RESUMO
Genomic imprinting is an epigenetic regulation mechanism in mammals resulting in the parentally dependent monoallelic expression of genes. Imprinting disorders in humans are associated with several congenital syndromes and cancers and remain the focus of many medical studies. Cattle is a better model organism for investigating human embryo development than mice. Imprinted genes usually cluster on chromosomes and are regulated by different methylation regions (DMRs) located in imprinting control regions that control gene expression in cis. There is an imprinted locus on human chromosome 16q24.1 associated with congenital lethal developmental lung disease in newborns. However, genomic imprinting on bovine chromosome 18, which is homologous with human chromosome 16 has not been systematically studied. The aim of this study was to analyze the allelic expressions of eight genes (CDH13, ATP2C2, TLDC1, COTL1, CRISPLD2, ZDHHC7, KIAA0513, and GSE1) on bovine chromosome 18 and to search the DMRs associated gene allelic expression. Three transcript variants of the ZDHHC7 gene (X1, X2, and X5) showed maternal imprinting in bovine placentas. In addition, the monoallelic expression of X2 and X5 was tissue-specific. Five transcripts of the KIAA0513 gene showed tissue- and isoform-specific monoallelic expression. The CDH13, ATP2C2, and TLDC1 genes exhibited tissue-specific imprinting, however, COTL1, CRISLPLD2, and GSE1 escaped imprinting. Four DMRs, established after fertilization, were found in this region. Two DMRs were located between the ZDHHC7 and KIAA0513 genes, and two were in exon 1 of the CDH13 and ATP2C2 genes, respectively. The results from this study support future studies on the molecular mechanism to regulate the imprinting of candidate genes on bovine chromosome 18.
Assuntos
Metilação de DNA , Epigênese Genética , Recém-Nascido , Gravidez , Feminino , Humanos , Bovinos/genética , Animais , Camundongos , Metilação de DNA/genética , Cromossomos Humanos Par 18 , Impressão Genômica/genética , Cromossomos , Mamíferos/genética , Proteínas do Tecido Nervoso/genéticaRESUMO
The PI3K/AKT/mTOR (PAM) signaling pathway is a highly conserved signal transduction network in eukaryotic cells that promotes cell survival, cell growth, and cell cycle progression. Growth factor signalling to transcription factors in the PAM axis is highly regulated by multiple cross-interactions with several other signaling pathways, and dysregulation of signal transduction can predispose to cancer development. The PAM axis is the most frequently activated signaling pathway in human cancer and is often implicated in resistance to anticancer therapies. Dysfunction of components of this pathway such as hyperactivity of PI3K, loss of function of PTEN, and gain-of-function of AKT, are notorious drivers of treatment resistance and disease progression in cancer. In this review we highlight the major dysregulations in the PAM signaling pathway in cancer, and discuss the results of PI3K, AKT and mTOR inhibitors as monotherapy and in co-administation with other antineoplastic agents in clinical trials as a strategy for overcoming treatment resistance. Finally, the major mechanisms of resistance to PAM signaling targeted therapies, including PAM signaling in immunology and immunotherapies are also discussed.
Assuntos
Neoplasias , Fosfatidilinositol 3-Quinases , Humanos , Proteínas Proto-Oncogênicas c-akt , Transdução de Sinais , Serina-Treonina Quinases TOR , Neoplasias/tratamento farmacológico , Neoplasias/genéticaRESUMO
The development of tissues and organs requires close interaction of cells. To achieve this, cells express adhesion proteins such as the neural cell adhesion molecule (NCAM) or its Drosophila ortholog Fasciclin 2 (Fas2). Both are members of the Ig-domain superfamily of proteins that mediate homophilic adhesion. These proteins are expressed as isoforms differing in their membrane anchorage and their cytoplasmic domains. To study the function of single isoforms, we have conducted a comprehensive genetic analysis of Fas2 We reveal the expression pattern of all major Fas2 isoforms, two of which are GPI anchored. The remaining five isoforms carry transmembrane domains with variable cytoplasmic tails. We generated Fas2 mutants expressing only single isoforms. In contrast to the null mutation, which causes embryonic lethality, these mutants are viable, indicating redundancy among the different isoforms. Cell type-specific rescue experiments showed that glial-secreted Fas2 can rescue the Fas2 mutant phenotype to viability. This demonstrates that cytoplasmic Fas2 domains have no apparent essential functions and indicate that Fas2 has function(s) other than homophilic adhesion. In conclusion, our data suggest novel mechanistic aspects of a long-studied adhesion protein.
Assuntos
Moléculas de Adesão Celular Neuronais/metabolismo , Drosophila melanogaster/citologia , Drosophila melanogaster/metabolismo , Transdução de Sinais , Animais , Adesão Celular , Moléculas de Adesão Celular Neuronais/química , Moléculas de Adesão Celular Neuronais/genética , Movimento Celular , Drosophila melanogaster/embriologia , Drosophila melanogaster/genética , Embrião não Mamífero/citologia , Embrião não Mamífero/metabolismo , Edição de Genes , Regulação da Expressão Gênica no Desenvolvimento , Glicosilfosfatidilinositóis/metabolismo , Mutação/genética , Neuroglia/metabolismo , Domínios Proteicos , Isoformas de Proteínas/metabolismo , Traqueia/embriologia , Traqueia/metabolismoRESUMO
Gain or loss of appetite and resulting body weight changes are commonly observed in major depressive disorders (MDDs). Brain-derived neurotrophic factor (BDNF) is broadly expressed in the brain and is thought to play a role in the pathophysiology of MDDs and obesity. Congenital loss of function of BDNF causes weight gain in both humans and rodents; however, it is not clear whether acquired loss of function of BDNF also affects body weight. Thus, we exploited mutant mice in which the Bdnf expression level is regulated by the tetracycline-dependent transcriptional silencer (tTS)-tetracycline operator sequence (tetO) system. Time-controlled Bdnf expression using this system allowed us to establish congenital and acquired loss of function of Bdnf in mice. We demonstrated that changes in Bdnf expression influenced body weight during not only the developmental stage but also the adult stage of mice. Although it is still unclear whether acquired Bdnf loss of function in rodents mimics the pathology of MDD, our findings may bridge the mechanistic gap between MDDs and body weight gain in line with BDNF dysfunction.
Assuntos
Fator Neurotrófico Derivado do Encéfalo/metabolismo , Transtorno Depressivo Maior , Adulto , Animais , Peso Corporal , Regulação para Baixo , Humanos , Camundongos , Tetraciclinas , Aumento de PesoRESUMO
The transcription factor p53 exerts its tumour suppressive effect through transcriptional activation of numerous target genes controlling cell cycle arrest, apoptosis, cellular senescence and DNA repair. In addition, there is evidence that p53 influences the translation of specific mRNAs, including translational inhibition of ribosomal protein synthesis and translational activation of MDM2. A challenge in the analysis of translational control is that changes in mRNA abundance exert a kinetic (passive) effect on ribosome densities. In order to separate these passive effects from active regulation of translation efficiency in response to p53 activation, we conducted a comprehensive analysis of translational regulation by comparative analysis of mRNA levels and ribosome densities upon DNA damage induced by neocarzinostatin in wild-type and TP53-/- HCT116 colorectal carcinoma cells. Thereby, we identified a specific group of mRNAs that are preferentially translated in response to p53 activation, many of which correspond to p53 target genes including MDM2, SESN1 and CDKN1A. By subsequent polysome profile analysis of SESN1 and CDKN1A mRNA, we could demonstrate that p53-dependent translational activation relies on a combination of inducing the expression of translationally advantageous isoforms and trans-acting mechanisms that further enhance the translation of these mRNAs.
Assuntos
Ribossomos , Proteína Supressora de Tumor p53 , Pontos de Checagem do Ciclo Celular , Regulação da Expressão Gênica , Humanos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ribossomos/genética , Ribossomos/metabolismo , Fatores de Transcrição/metabolismo , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismoRESUMO
Bitter taste receptors (TAS2Rs) are expressed by oral cavity cells in mammals and classically function as sensors for bitter compounds. There are 25 functional isoforms of human TAS2Rs, with individual bitter ligands. Each human TAS2R isoform is distributed in several tissues, such as the airway epithelia and gastrointestinal tract, and plays an important role in physiological functions. However, quantification of each isoform is difficult because of highly homologous sequences between some TAS2R isoforms. Therefore, differentiating the isoforms by their expression levels is suitable for clarifying the tissue-specific effects of bitter compounds. In this study, we developed a real-time quantitative PCR (qPCR) method to determine the expression of each TAS2R isoform. Using plasmid standards harboring each isoform, we confirmed that the current assay can quantify the gene expression of each isoform, with negligible interference from other isoforms. In addition, our methods can successfully discriminate between the mRNA expression of each isoform in human cell lines and tissues. Therefore, this qPCR method can successfully quantify the mRNA level of each TAS2R isoform. This method will contribute to a better understanding of the molecular mechanisms underlying the TAS2R ligand-activated signal transduction.
Assuntos
Isoformas de Proteínas , Receptores Acoplados a Proteínas G , Paladar , Animais , Humanos , Ligantes , Isoformas de Proteínas/genética , RNA Mensageiro , Reação em Cadeia da Polimerase em Tempo Real , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Transcrição GênicaRESUMO
Protein kinase A (PKA) holoenzyme, comprised of a cAMP-binding regulatory (R)-subunit dimer and 2 catalytic (C)-subunits, is the master switch for cAMP-mediated signaling. Of the 4 R-subunits (RIα, RIß, RIIα, RIIß), RIα is most essential for regulating PKA activity in cells. Our 2 RIα2C2 holoenzyme states, which show different conformations with and without ATP, reveal how ATP/Mg2+ functions as a negative orthosteric modulator. Biochemical studies demonstrate how the removal of ATP primes the holoenzyme for cAMP-mediated activation. The opposing competition between ATP/cAMP is unique to RIα. In RIIß, ATP serves as a substrate and facilitates cAMP-activation. The isoform-specific RI-holoenzyme dimer interface mediated by N3A-N3A' motifs defines multidomain cross-talk and an allosteric network that creates competing roles for ATP and cAMP. Comparisons to the RIIß holoenzyme demonstrate isoform-specific holoenzyme interfaces and highlights distinct allosteric mechanisms for activation in addition to the structural diversity of the isoforms.
Assuntos
Subunidade RIIbeta da Proteína Quinase Dependente de AMP Cíclico/química , Subunidade RIalfa da Proteína Quinase Dependente de AMP Cíclico/química , Proteínas Quinases Dependentes de AMP Cíclico/química , Estrutura Quaternária de Proteína , Trifosfato de Adenosina/química , Trifosfato de Adenosina/genética , Regulação Alostérica/genética , Sequência de Aminoácidos/genética , Cristalografia por Raios X , AMP Cíclico/química , AMP Cíclico/genética , Subunidade RIIbeta da Proteína Quinase Dependente de AMP Cíclico/genética , Subunidade RIalfa da Proteína Quinase Dependente de AMP Cíclico/genética , Proteínas Quinases Dependentes de AMP Cíclico/genética , Regulação Enzimológica da Expressão Gênica/genética , Holoenzimas/química , Holoenzimas/genética , Humanos , Ligação Proteica/genética , Subunidades Proteicas/química , Subunidades Proteicas/genética , Transdução de Sinais/genéticaRESUMO
Cutaneous squamous cell carcinomas (cSCCs) account for about 20% of keratinocyte carcinomas, the most common cancer in the UK. Therapeutic options for cSCC patients who develop metastasis are limited and a better understanding of the biochemical pathways involved in cSCC development/progression is crucial to identify novel therapeutic targets. Evidence indicates that the phosphoinositide 3-kinases (PI3Ks)/Akt pathway plays an important role, in particular in advanced cSCC. Questions remain of whether all four PI3K isoforms able to activate Akt are involved and whether selective inhibition of specific isoform(s) might represent a more targeted strategy. Here we determined the sensitivity of four patient-derived cSCC cell lines to isoform-specific PI3K inhibitors to start investigating their potential therapeutic value in cSCC. Parallel experiments were performed in immortalized keratinocyte cell lines. We observed that pan PI3Ks inhibition reduced the growth/viability of all tested cell lines, confirming the crucial role of this pathway. Selective inhibition of the PI3K isoform p110α reduced growth/viability of keratinocytes and of two cSCC cell lines while affecting the other two only slightly. Importantly, p110α inhibition reduced Akt phosphorylation in all cSCC cell lines. These data indicate that growth and viability of the investigated cSCC cells display differential sensitivity to isoform-specific PI3K inhibitors.
Assuntos
Carcinoma de Células Escamosas/tratamento farmacológico , Fosfatidilinositol 3-Quinases/metabolismo , Inibidores de Fosfoinositídeo-3 Quinase/farmacologia , Neoplasias Cutâneas/tratamento farmacológico , Carcinoma de Células Escamosas/enzimologia , Carcinoma de Células Escamosas/patologia , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Cromonas/farmacologia , Humanos , Imidazóis/farmacologia , Isoenzimas , Queratinócitos/efeitos dos fármacos , Queratinócitos/enzimologia , Morfolinas/farmacologia , Proteínas Proto-Oncogênicas c-akt/metabolismo , Neoplasias Cutâneas/enzimologia , Neoplasias Cutâneas/patologia , Serina-Treonina Quinases TOR/antagonistas & inibidores , Serina-Treonina Quinases TOR/metabolismo , Tiazóis/farmacologia , Tiazolidinedionas/farmacologiaRESUMO
Neuropathic pain (NP) is a chronic condition that results from a lesion or disease of the nervous system, greatly impacting patients' quality of life. Current pharmacotherapy options deliver inadequate and/or insufficient responses and thus a significant unmet clinical need remains for alternative treatments in NP. Neuroinflammation, oxidative stress and their reciprocal relationship are critically involved in NP pathophysiology. In this context, new pharmacological approaches, aiming at enhancing the resolution phase of inflammation and/or restoring redox balance by targeting specific reactive oxygen species (ROS) sources, are emerging as potential therapeutic strategies for NP, with improved efficacy and safety profiles. Several reports have demonstrated that administration of exogenous specialized pro-resolving mediators (SPMs) ameliorates NP pathophysiology. Likewise, deletion or inhibition of the ROS-generating enzyme NADPH oxidase (NOX), particularly its isoforms 2 and 4, results in beneficial effects in NP models. Notably, SPMs also modulate oxidative stress and NOX also regulates neuroinflammation. By targeting neuroinflammatory and oxidative pathways, both SPMs analogues and isoform-specific NOX inhibitors are promising therapeutic strategies for NP.
Assuntos
Anti-Inflamatórios/uso terapêutico , NADPH Oxidases/antagonistas & inibidores , Neuralgia/tratamento farmacológico , Estresse Oxidativo/efeitos dos fármacos , Fatores Etários , Animais , Humanos , Inflamação/tratamento farmacológico , Caracteres SexuaisRESUMO
Because of their importance in maintaining protein homeostasis, molecular chaperones, including heat-shock protein 90 (Hsp90), represent attractive drug targets. Although a number of Hsp90 inhibitors are in preclinical/clinical development, none strongly differentiate between constitutively expressed Hsp90ß and stress-induced Hsp90α, the two cytosolic paralogs of this molecular chaperone. Thus, the importance of inhibiting one or the other paralog in different disease states remains unknown. We show that the natural product, gambogic acid (GBA), binds selectively to a site in the middle domain of Hsp90ß, identifying GBA as an Hsp90ß-specific Hsp90 inhibitor. Furthermore, using computational and medicinal chemistry, we identified a GBA analog, referred to as DAP-19, which binds potently and selectively to Hsp90ß. Because of its unprecedented selectivity for Hsp90ß among all Hsp90 paralogs, GBA thus provides a new chemical tool to study the unique biological role of this abundantly expressed molecular chaperone in health and disease.
Assuntos
Proteínas de Choque Térmico HSP90/antagonistas & inibidores , Proteínas de Choque Térmico HSP90/química , Xantonas/farmacologia , Simulação por Computador , Células HEK293 , Humanos , Mutagênese Sítio-Dirigida , Domínios Proteicos , Isoformas de Proteínas , Xantonas/metabolismoRESUMO
BACKGROUND: Aberrant mutations in KRAS play a critical role in tumor initiation and progression, and are a negative prognosis factor in lung adenocarcinoma (LUAD). RESULTS: Using genomic analysis for K-Ras isoforms (K-Ras4A and K-Ras4B) and large-scale multi-omics data, we inspected the overall survival (OS) and disease-free survival (DFS) of LUAD patients based on the abundance of transcript variants by analyzing RNA expression and somatic mutation data from The Cancer Genome Atlas (n = 516). The expression of the minor transcript K-Ras4A and its proportion were positively correlated with the presence of KRAS mutations in LUAD. We found that both K-Ras4A abundance measures (expression and proportion) have a strong association with poor OS (p = 0.0149 and p = 3.18E-3, respectively) and DFS (p = 3.03E-4 and p = 0.0237, respectively), but only in patients harboring KRAS mutations. A Cox regression analysis showed significant results in groups with low expression (hazard ratio (HR) = 2.533, 95% confidence interval (CI) = 1.380-4.651, p = 2.72E-3) and low proportion (HR = 2.549, 95% CI = 1.387-4.684, p = 2.58E-3) of K-Ras4A. CONCLUSIONS: Based on the above results, we report the possible use of abundance measures for K-Ras4A for predicting the survival of LUAD patients with KRAS mutations.
Assuntos
Adenocarcinoma de Pulmão/mortalidade , Neoplasias Pulmonares/mortalidade , Proteínas Proto-Oncogênicas p21(ras)/genética , Adenocarcinoma de Pulmão/genética , Adenocarcinoma de Pulmão/metabolismo , Adenocarcinoma de Pulmão/terapia , Idoso , Intervalo Livre de Doença , Feminino , Expressão Gênica , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/terapia , Masculino , Pessoa de Meia-Idade , Mutação , Prognóstico , Modelos de Riscos Proporcionais , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismoRESUMO
Long-term treatment with the potent immunosuppressive drug cyclosporine A (CsA) results in chronic nephrotoxicity. Its immunosuppressive properties are due to the inhibition of the calcium- and calmodulin-dependent phosphatase protein calcineurin A (CnA) which has three catalytic isoforms. Of those, the CnAα and ß isoforms are ubiquitously expressed, particularly in the kidney. Additionally, chronic nephrotoxicity has been associated with an imbalance of extracellular matrix (ECM) synthesis and degradation resulting in an accumulation of ECM molecules. This study evaluates whether the expressions of matrix metalloproteinases (MMP-2 and MMP-9) induced by CsA are calcineurin isoform specific. Wild-type (WT), CnAα knockout (CnAα-/-) and CnAß knockout (CnAß-/-) kidney fibroblast cell lines (an in vitro innovative tool that was previously created in our lab) were treated with CsA at 10â¯ng/ml for 48â¯h. ELISA analysis demonstrated that the CsA-induced secretion profile of MMP-9 was highest in CnAα-/- cells and lowest in CnAß-/- cells vs. WT cells. In contrast, CsA did not induce an increase in MMP-2 protein levels in WT, CnAα-/- nor CnAß-/- renal fibroblasts. These results indicate that MMP-9 secretion is CnA-isoform specific, i.e. the CnAß isoform contributes to the CsA-induced upregulation of MMP-9 while the CnAα does not. As such, understanding the role of calcineurin A isoforms in the regulation of the homeostasis of ECM degradation in the kidney after long-term CsA treatment needs to be further investigated.
Assuntos
Fibroblastos/metabolismo , Rim/citologia , Metaloproteinase 9 da Matriz/metabolismo , Animais , Calcineurina/efeitos dos fármacos , Calcineurina/metabolismo , Linhagem Celular , Ciclosporina/farmacologia , Expressão Gênica , Humanos , Rim/enzimologia , Metaloproteinases da Matriz/metabolismo , Isoformas de Proteínas/efeitos dos fármacosRESUMO
Gene regulatory networks orchestrate the assembly of functionally related cells within a cellular network. Subtle differences often exist among functionally related cells within such networks. How differences are created among cells with similar functions has been difficult to determine due to the complexity of both the gene and the cellular networks. In Caenorhabditis elegans, the DD and VD motor neurons compose a cross-inhibitory, GABAergic network that coordinates dorsal and ventral muscle contractions during locomotion. The Pitx2 homologue, UNC-30, acts as a terminal selector gene to create similarities and the Coup-TFII homologue, UNC-55, is necessary for creating differences between the two motor neuron classes. What is the organizing gene regulatory network responsible for initiating the expression of UNC-55 and thus creating differences between the DD and VD motor neurons? We show that the unc-55 promoter has modules that contain Meis/UNC-62 binding sites. These sites can be subdivided into regions that are capable of activating or repressing UNC-55 expression in different motor neurons. Interestingly, different isoforms of UNC-62 are responsible for the activation and the stabilization of unc-55 transcription. Furthermore, specific isoforms of UNC-62 are required for proper synaptic patterning of the VD motor neurons. Isoform specific regulation of differentiating neurons is a relatively unexplored area of research and presents a mechanism for creating differences among functionally related cells within a network.
Assuntos
Proteínas de Caenorhabditis elegans/fisiologia , Caenorhabditis elegans/genética , Neurônios GABAérgicos/citologia , Proteínas de Homeodomínio/fisiologia , Neurônios Motores/citologia , Receptores de Superfície Celular/fisiologia , Receptores Citoplasmáticos e Nucleares/fisiologia , Animais , Animais Geneticamente Modificados , Sistemas CRISPR-Cas , Caenorhabditis elegans/fisiologia , Proteínas de Caenorhabditis elegans/biossíntese , Regulação da Expressão Gênica no Desenvolvimento , Redes Reguladoras de Genes/genética , Genes Reporter , Neurônios Motores/classificação , Neurogênese/genética , Regiões Promotoras Genéticas/genética , Isoformas de Proteínas/fisiologia , RNA Guia de Cinetoplastídeos/genética , RNA de Helmintos/biossíntese , RNA de Helmintos/genética , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , Receptores de Superfície Celular/biossíntese , Receptores Citoplasmáticos e Nucleares/biossíntese , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Fatores de Transcrição , Transcrição Gênica/genéticaRESUMO
The temporal control mechanisms that precisely control animal development remain largely elusive. The timing of major developmental transitions in insects, including molting and metamorphosis, is coordinated by the steroid hormone 20-hydroxyecdysone (20E). 20E involves feedback loops to maintain pulses of ecdysteroid biosynthesis leading to its upsurge, whereas the underpinning molecular mechanisms are not well understood. Using the silkworm Bombyx mori as a model, we demonstrated that E75, the 20E primary response gene, mediates a regulatory loop between ecdysteroid biosynthesis and 20E signaling. E75 isoforms A and C directly bind to retinoic acid receptor-related response elements in Halloween gene promoter regions to induce gene expression thus promoting ecdysteroid biosynthesis and developmental transition, whereas isoform B antagonizes the transcriptional activity of isoform A/C through physical interaction. As the expression of E75 isoforms is differentially induced by 20E, the E75-mediated regulatory loop represents a fine autoregulation of steroidogenesis, which contributes to the precise control of developmental timing.
Assuntos
Bombyx/embriologia , Ecdisterona/metabolismo , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Genes de Insetos/fisiologia , Proteínas de Insetos/biossíntese , Metamorfose Biológica/fisiologia , Animais , Bombyx/genética , Ecdisterona/genética , Proteínas de Insetos/genética , Isoformas de ProteínasRESUMO
Akt/PKB plays a pivotal role in cell proliferation and survival. However, the isotype-specific roles of Akt in mitochondrial function have not been fully addressed. In this study, we explored the role of Akt in mitochondrial function after stable knockdown of the Akt isoforms in EJ human bladder cancer cells. We found that the mitochondrial mass was significantly increased in the Akt1- and Akt3-knockdown cells, and this increase was accompanied by an increase in TFAM and NRF1. Akt2 knockdown did not cause a similar effect. Interestingly, Akt3 knockdown also led to severe structural defects in the mitochondria, an increase in doxorubicin-induced senescence, and impairment of cell proliferation in galactose medium. Consistent with these observations, the mitochondrial oxygen consumption rate was significantly reduced in the Akt3-knockdown cells. An Akt3 deficiency-induced decrease in mitochondrial respiration was also observed in A549 lung cancer cells. Collectively, these results suggest that the Akt isoforms play distinct roles in mitochondrial function and that Akt3 is critical for proper mitochondrial respiration in human cancer cells.
Assuntos
Neoplasias Pulmonares/metabolismo , Mitocôndrias/metabolismo , Proteínas Proto-Oncogênicas c-akt/antagonistas & inibidores , Neoplasias da Bexiga Urinária/metabolismo , Células A549 , Linhagem Celular Tumoral , Técnicas de Silenciamento de Genes , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Microscopia Eletrônica de Transmissão , Mitocôndrias/patologia , Consumo de Oxigênio , Proteínas Proto-Oncogênicas c-akt/genética , Proteínas Proto-Oncogênicas c-akt/metabolismo , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/patologiaRESUMO
Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify â¼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
Assuntos
Proteômica , RNA Mensageiro/genética , Análise de Sequência de RNA , Células Cultivadas , Códon , Éxons , Humanos , Fases de Leitura Aberta , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Splicing de RNA , Espectrometria de Massas em TandemRESUMO
The AMP-activated protein kinase (AMPK) regulates cellular and whole-body energy balance in response to changes in adenylate charge and hormonal signals. Activation of AMPK in tissues such as skeletal muscle and liver reverses many of the metabolic defects associated with obesity and Type 2 diabetes. Here we report a bi-quinoline (JJO-1) that allosterically activates all AMPK αßγ isoforms in vitro except complexes containing the γ3 subunit. JJO-1 does not directly activate the autoinhibited α subunit kinase domain and differs among other known direct activators of AMPK in that allosteric activation occurs only at low ATP concentrations, and is not influenced by either mutation of the γ subunit adenylate-nucleotide binding sites or deletion of the ß subunit carbohydrate-binding module. Our findings indicate that AMPK has multiple modes of allosteric activation that may be exploited to design isoform-specific activators as potential therapeutics for metabolic diseases.
Assuntos
Proteínas Quinases Ativadas por AMP/metabolismo , Trifosfato de Adenosina/metabolismo , Quinolinas/farmacologia , Transdução de Sinais/fisiologia , Animais , Células COS , Chlorocebus aethiops , Ativação Enzimática/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacosRESUMO
Clonorchis sinensis or the Chinese liver fluke is one of the most prevalent parasites affecting a major population in the oriental countries. The parasite lacks lipid generating mechanisms but is exposed to fatty acid rich bile in the liver. A secretory phospholipase A2, an enzyme that breaks down complex lipids, is important for the growth of the parasite. The enzyme is also implicated in the pathogenesis leading up to the hepatic fibrosis and its complications including cancer. The five isoforms of this particular enzyme from the parasite therefore qualify as potential drug targets. In this study, a detailed structural and ligand binding analysis of the isoforms has been done by modeling. The overall three dimensional structures of the isoforms are well conserved with three helices and a ß-wing stabilized by four disulfide bonds. There are characteristic differences at the calcium binding loop, hydrophobic channel and the C-terminal domain that can potentially be exploited for drug binding. But the most significant feature pertains to the catalytic site where the isoforms exhibit three variations of either a histidine-aspartate-tyrosine or histidine-glutamate-tyrosine or histidine-aspartate-phenylalanine. Molecular docking studies show that isoform specific residues and their conformations in the substrate binding hydrophobic channel make unique interactions with certain inhibitor molecules resulting in a perfect tight fit. The proposed ligand molecules have a predicted affinity in micro-molar to nano-molar range. Interestingly, few of the ligand binding interaction patterns is in accordance to the phylogenetic studies to thereby establish the usefulness of evolutionary mechanisms in aiding ligand design. The molecular diversity of the parasitic PLA2 described in this study provides a platform for personalized medicine in the therapeutics of clonorchiasis.
RESUMO
The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms of PI3K, as they demonstrate better specificity and reduced toxicity in comparison to existing inhibitors. A ligand-based and target-based rational drug design strategy was employed to build a virtual library of 105 new compounds. Through this strategy, the four isoforms were compared regarding their activity pocket availability, amino acid sequences, and prone interactions. Additionally, a known active scaffold was used as a molecular base to design new derivatives. The virtual screening of the resultant library toward the four isoforms points to the obtention of 19 selective inhibitors for the PI3Kα and PI3Kγ targets. Three selective ligands, one for α-isoform and two for γ-isoform, present a ∆ (∆Gbinding) equal or greater than 1.5 Kcal/mol and were identified as the most promising candidates. A principal component analysis was used to establish correlations between the affinity data and some of the physicochemical and structural properties of the ligands. The binding modes and interactions established by the selective ligands in the active centre of the α and γ isoforms of PI3K were also investigated. After modelling studies, a synthetic approach to generate selective ligands was developed and applied in synthesising a set of derivatives that were obtained in good to excellent yield.
RESUMO
Following gene expansion during evolution, today's phylogenetic tree of the NR2F family of nuclear orphan receptors in mammals is represented by three different isoforms: NR2F1, NR2F2, and NR2F6. Structural analysis of the NR2F family members has revealed that NR2F1 and NR2F2 are closely related and grouped together apart from NR2F6, which is more divergent in its biochemical characteristics. In this review, we highlight current knowledge on the cellular functions of NR2F family members. NR2F family members have been reported to be causally involved in carcinogenesis. Mechanistically, NR2F proteins are localized in the nucleus, where they bind to target DNA enhancer sequences and have been implicated in the regulation of de novo gene transcription, though this is not sufficiently understood. Based on apparently divergent and non-uniform expression patterns of the NR2F isoforms in different tissues and cell types, non-redundant functions of the individual family members appear to exist. Notably, NR2F2 appears to be more closely related functionally to NR2F6 than NR2F1. Along these lines, NR2F2 and NR2F6 have been reported to be involved in cellular neoplasia. Furthermore, enhanced expression of NR2F isoforms has been established as prognostic biomarkers in various cancer entities. Therefore, it is tempting to speculate that NR2F isoforms represent innovative targets for therapeutic intervention in defined types of cancer. Thus, NR2F family nuclear receptors can be viewed as gatekeepers balancing cell type-specific regulation of proliferation and the suppression of terminal differentiation in health and disease.