantes , Humanos , Neoplasias Pulmonares/patología , Quinasas de Proteína Quinasa Activadas por Mitógenos/antagonistas & inhibidores , Quinasas de Proteína Quinasa Activadas por Mitógenos/metabolismo , Metástasis de la Neoplasia , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico , Transducción de Señal
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