101 results on '"MANGIULLI, M."'
Search Results
2. Uricemia and homocysteinemia: nontraditional risk factors in the early stages of chronic kidney disease - Preliminary data
- Author
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Lai, S., Mariotti, A., Coppola, B., Lai, C., Aceto, P., Dimko, M., Alessandro Galani, Innico, G., Frassetti, N., Mangiulli, M., and Cianci, R.
- Subjects
Brachial artery flow-mediated dilation ,Uricemia and homocysteinemia ,Chronic kidney disease ,Carotid intima-media thickness ,Endothelial dysfunction ,uricemia and homocysteinemia ,brachial artery flow-mediated dilation ,endothelial dysfunction ,carotid intima-media thickness ,chronic kidney disease - Published
- 2014
3. Reduction in Heart Rate Variability in Autosomal Dominant Polycystic Kidney Disease.
- Author
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Lai S, Mangiulli M, Perrotta AM, Di Lazzaro Giraldi G, Testorio M, Rosato E, Cianci R, and Gigante A
- Subjects
- Adult, Aged, Female, Humans, Male, Middle Aged, Heart Rate physiology, Polycystic Kidney, Autosomal Dominant physiopathology
- Abstract
Introduction: Cardiovascular disease is one of the main causes of morbidity and mortality in patients with autosomal dominant polycystic kidney disease (ADPKD). Autonomic dysfunction is associated with an increased risk for all cardiovascular events in the general population and can be evaluated with heart rate variability (HRV)., Objective: To evaluate HRV in ADPKD patients with mild hypertension versus hypertensive patients with organ damage and healthy controls (HC)., Materials and Methods: We have enrolled 65 patients: 21 ADPKD patients (10 males), 20 patients with hypertension (14 males), and 24 HC (10 males). Biochemical analysis, clinical evaluation, anthropometric data, intima-media thickness, 24-h ECG Holter recording, and echocardiography were investigated at the time of enrollment., Results: No significant differences in HRV parameters were found between ADPKD with mild hypertension and hypertensive patients with organ damage. The median of HRV variables in time domain as SDNN (global autonomic activity) was significantly lower in ADPKD and hypertensive patients than HC (p < 0.05). In the frequency domain analysis, low frequency (LF), which mainly reflects the sympathetic component, showed higher values in ADPKD and hypertensive patients than HC during the night (p < 0.01). During the night, the sympathovagal balance, LF/high frequency (HF), showed higher values in ADPKD and hypertensive patients than HC (p < 0.0001). Conversely, LF day was lower in ADPKD and hypertensive patients than HC (p < 0.01). HF, which mainly reflects the parasympathetic component, was lower in ADPKD and hypertensive patients during the night than HC (p < 0.0001)., Conclusions: HRV reduction is present in ADPKD patients with mild hypertension in the absence of organ damage. The evaluation of sympathovagal balance can provide novel information on the cardiovascular risk in ADPKD patients in addition to classical risk factors., (© 2019 The Author(s) Published by S. Karger AG, Basel.)
- Published
- 2019
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4. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
- Author
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Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, RIZZI, RAFFAELLA, Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, and RIZZI, RAFFAELLA
- Abstract
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256939 protein variants from 17191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
- Published
- 2011
5. Chronic kidney disease and urological disorders: systematic use of uroflowmetry in nephropathic patients.
- Author
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Lai S, Pastore S, Piloni L, Mangiulli M, Esposito Y, Pierella F, Galani A, Pintus G, Mastroluca D, Shahabadi H, Ciccariello M, Salciccia S, and Von Heland M
- Abstract
Background: Chronic kidney disease (CKD) is a highly prevalent condition. Urologic disorders are known causes of CKD, but often remain undiagnosed and underestimated also for their insidious onset and slow progression. We aimed to evaluate the prevalence of urological unrecognized diseases in CKD patients by uroflowmetry., Methods: We enrolled consecutive stable CKD outpatients. The patients carried out two questionnaires, the International Prostate Symptom Score and Incontinence Questionnaire-Short Form, and they also underwent uroflowmetry, evaluating max flow rate ( Q
max ), voiding time and voided volume values., Results: A total of 83 patients (43 males, mean age of 59.8 ± 13.3 years) were enrolled. Our study showed 28 males and 10 females with a significant reduction of Qmax (P < 0.001) while 21 females reported a significant increase of Qmax (P < 0.001) with a prevalence of 49.5% of functional urological disease. Moreover, we showed a significant association between Qmax and creatinine (P = 0.013), estimated glomerular filtration rate (P = 0.029) and voiding volume (P = 0.05). We have not shown significant associations with age (P = 0.215), body mass index (P = 0.793), systolic blood pressure (P = 0.642) or diastolic blood pressure (P = 0.305). Moreover, Pearson's chi-squared test showed a significant association between Qmax altered with CKD (χ2 = 1.885, P = 0.170) and recurrent infection (χ2 = 8.886, P = 0.012), while we have not shown an association with proteinuria (χ2 = 0.484, P = 0.785), diabetes (χ2 = 0.334, P = 0.563) or hypertension (χ2 = 1.885, P = 0.170)., Conclusions: We showed an elevated prevalence of urological diseases in nephropathic patients; therefore, we suggest to include uroflowmetry in CKD patient assessment, considering the non-invasiveness, repeatability and low cost of examination. Uroflowmetry could be used to identify previously unrecognized urological diseases, which may prevent the onset of CKD or progression to end-stage renal disease and reduce the costs of management.- Published
- 2018
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6. ASPicDB: A database resource for alternative splicing analysis
- Author
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Castrignanò, T, D'Antonio, M, Anselmo, A, Carrabino, D, D'Onorio De Meo, A, D'Erchia, A, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Riva, A, Rizzi, R, Bonizzoni, P, Pesole, G, D'Erchia, AM, RIZZI, RAFFAELLA, Pesole, G., BONIZZONI, PAOLA, Castrignanò, T, D'Antonio, M, Anselmo, A, Carrabino, D, D'Onorio De Meo, A, D'Erchia, A, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Riva, A, Rizzi, R, Bonizzoni, P, Pesole, G, D'Erchia, AM, RIZZI, RAFFAELLA, Pesole, G., and BONIZZONI, PAOLA
- Abstract
Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they provide that prevent the full exploitation of the available data. Furthermore, current resources provide limited query and download facilities. Results: ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. Splice-site detection and full-length transcript modeling have been carried out by a genome-wide application of the ASPic algorithm, based on the multiple alignments of gene-related transcripts (typically a Unigene cluster) to the genomic sequence, a strategy that greatly improves prediction accuracy compared to methods based on independent and progressive alignments. Enhanced query and download facilities for annotations and sequences allow users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB, which is regularly updated on a monthly basis, also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST sequences and their library source annotation. © The Author 2008. Published by Oxford University Press. All rights reserved.
- Published
- 2008
7. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
- Author
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Martelli, P. L., primary, D'Antonio, M., additional, Bonizzoni, P., additional, Castrignano, T., additional, D'Erchia, A. M., additional, D'Onorio De Meo, P., additional, Fariselli, P., additional, Finelli, M., additional, Licciulli, F., additional, Mangiulli, M., additional, Mignone, F., additional, Pavesi, G., additional, Picardi, E., additional, Rizzi, R., additional, Rossi, I., additional, Valletti, A., additional, Zauli, A., additional, Zambelli, F., additional, Casadio, R., additional, and Pesole, G., additional
- Published
- 2010
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8. A platform independent RNA-Seq protocol for the detection of transcriptome complexity.
- Author
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Calabrese C, Mangiulli M, Manzari C, Paluscio AM, Caratozzolo MF, Marzano F, Kurelac I, D'Erchia AM, D'Elia D, Licciulli F, Liuni S, Picardi E, Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, and Tullo A
- Subjects
- Animals, Cell Line, Tumor, Chromosome Mapping, Expressed Sequence Tags, Gene Expression Regulation, Heterografts, Humans, Mice, Molecular Sequence Annotation, Gene Expression Profiling methods, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA methods, Transcriptome
- Abstract
Background: Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein coding genes and their splice variants. Indeed, most transcripts are the result of antisense, overlapping and non-coding RNA expression. In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the choice of the strategy for cDNA library construction. The protocols developed so far provide the utilization of the entire library for a single sequencing run with a specific platform., Results: We set up a unique protocol to generate and amplify a strand-specific cDNA library representative of all RNA species that may be implemented with all major platforms currently available on the market (Roche 454, Illumina, ABI/SOLiD). Our method is reproducible, fast, easy-to-perform and even allows to start from low input total RNA. Furthermore, we provide a suitable bioinformatics tool for the analysis of the sequences produced following this protocol., Conclusion: We tested the efficiency of our strategy, showing that our method is platform-independent, thus allowing the simultaneous analysis of the same sample with different NGS technologies, and providing an accurate quantitative and qualitative portrait of complex whole transcriptomes.
- Published
- 2013
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9. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
- Author
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Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, and Pesole G
- Subjects
- Exons, Genetic Variation, Humans, Protein Isoforms chemistry, Protein Isoforms genetics, RNA, Messenger chemistry, Sequence Analysis, Protein, User-Computer Interface, Alternative Splicing, Databases, Genetic, Proteins chemistry, Proteins genetics
- Abstract
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
- Published
- 2011
- Full Text
- View/download PDF
10. Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation.
- Author
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Valletti A, Anselmo A, Mangiulli M, Boria I, Mignone F, Merla G, D'Angelo V, Tullo A, Sbisà E, D'Erchia AM, and Pesole G
- Subjects
- Alternative Splicing genetics, Genome-Wide Association Study, Humans, Computational Biology methods, Expressed Sequence Tags, Genome, Human genetics, Neoplasms genetics
- Abstract
Background: Many evidences report that alternative splicing, the mechanism which produces mRNAs and proteins with different structures and functions from the same gene, is altered in cancer cells. Thus, the identification and characterization of cancer-specific splice variants may give large impulse to the discovery of novel diagnostic and prognostic tumour biomarkers, as well as of new targets for more selective and effective therapies., Results: We present here a genome-wide analysis of the alternative splicing pattern of human genes through a computational analysis of normal and cancer-specific ESTs from seventeen anatomical groups, using data available in AspicDB, a database resource for the analysis of alternative splicing in human. By using a statistical methodology, normal and cancer-specific genes, splice sites and cassette exons were predicted in silico. The condition association of some of the novel normal/tumoral cassette exons was experimentally verified by RT-qPCR assays in the same anatomical system where they were predicted. Remarkably, the presence in vivo of the predicted alternative transcripts, specific for the nervous system, was confirmed in patients affected by glioblastoma., Conclusion: This study presents a novel computational methodology for the identification of tumor-associated transcript variants to be used as cancer molecular biomarkers, provides its experimental validation, and reports specific biomarkers for glioblastoma.
- Published
- 2010
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11. Identification and functional characterization of two new transcriptional variants of the human p63 gene.
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Mangiulli M, Valletti A, Caratozzolo MF, Tullo A, Sbisà E, Pesole G, and D'Erchia AM
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- Algorithms, Alternative Splicing, Amino Acid Sequence, Cell Differentiation, Cell Line, Cell Proliferation, Cells, Cultured, Humans, Keratinocytes cytology, Keratinocytes metabolism, Molecular Sequence Data, Nuclear Proteins analysis, Protein Isoforms genetics, Protein Isoforms metabolism, Trans-Activators genetics, Transcription Factors, Transcription, Genetic, Transcriptional Activation, Tumor Suppressor Proteins genetics, Trans-Activators metabolism, Tumor Suppressor Proteins metabolism
- Abstract
p63 belongs to a family of transcription factors, which, while demonstrating striking conservation of functional domains, regulate distinct biological functions. Its principal role is in the regulation of epithelial commitment, differentiation and maintenance programs, during embryogenesis and in adult tissues. The p63 gene has a complex transcriptional pattern, producing two subclasses of N-terminal isoforms (TA and DeltaN) which are alternatively spliced at the C-terminus. Here, we report the identification of two new C-terminus p63 variants, we named p63 delta and epsilon, that increase from 6 to 10 the number of the p63 isoforms. Expression analysis of all p63 variants demonstrates a tissue/cell-type-specific nature of p63 alternative transcript expression, probably related to their different cellular functions. We demonstrate that the new p63 variants as DeltaN isoforms are active as transcription factors as they have nuclear localization and can modulate the expression of p63 target genes. Moreover, we report that, like DeltaNp63alpha, DeltaNp63delta and epsilon sustain cellular proliferation and that their expression decreases during keratinocyte differentiation, suggesting their involvement in this process. Taken together, our results demonstrate the existence of novel p63 proteins whose expression should be considered in future studies on the roles of p63 in the regulation of cellular functions.
- Published
- 2009
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12. Uricemia and homocysteinemia: nontraditional risk factors in the early stages of chronic kidney disease--preliminary data
- Author
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Lai S, Mariotti A, Coppola B, Lai C, Aceto P, Dimko M, Alessandro Galani, Innico G, Frassetti N, Mangiulli M, and Cianci R
- Subjects
Adult ,Male ,Brachial Artery ,Hyperhomocysteinemia ,Hyperuricemia ,Middle Aged ,Atherosclerosis ,Carotid Intima-Media Thickness ,Vasodilation ,Regional Blood Flow ,Risk Factors ,Case-Control Studies ,Humans ,Female ,Renal Insufficiency, Chronic ,Aged - Abstract
Patients with chronic kidney disease (CKD) show a risk of cardiovascular death, which is 10-100 times higher than that in the general population. This increase is not completely explained by the traditional cardiovascular risk factors. Hyperuricemia and hyperhomocysteinemia are highly prevalent in CKD. Patients suffering from these complications present accelerated atherosclerosis, determined mainly from the endothelial dysfunction that carries out a central role in the pathogenesis of cardiovascular diseases.The hypothesis was that brachial artery flow mediated dilation (FMD) and carotid intima-media thickness (cIMT) evaluation can be considered as early and systemic markers of atherosclerosis and that nontraditional risk factors, such as hyperhomocysteinemia and hyperuricemia, are associated with early endothelial dysfunction and vascular damage in patients suffering from first- and second-stage CKD.The study comprised 50 patients, 10 for each CKD stage, and 15 age- and sex-matched healthy controls. We compared the traditional and nontraditional factors for cardiovascular diseases with alterations of vascular reactivity, such as cIMT, and brachial artery FMD, in patients affected by CKD with those in the control group.In our study, hyperuricemia was significantly and independently associated with brachial artery FMD reduction (p = 0.007), while hyperhomocysteinemia was significantly and independently associated with carotid intima-media thickening (p = 0.021) in patients at Stage I and II KDOQI (Kidney Disease Outcomes Quality Initiative).In our study, we found a progressive increase in the inflammatory indices and endothelial dysfunction at the early stages of CKD. Hyperuricemia and hyperhomocysteinemia were associated with IMT and FMD at Stage I-III KDOQI, and can be used as markers of subclinical atherosclerosis, especially in nephropathic patients with high cardiovascular risk.
13. An unsuspected histopathological finding -- concomitant IgA nephropathy in a patient with ANCA-associated vasculitis: a case report and literature review.
- Author
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Tota, Maciej, Donizy, Piotr, Byrska, Martyna, Krajewska, Magdalena, and Kusztal, Mariusz
- Subjects
IGA glomerulonephritis ,LITERATURE reviews ,HISTOPATHOLOGY ,VASCULITIS ,RENAL biopsy - Abstract
Although associations of IgA nephropathy (IgAN) and ANCA-associated vasculitis (AAV) have been described, this coexistence scarcely occurs and requires multidisciplinary management. Herein, we discuss a course of treatment introduced in a patient with two exacerbations. Furthermore, alterations in histopathological images between two kidney biopsies are presented. The applicability of traditional inflammatory markers, e.g., CRP, in monitoring disease severity in AAV and IgAN is limited. Based on our patient and current literature, we suggest ANCA testing in patients with rapidly progressing IgAN for therapeutic and prognostic purposes. As regards the therapy of IgAN associated with AAV, aggressive immunosuppressive regimens with methylprednisolone and cyclophosphamide are recommended. Alternatively, methylprednisolone with rituximab, plasma exchange, mycophenolate mofetil, and intravenous immunoglobulin (IVIG) could also be considered. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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14. Whole-Exome and Transcriptome Sequencing Expands the Genotype of Majewski Osteodysplastic Primordial Dwarfism Type II.
- Author
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Marzano, Flaviana, Chiara, Matteo, Consiglio, Arianna, D'Amato, Gabriele, Gentile, Mattia, Mirabelli, Valentina, Piane, Maria, Savio, Camilla, Fabiani, Marco, D'Elia, Domenica, Sbisà, Elisabetta, Scarano, Gioacchino, Lonardo, Fortunato, Tullo, Apollonia, Pesole, Graziano, and Faienza, Maria Felicia
- Subjects
NUCLEOTIDE sequencing ,GENE expression ,DWARFISM ,GROWTH disorders ,GENETIC variation ,RECESSIVE genes - Abstract
Microcephalic Osteodysplastic Primordial Dwarfism type II (MOPDII) represents the most common form of primordial dwarfism. MOPD clinical features include severe prenatal and postnatal growth retardation, postnatal severe microcephaly, hypotonia, and an increased risk for cerebrovascular disease and insulin resistance. Autosomal recessive biallelic loss-of-function genomic variants in the centrosomal pericentrin (PCNT) gene on chromosome 21q22 cause MOPDII. Over the past decade, exome sequencing (ES) and massive RNA sequencing have been effectively employed for both the discovery of novel disease genes and to expand the genotypes of well-known diseases. In this paper we report the results both the RNA sequencing and ES of three patients affected by MOPDII with the aim of exploring whether differentially expressed genes and previously uncharacterized gene variants, in addition to PCNT pathogenic variants, could be associated with the complex phenotype of this disease. We discovered a downregulation of key factors involved in growth, such as IGF1R, IGF2R, and RAF1, in all three investigated patients. Moreover, ES identified a shortlist of genes associated with deleterious, rare variants in MOPDII patients. Our results suggest that Next Generation Sequencing (NGS) technologies can be successfully applied for the molecular characterization of the complex genotypic background of MOPDII. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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15. The Effect of Caffeine on Heart Rate Variability in Newborns: A Pilot Study.
- Author
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Lenasi, Helena, Rihar, Eva, Filipič, Jerneja, Klemenc, Matjaž, and Fister, Petja
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HEART beat ,AUTONOMIC nervous system ,CAFFEINE ,NEWBORN infants ,DRUG dosage ,FOURIER transforms - Abstract
Neonatal apnoea can be treated with caffeine, which affects the central nervous and cardiovascular systems. Heart rate variability (HRV) reflects the activity of the autonomic nervous system (ANS) and might be used as a measure of ANS maturation in newborns. We aimed to establish the effect of caffeine on HRV in newborns and investigated the potential correlation between HRV and postmenstrual age (PMA). In 25 haemodynamically stable newborns hospitalized due to apnoea and treated with caffeine (2.5 mg/kg), we assessed breathing frequency, arterial oxygen saturation, body temperature, and the heart rate while they were sleeping. We assessed HRV by spectral analysis using fast Fourier transformation. The same protocol was reapplied 100 h after caffeine withdrawal to assess the control parameters. Caffeine increased breathing frequency (p = 0.023) but did not affect any other parameter assessed including HRV. We established a positive correlation between postmenstrual age and HRV during treatment with caffeine as well as after caffeine had been withdrawn (total power: p = 0.044; low-frequency band: p = 0.039). Apparently, the maintenance dose of caffeine is too low to affect the heart rate and HRV. A positive correlation between PMA and HRV might reflect maturation of the ANS, irrespective of caffeine treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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16. Assessment of Cardiovascular Disease in Autosomal Dominant Polycystic Kidney Disease.
- Author
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Gigante, Antonietta, Perrotta, Adolfo Marco, Tinti, Francesca, Assanto, Eleonora, Muscaritoli, Maurizio, Lai, Silvia, and Cianci, Rosario
- Subjects
POLYCYSTIC kidney disease ,CARDIOVASCULAR diseases ,KIDNEY failure ,GENETIC disorders - Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited kidney disease which leads to progressive kidney failure. About 5–10% of patients requiring renal replacement therapy are affected by ADPKD. Cardiovascular diseases are the main causes of morbidity and mortality in these patients with ADPKD; arterial hypertension (AH) is the first symptom with a very early onset. Anyway, some other cardiovascular abnormalities have been reported in ADPKD regardless of the presence of AH. With this background, we conducted a systematic review, collecting all randomized controlled trials (RCTs) and quasi-RCTs found on the main databases; we evaluated the evidence about different imaging techniques to grade the cardiovascular risk in a very early stage of disease. This review aims to describe all cardiovascular assessments in ADPKD patients to improve clinicians' ability to discover cardiovascular involvement early, allowing appropriate therapies promptly. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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17. The dual role of p63 in cancer.
- Author
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Yongfeng Xu, Xiaojuan Yang, Qunli Xiong, Junhong Han, and Qing Zhu
- Subjects
DNA repair ,CANCER stem cells ,CELL physiology ,CANCER invasiveness ,DNA damage - Abstract
The p53 family is made up of three transcription factors: p53, p63, and p73. These proteins are well-known regulators of cell function and play a crucial role in controlling various processes related to cancer progression, including cell division, proliferation, genomic stability, cell cycle arrest, senescence, and apoptosis. In response to extra- or intracellular stress or oncogenic stimulation, all members of the p53 family are mutated in structure or altered in expression levels to affect the signaling network, coordinating many other pivotal cellular processes. P63 exists as two main isoforms (TAp63 and DNp63) that have been contrastingly discovered; the TA and DN isoforms exhibit distinguished properties by promoting or inhibiting cancer progression. As such, p63 isoforms comprise a fully mysterious and challenging regulatory pathway. Recent studies have revealed the intricate role of p63 in regulating the DNA damage response (DDR) and its impact on diverse cellular processes. In this review, we will highlight the significance of how p63 isoforms respond to DNA damage and cancer stem cells, as well as the dual role of TAp63 and DNp63 in cancer. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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18. Contrast-Induced Acute Kidney Injury and Endothelial Dysfunction: The Role of Vascular and Biochemical Parameters.
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Perrotta, Adolfo Marco, Gigante, Antonietta, Rotondi, Silverio, Menè, Paolo, Notturni, Adriano, Schiavetto, Stefano, Tanzilli, Gaetano, Pellicano, Chiara, Guaglianone, Giuseppe, Tinti, Francesca, Palange, Paolo, Mazzaferro, Sandro, Cianci, Rosario, and Lai, Silvia
- Subjects
ACUTE kidney failure ,ENDOTHELIUM diseases ,CAROTID intima-media thickness ,TYPE 2 diabetes ,CORONARY angiography - Abstract
Introduction: Contrast-induced acute kidney injury (CIAKI) is one of the main causes of acute renal failure in hospitalized patients, following the administration of iodinated contrast medium used for CT scans and angiographic procedures. CIAKI determines a high cardiovascular risk and appears to be one of the most feared complications of coronary angiography, causing a notable worsening of the prognosis with high morbidity and mortality. Aim: To evaluate a possible association between the renal resistive index (RRI) and the development of CIAKI, as well as an association with the main subclinical markers of atherosclerosis and the main cardiovascular risk factors. Materials and Methods: We enrolled 101 patients with an indication for coronary angiography. Patients underwent an assessment of renal function (serum nitrogen and basal creatinine, 48 and 72 h after administration of contrast medium), inflammation (C reactive protein (CRP), serum calcium and phosphorus, intact parathormone (iPTH), 25-hydroxyvitaminD (25-OH-VitD), serum uric acid (SUA), total cholesterol, serum triglycerides, serum glucose and insulin). All patients also carried out an evaluation of RRI, intima-media thickness (IMT), interventricular septum (IVS) and the ankle-brachial index (ABI). Results: 101 patients (68 male), with a mean age of 73.0 ± 15.0 years, were enrolled for the study; 35 are affected by type 2 diabetes mellitus. A total of 19 cases of CIAKI were reported (19%), while among diabetic patients we reported an incidence of 23% (8 patients). In our study, patients with CIAKI had significantly higher RRI (p < 0.001) and IMT (p < 0.001) with respect to the patients who did not develop CIAKI. Furthermore, patients with CIAKI had significantly higher CRP (p < 0.001) and SUA (p < 0.006). Conclusions: We showed a significant difference in RRI, IMT, SUA and CRP values between the population developing CIAKI and patients without CIAKI. This data appears relevant considering that RRI and IMT are low-cost, non-invasive and easily reproducible markers of endothelial dysfunction and atherosclerosis. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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19. Circular RNA ARHGAP5 inhibits cisplatin resistance in cervical squamous cell carcinoma by interacting with AUF1.
- Author
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Deng, Sisi, Qian, Lili, Liu, Luwen, Liu, Hanyuan, Xu, Zhihao, Liu, Yujie, Wang, Yingying, Chen, Liang, and Zhou, Ying
- Abstract
Cervical squamous cell carcinoma (CSCC) is one of the leading causes of cancer death in women worldwide. Patients with advanced cervical carcinoma always have a poor prognosis once resistant to cisplatin due to the lack of effective treatment. It is urgent to investigate the molecular mechanisms of cisplatin resistance. Circular RNAs (circRNAs) are known to exert their regulatory functions in a series of malignancies. However, their effects on CSCC remain to be elucidated. Here, we found that cytoplasmic circARHGAP5, derived from second and third exons of the ARHGAP5 gene, was downregulated in cisplatin‐resistant tissues compared with normal cervix tissues and untreated cervical cancer tissues. In addition, experiments from overexpression/knockdown cell lines revealed that circARHGAP5 could inhibit cisplatin‐mediated cell apoptosis in CSCC cells both in vitro and in vivo. Mechanistically, circARHGAP5 interacted with AU‐rich element RNA‐binding protein (AUF1) directly. Overexpression of AUF1 could also inhibit cell apoptosis mediated by cisplatin. Furthermore, we detected the potential targets of AUF1 related to the apoptotic pathway and found that bcl‐2‐like protein 11 (BIM) was not only negatively regulated by AUF1 but positively regulated by circARHGAP5, which indicated that BIM mRNA might be degraded by AUF1 and thereby inhibited tumor cell apoptosis. Collectively, our data indicated that circARHGAP5 directly bound to AUF1 and prevented AUF1 from interacting with BIM mRNA, thereby playing a pivotal role in cisplatin resistance in CSCC. Our study provides insights into overcoming cancer resistance to cisplatin treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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20. TP63 Functions as a Tumor Suppressor Regulated by GAS5/miR-221-3p Signaling Axis in Human Non-Small Cell Lung Cancer Cells.
- Author
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Shen, Qiming, Wang, Haoyou, and Zhang, Lin
- Subjects
NON-small-cell lung carcinoma ,CANCER cells ,GIANT cell tumors ,TUMOR proteins ,INHIBITION of cellular proliferation ,GROWTH arrest-specific 5 - Abstract
Background: Tumor protein p63 (TP63) has been proven to play a role as a tumor suppressor in some human cancers, including non-small cell lung cancer (NSCLC). This study aimed to investigate the mechanism of TP63 and analyze the underlying pathway dysregulating TP63 in NSCLC. Methods: RT-qPCR and Western blotting assays were used to determine gene expression in NSCLC cells. The luciferase reporter assay was performed to explore the transcriptional regulation. Flow cytometry was used to analyze the cell cycle and cell apoptosis. Transwell and CCK-8 assays were performed to test cell invasion and cell proliferation, respectively. Results: GAS5 interacted with miR-221-3p, and its expression was significantly reduced in NSCLC. GAS5, as a molecular sponge, upregulated the mRNA and protein levels of TP63 by inhibiting miR-221-3p in NSCLC cells. The upregulation of GAS5 inhibited cell proliferation, apoptosis, and invasion, which was partially reversed by the knockdown of TP63. Interestingly, we found that GAS5-induced TP63 upregulation promoted tumor chemotherapeutic sensitivity to cisplatin therapy in vivo and in vitro. Conclusion: Our results revealed the mechanism by which GAS5 interacts with miR-221-3p to regulate TP63, and targeting GAS5/miR-221-3p/TP63 may be a potential therapeutic strategy for NSCLC cells. Graphical [ABSTRACT FROM AUTHOR]
- Published
- 2023
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21. ΔNp63α-mediated epigenetic regulation in keratinocyte senescence.
- Author
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Linghan Kuang and Chenghua Li
- Subjects
KERATINOCYTE differentiation ,KERATINOCYTES ,EPIGENETICS ,SKIN aging ,CELLULAR aging ,CELL cycle - Abstract
Keratinocyte senescence contributes to skin ageing and epidermal dysfunction. According to the existing knowledge, the transcription factor Np63a plays pivotal roles in differentiation and proliferation of keratinocytes. It is traditionally accepted that p63a exerts its functions via binding to promoter regions to activate or repress gene transcription. However, accumulating evidence demonstrates that Np63a can bind to elements away from promoter regions of its target genes, mediating epigenetic regulation. On the other hand, several epigenetic alterations, including DNA methylation, histone modification and variation, chromatin remodelling, as well as enhancer-promoter looping, are found to be related to cell senescence. To systematically elucidate how Np63a affects keratinocyte senescence via epigenetic regulation, we comprehensively compiled the literatures on the roles of Np63a in keratinocyte senescence, epigenetics in cellular senescence, and the relation between Np63a-mediated epigenetic regulation and keratinocyte senescence. Based on the published data, we conclude that Np63a mediates epigenetic regulation via multiple mechanisms: recruiting epigenetic enzymes to modify DNA or histones, coordinating chromatin remodelling complexes (CRCs) or regulating their expression, and mediating enhancer-promoter looping. Consequently, the expression of genes related to cell cycle is modulated, and proliferation of keratinocytes and renewal of stem cells are maintained, by Np63a. During skin inflammaging, the decline of Np63a may lead to epigenetic dysregulation, resultantly deteriorating keratinocyte senescence. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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22. Dietary Aspects and Drug-Related Side Effects in Autosomal Dominant Polycystic Kidney Disease Progression.
- Author
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Quiroga, Borja and Torra, Roser
- Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most commonly inherited kidney disease. In the absence of targeted therapies, it invariably progresses to advanced chronic kidney disease. To date, the only approved treatment is tolvaptan, a vasopressin V2 receptor antagonist that has been demonstrated to reduce cyst growth and attenuate the decline in kidney function. However, it has various side effects, the most frequent of which is aquaresis, leading to a significant discontinuation rate. The strategies proposed to combat aquaresis include the use of thiazides or metformin and a reduction in the dietary osmotic load. Beyond the prescription of tolvaptan, which is limited to those with a rapid and progressive decline in kidney function, dietary interventions have been suggested to protect against disease progression. Moderate sodium restriction, moderate protein intake (up to 0.8 g/kg/day), avoidance of being overweight, and increased water consumption are recommended in ADPKD guidelines, though all with low-grade evidence. The aim of the present review is to critically summarize the evidence on the effect of dietary modification on ADPKD and to offer some strategies to mitigate the adverse aquaretic effects of tolvaptan. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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23. Beyond Loss of Kidney Function: Patient Care in Autosomal Dominant Polycystic Kidney Disease.
- Author
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Hogan MC, Simmons K, Ullman L Jr, Gondal M, and Dahl NK
- Subjects
- Humans, Kidney, Patient Care, Polycystic Kidney, Autosomal Dominant diagnosis, Polycystic Kidney, Autosomal Dominant therapy, Kidney Transplantation, Kidney Calculi
- Abstract
Patients with autosomal dominant polycystic kidney disease benefit from specialized care over their lifetimes, starting with diagnosis of the condition with ongoing discussion of both the renal course and extra-renal issues. Both renal and extra-renal issues may continue to cause major morbidity even after successful kidney transplant or initiation of RRT, and extra-renal disease aspects should always be considered as part of routine management. In this review, we will focus on updates in pain/depression screening, cardiac manifestations, liver and pancreatic cysts, kidney stone management, and genetic counseling. In some instances, we have shared our current clinical practice rather than an evidence-based guideline. We anticipate more standardization of care after the release of the Kidney Disease Improving Global Outcomes guidelines for management in autosomal dominant polycystic kidney disease later this year., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Society of Nephrology.)
- Published
- 2023
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24. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
- Author
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Pier L. Martelli1, Mattia D'Antonio2, Paola Bonizzoni3, Tiziana Castrignano` 2, Anna M. D'Erchia4, Paolo D'Onorio De Meo2, Piero Fariselli1, Michele Finelli5, Flavio Licciulli6, Marina Mangiulli4, Flavio Mignone7, Giulio Pavesi8, Ernesto Picardi3, Raffaella Rizzi3, Ivan Rossi5, Alessio Valletti4, Andrea Zauli5, Federico Zambelli8, Rita Casadio1, Graziano Pesole4, 9, Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli P.L., D'Antonio M., Bonizzoni P., Castrignanò T., D'Erchia A.M., D'Onorio De Meo P., Fariselli P., Finelli M., Licciulli F., Mangiulli M., Mignone F., Pavesi G., Picardi E., Rizzi R., Rossi I., Valletti A., Zauli A., Zambelli F., Casadio R., and Pesole G.
- Subjects
Signal peptide ,ANNOTATION PIPELINE ,PROTEIN ANNOTATION ,Biology ,transcriptomics ,Exon ,User-Computer Interface ,Protein Annotation ,Sequence Analysis, Protein ,Databases, Genetic ,Genetics ,Humans ,Protein Isoforms ,RNA, Messenger ,Gene ,database ,transcript ,Alternative splicing ,Genetic Variation ,Proteins ,INF/01 - INFORMATICA ,Articles ,Exons ,bioinformatics ,BIO/11 - BIOLOGIA MOLECOLARE ,Transmembrane protein ,ALTERNATIVE SPLICING ,Proteome ,RNA splicing ,protein - Abstract
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
- Published
- 2011
25. ΔNp63α promotes Epstein-Barr virus latency in undifferentiated epithelial cells.
- Author
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Van Sciver, Nicholas, Ohashi, Makoto, Nawandar, Dhananjay M., Pauly, Nicholas P., Lee, Denis, Makielski, Kathleen R., Bristol, Jillian A., Tsao, Sai Wah, Lambert, Paul F., Johannsen, Eric C., and Kenney, Shannon C.
- Subjects
EPSTEIN-Barr virus ,DIFFUSE large B-cell lymphomas ,EPITHELIAL cells ,LATENT infection ,EPITHELIAL cell tumors ,B cell lymphoma ,MONONUCLEOSIS ,VIRUS diseases - Abstract
Epstein-Barr virus (EBV) is a human herpesvirus that causes infectious mononucleosis and contributes to both B-cell and epithelial-cell malignancies. EBV-infected epithelial cell tumors, including nasopharyngeal carcinoma (NPC), are largely composed of latently infected cells, but the mechanism(s) maintaining viral latency are poorly understood. Expression of the EBV BZLF1 (Z) and BRLF1 (R) encoded immediate-early (IE) proteins induces lytic infection, and these IE proteins activate each other's promoters. ΔNp63α (a p53 family member) is required for proliferation and survival of basal epithelial cells and is over-expressed in NPC tumors. Here we show that ΔNp63α promotes EBV latency by inhibiting activation of the BZLF1 IE promoter (Zp). Furthermore, we find that another p63 gene splice variant, TAp63α, which is expressed in some Burkitt and diffuse large B cell lymphomas, also represses EBV lytic reactivation. We demonstrate that ΔNp63α inhibits the Zp promoter indirectly by preventing the ability of other transcription factors, including the viral IE R protein and the cellular KLF4 protein, to activate Zp. Mechanistically, we show that ΔNp63α promotes viral latency in undifferentiated epithelial cells both by enhancing expression of a known Zp repressor protein, c-myc, and by decreasing cellular p38 kinase activity. Furthermore, we find that the ability of cis-platinum chemotherapy to degrade ΔNp63α contributes to the lytic-inducing effect of this agent in EBV-infected epithelial cells. Together these findings demonstrate that the loss of ΔNp63α expression, in conjunction with enhanced expression of differentiation-dependent transcription factors such as BLIMP1 and KLF4, induces lytic EBV reactivation during normal epithelial cell differentiation. Conversely, expression of ΔNp63α in undifferentiated nasopharyngeal carcinoma cells and TAp63α in Burkitt lymphoma promotes EBV latency in these malignancies. Author summary: Epstein-Barr virus (EBV) is an important cause of both epithelial cell and B cell human cancers. EBV-infected tumors have predominantly latent viral infection, allowing them to escape the cell killing that occurs during lytic viral infection. EBV is highly lytic in normal differentiated oral epithelial cells. Thus, an important question is how the virus maintains the latent form of viral infection in EBV-associated epithelial cell tumors such as undifferentiated nasopharyngeal carcinoma (NPC). This study demonstrates that the cellular transcription factor ΔNp63ɑ, which is specifically expressed in undifferentiated basal epithelial cells and is over-expressed in NPC tumors, maintains EBV latency by inhibiting the activity of the viral immediate-early (IE) promoter (Zp) that drives expression of the BZLF1 IE protein. A related splice variant, TAp63α, found in some EBV+ lymphomas, has a similar inhibitory effect. Our findings reveal that ΔNp63ɑ and TAp63α contribute to EBV latency in both epithelial and B cell tumors. Furthermore, since differentiation results in loss of ΔNp63ɑ expression, our results help to explain why lytic EBV reactivation is promoted by epithelial cell differentiation. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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26. Insights Into the Function and Clinical Application of HDAC5 in Cancer Management.
- Author
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Yang, Jun, Gong, Chaoju, Ke, Qinjian, Fang, Zejun, Chen, Xiaowen, Ye, Ming, and Xu, Xi
- Subjects
HISTONE deacetylase ,CELL physiology ,CELL proliferation ,ANTINEOPLASTIC agents ,IMMUNE response - Abstract
Histone deacetylase 5 (HDAC5) is a class II HDAC. Aberrant expression of HDAC5 has been observed in multiple cancer types, and its functions in cell proliferation and invasion, the immune response, and maintenance of stemness have been widely studied. HDAC5 is considered as a reliable therapeutic target for anticancer drugs. In light of recent findings regarding the role of epigenetic reprogramming in tumorigenesis, in this review, we provide an overview of the expression, biological functions, regulatory mechanisms, and clinical significance of HDAC5 in cancer. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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27. E47 upregulates ΔNp63α to promote growth of squamous cell carcinoma.
- Author
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Xu, Jing, Li, Fengtian, Gao, Ya, Guo, Rongtian, Ding, Liangping, Fu, Mengyuan, Yi, Yong, Chen, Hu, Xiao, Zhi-Xiong Jim, and Niu, Mengmeng
- Published
- 2021
- Full Text
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28. Pin1 and JNK1 cooperatively modulate TAp63γ.
- Author
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Fan, Xueying, He, Wei, Hu, Ke, Chen, Huimin, Chen, Li, Fan, Shijie, and Li, Chenghua
- Subjects
TRANSCRIPTION factors ,CARRIER proteins ,PHOSPHORYLATION ,GENES ,ISOMERASES - Abstract
The p63 gene encodes at least 10 isoforms, which can be classified into TA and ∆N isotypes (TAp63 and ∆Np63 proteins) according to their differences at the N termini. TAp63γ is an important transcription factor. We previously reported that peptidyl‐prolyl isomerase (PPI) Pin1 directly binds to TAp63γ protein and identified that serine 12 (S12) in the transactivation domain (TAD) of TAp63γ is required for regulation of its transcriptional activity. In the present study, we report that Pin1 stimulates transcriptional and pro‐apoptotic activities of TAp63γ; this Pin1‐mediated stimulation may depend on phosphorylation of S12 mediated by JNK1 and results in striking activation of TAp63γ. JNK1 represses transactivity of TAp63γ in cells without abundant Pin1 proteins and enhances it in the presence of sufficient levels of Pin1. Collectively, our data suggest a novel mechanism for regulation of TAp63γ transactivity: TAp63γ with unphosphorylated S12 is moderately active, phosphorylation at this residue (pS12) makes it hypoactive, and Pin1 binds to the pS12‐P13 motif and makes TAp63γ hyperactive. Our findings will aid in the elucidation of the mechanism underlying modulation of TAp63γ. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
29. An NKX2-1GFP and TP63tdTomato dual fluorescent reporter for the investigation of human lung basal cell biology.
- Author
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Goh, Kim Jee, Tan, Ee Kim, Lu, Hao, Roy, Sudipto, and Dunn, N. Ray
- Subjects
GREEN fluorescent protein ,CYTOLOGY ,MULTIPOTENT stem cells ,EPITHELIAL cells ,LABORATORY mice - Abstract
Basal cells are multipotent stem cells responsible for the repair and regeneration of all the epithelial cell types present in the proximal lung. In mice, the elusive origins of basal cells and their contribution to lung development were recently revealed by high-resolution, lineage tracing studies. It however remains unclear if human basal cells originate and participate in lung development in a similar fashion, particularly with mounting evidence for significant species-specific differences in this process. To address this outstanding question, in the last several years differentiation protocols incorporating human pluripotent stem cells (hPSC) have been developed to produce human basal cells in vitro with varying efficiencies. To facilitate this endeavour, we introduced tdTomato into the human TP63 gene, whose expression specifically labels basal cells, in the background of a previously described hPSC line harbouring an NKX2-1
GFP reporter allele. The functionality and specificity of the NKX2-1GFP ;TP63tdTomato hPSC line was validated by directed differentiation into lung progenitors as well as more specialised lung epithelial subtypes using an organoid platform. This dual fluorescent reporter hPSC line will be useful for tracking, isolating and expanding basal cells from heterogenous differentiation cultures for further study. [ABSTRACT FROM AUTHOR]- Published
- 2021
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- View/download PDF
30. Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene.
- Author
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Kalinina, Marina, Skvortsov, Dmitry, Kalmykova, Svetlana, Ivanov, Timofei, Dontsova, Olga, and Pervouchine, Dmitri D
- Published
- 2021
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31. TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development.
- Author
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Yi, Mei, Tan, Yixin, Wang, Li, Cai, Jing, Li, Xiaoling, Zeng, Zhaoyang, Xiong, Wei, Li, Guiyuan, Li, Xiayu, Tan, Pingqing, and Xiang, Bo
- Subjects
SQUAMOUS cell carcinoma ,CELL differentiation ,CHROMATIN-remodeling complexes ,CHROMATIN - Abstract
Squamous cell carcinoma (SCC) is an aggressive malignancy that can originate from various organs. TP63 is a master regulator that plays an essential role in epidermal differentiation. It is also a lineage-dependent oncogene in SCC. ΔNp63α is the prominent isoform of TP63 expressed in epidermal cells and SCC, and overexpression promotes SCC development through a variety of mechanisms. Recently, ΔNp63α was highlighted to act as an epidermal-specific pioneer factor that binds closed chromatin and enhances chromatin accessibility at epidermal enhancers. ΔNp63α coordinates chromatin-remodeling enzymes to orchestrate the tissue-specific enhancer landscape and three-dimensional high-order architecture of chromatin. Moreover, ΔNp63α establishes squamous-like enhancer landscapes to drive oncogenic target expression during SCC development. Importantly, ΔNp63α acts as an upstream regulator of super enhancers to activate a number of oncogenic transcripts linked to poor prognosis in SCC. Mechanistically, ΔNp63α activates genes transcription through physically interacting with a number of epigenetic modulators to establish enhancers and enhance chromatin accessibility. In contrast, ΔNp63α also represses gene transcription via interacting with repressive epigenetic regulators. ΔNp63α expression is regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances of p63 in epigenomic and transcriptional control, as well as the mechanistic regulation of p63. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
32. lncRNA PART1 and MIR17HG as ΔNp63α direct targets regulate tumor progression of cervical squamous cell carcinoma.
- Author
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Liu, Hanyuan, Zhu, Chenchen, Xu, Zhihao, Wang, Juan, Qian, Lili, Zhou, Qingqing, Shen, Zhen, Zhao, Weidong, Xiao, Weihua, Chen, Liang, and Zhou, Ying
- Abstract
Cervical cancer (CC) remains one of the leading causes of mortality of female cancers worldwide, with more than 90% being cervical squamous cell carcinoma (CSCC). ΔNp63α is the predominant isoform expressed in cervical epithelial tissues and exerts its antitumor function in CSCC. In this study, we have identified 39 long noncoding RNAs as ΔNp63α targets in CSCC through RNA sequencing and chromatin immunoprecipitation sequencing, in which we further confirmed and focused on the two tumor‐related long noncoding RNAs, PART1 (lncPART1) and MIR17HG (lncMIR17HG). Experiments from stable overexpression/knockdown cell lines revealed that lncPART1 and lncMIR17HG regulated cell proliferation, migration, and invasion. In vivo experiments further showed that lncPART1 suppresses tumor growth in CSCC‐derived tumors. Examinations of clinical tissues indicated that the expression of lncPART1 was positively correlated with ΔNp63α expression, while lncMIR17HG was negatively correlated with ΔNp63α expression, suggesting that ΔNp63α plays a central role via regulating its direct targets in the progression of CSCC. These findings provide novel insights in targeted therapy of cervical cancers. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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- View/download PDF
33. Kidney function and other factors and their association with falls : The screening for CKD among older people across Europe (SCOPE) study.
- Author
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Britting, Sabine, Artzi-Medvedik, Rada, Fabbietti, Paolo, Tap, Lisanne, Mattace-Raso, Francesco, Corsonello, Andrea, Lattanzio, Fabrizia, Ärnlöv, Johan, Carlsson, Axel C., Roller-Wirnsberger, Regina, Wirnsberger, Gerhard, Kostka, Tomasz, Guligowska, Agnieszka, Formiga, Francesc, Moreno-Gonzalez, Rafael, Gil, Pedro, Martinez, Sara Lainez, Kob, Robert, Melzer, Itshak, and Freiberger, Ellen
- Subjects
OLDER people ,CHRONIC kidney failure ,LOGISTIC regression analysis ,GLOMERULAR filtration rate - Abstract
Background: Reduced kidney function has become a major public health concern, especially among older people, as Chronic Kidney Disease (CKD) is associated with increased risk of end stage renal disease and mortality. Falls are a serious negative health outcome in older persons with one third of people aged 65 years experiencing a fall per year and increasing fall rates with increasing age. The impact of CKD on falls in older community-dwelling persons is not well investigated. Additionally, lower urinary tract symptoms (LUTS) may also increase the risk of falls. Therefore, our aim was to investigate the impact of CKD and LUTS on falls as well as on injurious falls.Methods: The SCOPE study is an observational, multinational, multicenter, prospective cohort study involving community-dwelling older persons aged 75 years and more recruited from August 2016 to March 2018 in seven European countries. The main outcomes of the present study were any falls and any injurious falls during the 12 months before enrolment. The cross-sectional association of estimated glomerular filtration rate (eGFR) and LUTS with study outcomes was investigated by logistic regression analysis adjusted for baseline characteristics of enrolled subjects.Results: Our series consisted of 2256 SCOPE participants (median age = 79.5 years, 55.7% female). Of them, 746 participants experienced a fall and 484 reported an injurious fall in the 12 months prior to baseline assessment. CKD was not significantly associated with falls (OR = 0.95, 95%CI = 0.79-1.14 for eGFR< 60; OR = 1.02, 95%CI = 0.81-1.28 for eGFR< 45; OR = 1.08, 95%CI = 0.74-1.57 for eGFR< 30) or injurious falls (OR = 0.91, 95%CI = 0.67-1.24 for eGFR< 60; OR = 0.93, 95%CI = 0.63-1.37 for eGFR< 45; OR = 1.19, 95%CI = 0.62-2.29 for eGFR< 30). LUTS were found significantly associated with both falls (OR = 1.56, 95%CI = 1.29-1.89) and injurious falls (OR = 1.58, 95%CI = 1.14-2.19), and such associations were confirmed in all multivariable models.Conclusions: Cross-sectional data suggest that CKD may not be associated with history of falls or injurious falls, whereas LUTS is significantly associated with the outcomes.Trial Registration: This study was registered on 25th February 2016 at clinicaltrials.gov ( NCT02691546 ). [ABSTRACT FROM AUTHOR]- Published
- 2020
- Full Text
- View/download PDF
34. PAN-P63 BUT NOT ΔNP63 (P40) EXPRESSION IN UNDIFFERENTIATED CARCINOMA OF THE PANCREAS.
- Author
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LISZKA, ŁUKASZ
- Abstract
Undifferentiated carcinoma of the pancreas (UC) is a carcinoma without a definitive direction of differentiation. Tumour protein p63 is a regulator of squamous phenotype, which may also be engaged in tumour development. N-terminal isoforms of p63 are TAp63 and ΔNp63. Pan-p63 antibodies are able to detect both isoforms, whereas p40 antibodies recognise the ΔNp63 isoform only. The aim of the study was to describe pan-p63/p40 immunohistochemical expression patterns in pancreatic neoplasms: UC, ductal adenocarcinomas, neuroendocrine tumours, neuroendocrine carcinomas, serous cystic neoplasms, and solid pseudopapillary neoplasms. DAK-p63 and BC28 antibodies were used for pan-p63 and p40 detection, respectively. Moderate-to-strong pan-p63 was found in anaplastic (pleomorphic giant cell) UC (n = 4), sarcomatoid UC (n = 2), UC with osteoclast-like giant cells (n = 3), and ductal carcinomas with partial squamous differentiation. Weak and focal pan-p63 expression was found in monomorphic UC (n = 3) and in the majority of neuroendocrine carcinomas (6/7 cases). Pan-p63 expression was infrequent in ductal carcinomas without squamous differentiation and in neuroendocrine tumours. Serous cystic and solid pseudopapillary neoplasms were pan-p63-negative. Ductal carcinomas with partial squamous differentiation were the only tumours with evident p40 expression. Pan-p63(+)/p40(-) immunohistochemical status may be supportive for UC diagnosis. The pan-p63 expression was not equivalent to squamous differentiation in pancreatic neoplasia. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
35. P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development.
- Author
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Monti, Paola, Ciribilli, Yari, Foggetti, Giorgia, Menichini, Paola, Bisio, Alessandra, Cappato, Serena, Inga, Alberto, Divizia, Maria Teresa, Lerone, Margherita, Bocciardi, Renata, and Fronza, Gilberto
- Subjects
GENE expression ,PROTEIN binding ,GENE families ,CHROMOSOMAL translocation ,CANCER ,RNA splicing ,CANCER invasiveness - Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (-N and TA isoforms); both transcripts are also subjected to alternative splicingmechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
36. TRIM8 Blunts the Pro-proliferative Action of ΔNp63α in a p53 Wild-Type Background.
- Author
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Caratozzolo, Mariano Francesco, Marzano, Flaviana, Abbrescia, Daniela Isabel, Mastropasqua, Francesca, Petruzzella, Vittoria, Calabrò, Viola, Pesole, Graziano, Sbisà, Elisabetta, Guerrini, Luisa, and Tullo, Apollonia
- Subjects
TUMOR suppressor proteins ,ONCOGENIC proteins ,P53 antioncogene ,GENE regulatory networks ,GENE families ,GENE expression - Abstract
The p53 gene family network plays a pivotal role in the control of many biological processes and therefore the right balance between the pro-apoptotic and pro-survival isoforms is key to maintain cellular homeostasis. The stability of the p53 tumor suppressor protein and that of oncogenic ΔNp63α, is crucial to control cell proliferation. The aberrant expression of p53 tumor suppressor protein and oncogenic ΔNp63α contributes to tumorigenesis and significantly affects anticancer drug response. Recently, we demonstrated that TRIM8 increases p53 stability, potentiating its tumor suppressor activity. In this paper, we show that TRIM8 simultaneously reduces the level of the pro-proliferative ΔNp63α protein, in both a proteasomal and caspase-1 dependent way, thereby playing a critical role in the cellular response to DNA damaging agents. Moreover, we provided evidence that ΔNp63α in turn, suppresses TRIM8 gene expression by preventing p53-mediated transactivation of TRIM8, therefore suggesting the existence of a negative feedback loop. These findings indicate that TRIM8 exerts its anticancer power through a joint action that provides on one hand, the activation of the p53 tumor suppressor role, and on the other the quenching of the oncogenic ΔNp63α protein activity. The enhancement of TRIM8 activity may offer therapeutic benefits and improve the management of chemoresistant tumors. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
37. Ectrodactyly-ectodermal dysplasia-clefting syndrome with unusual cutaneous vitiligoid and psoriasiform lesions due to a novel single point TP63 gene mutation.
- Author
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Wawrzycki, Bartłomiej, Pietrzak, Aldona, Chodorowska, Grażyna, Filip, Agata A., Petit, Veronique, Rudnicka, Lidia, Dybiec, Ewa, Rakowska, Adriana, Sobczyńska-Tomaszewska, Agnieszka, and Kanitakis, Jean
- Subjects
ECTODERMAL dysplasia ,GENETIC mutation ,ECTRODACTYLY - Published
- 2019
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- View/download PDF
38. Altered expression of p63 isoforms and expansion of p63- and club cell secretory protein-positive epithelial cells in the lung as novel features of aging.
- Author
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Fukumoto, Jutaro, Patil, Sahebgowda Sidramagowda, Krishnamurthy, Sudarshan, Saji, Smita, John, Irene, Narala, Venkata Ramireddy, Hernández-Cuervo, Helena, Alleyn, Matthew, Breitzig, Mason T., Galam, Lakshmi, Soundararajan, Ramani, Chaudhari, Uddhav K., Hansen, Barbara C., Lockey, Richard F., and Kolliputi, Narasaiah
- Subjects
PROTEIN C ,PROGENITOR cells ,RHESUS monkeys ,LUNGS ,EPITHELIAL cells ,LUNG diseases - Abstract
Aging is a key contributor for subclinical progression of late-onset lung diseases. Basal, club, and type II alveolar epithelial cells (AECs) are lung epithelial progenitors whose capacities of differentiation are extensively studied. The timely transition of these cells in response to environmental changes helps maintain the intricate organization of lung structure. However, it remains unclear how aging affects their behavior. This paper demonstrates that the protein expression profiles of a type II AEC marker, prosurfactant protein C (pro-SPC), and a basal cell marker, p63, are altered in the lungs of 14-mo-old versus 7- to 9-wk-old mice. Expression of NH2- terminal-truncated forms of p63 (ΔNp63), a basal cell marker, and claudin-10, a club cell marker, in cytoplasmic extracts of lungs of 14-mo-old mice was upregulated. In contrast, nuclear expression of full-length forms of p63 (TAp63) decreases with age. These alterations in protein expression profiles coincide with dramatic changes in lung functions including compliance. Whole tissue lysates of middle-aged versus aged rhesus monkey lungs display similar age-associated alterations in pro-SPC expression. An age-associated decrease of TAp63 in nuclear lysates was observed in aged monkey group. Moreover, the lungs of 14-mo-old versus 7- to 9-wk-old mice display a wider spreading of ΔNp63-positive CCSP-positive bronchiolar epithelial cells. This expansion did not involve upregulation of Ki67, a representative proliferation marker. Collectively, it is postulated that 1) this expansion is secondary to a transition of progenitor cells committed to club cells from ΔNp63- negative to ΔNp63-positive status, and 2) high levels of cytoplasmic ΔNp63 expression trigger club cell migration. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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39. TP63 Transcripts Play Opposite Roles in Chicken Skeletal Muscle Differentiation.
- Author
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Luo, Wen, Ren, Xueyi, Chen, Jiahui, Li, Limin, Lu, Shiyi, Chen, Tian, Nie, Qinghua, and Zhang, Xiquan
- Subjects
TUMOR proteins ,EMBRYOLOGY ,MYOBLASTS ,SKELETAL muscle ,CELL proliferation ,RNA sequencing - Abstract
Tumor protein 63 (TP63) comprises multiple isoforms and plays an important role during embryonic development. It has been shown that TP63 knockdown inhibits myogenic differentiation, but which isoform is involved in the underlying myogenic regulation remains uncertain. Here, we found that two transcripts of TP63 , namely, TAp63 α and Δ Np63 α, are expressed in chicken skeletal muscle. These two transcripts have distinct expression patterns and opposite functions in skeletal muscle development. TAp63 has higher expression in skeletal muscle than in other tissues, and its expression is gradually upregulated during chicken primary myoblast differentiation. Δ Np63 can be expressed in multiple tissues and exhibits stable expression during myoblast differentiation. TAp63 α overexpression inhibits myoblast proliferation, induces cell cycle arrest, and enhances myoblast differentiation. However, although Δ Np63 α has no significant effect on cell proliferation, the overexpression of Δ Np63 α inhibits myoblast differentiation. Using isoform-specific overexpression assays following RNA-sequencing, we identified potential downstream genes of TAp63 α and Δ Np63 α in myoblast. Bioinformatics analyses and experimental verification results showed that the differentially expressed genes (DEGs) between the TAp63 α and control groups were enriched in the cell cycle pathway, whereas the DEGs between the Δ Np63 α and control groups were enriched in muscle system process, muscle contraction, and myopathy. These findings provide new insights into the function and expression of TP63 during skeletal muscle development, and indicate that one gene may play two opposite roles during a single cellular process. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
40. Master regulatory role of p63 in epidermal development and disease.
- Author
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Soares, Eduardo and Zhou, Huiqing
- Subjects
TUMOR proteins ,GENE expression ,TRANSCRIPTION factors ,GENETIC mutation ,CELL proliferation ,KERATINOCYTES ,EPIGENETICS - Abstract
The transcription factor p63 is a master regulator of epidermal development. Mutations in p63 give rise to human developmental diseases that often manifest epidermal defects. In this review, we summarize major p63 isoforms identified so far and p63 mutation-associated human diseases that show epidermal defects. We discuss key roles of p63 in epidermal keratinocyte proliferation and differentiation, emphasizing its master regulatory control of the gene expression pattern and epigenetic landscape that define epidermal fate. We subsequently review the essential function of p63 during epidermal commitment and transdifferentiation towards epithelial lineages, highlighting the notion that p63 is the guardian of the epithelial lineage. Finally, we discuss current therapeutic development strategies for p63 mutation-associated diseases. Our review proposes future directions for dissecting p63-controlled mechanisms in normal and diseased epidermal development and for developing therapeutic options. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
41. A double dealing tale of p63: an oncogene or a tumor suppressor.
- Author
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Chen, Yonglong, Peng, Yougong, Fan, Shijie, Li, Yimin, Xiao, Zhi-Xiong, and Li, Chenghua
- Subjects
TUMOR proteins ,ONCOGENES ,TUMOR suppressor genes ,CANCER invasiveness ,CELL proliferation ,GENETICS - Abstract
As a member of tumor suppressor p53 family, p63, a gene encoding versatile protein variant, has been documented to correlate with cancer formation and progression, though it is rarely mutated in cancer patients. However, it has long been controversial on whether p63 is an oncogene or a tumor suppressor. Here, we comprehensively reviewed reports on roles of p63 in development, tumorigenesis and tumor progression. According to data from molecular cell biology, genetic models and clinic research, we conclude that p63 may act as either an oncogene or a tumor suppressor gene in different scenarios: TA isoforms of p63 gene are generally tumor-suppressive through repressing cell proliferation, survival and metastasis; ΔN isoforms, however, may initiate tumorigenesis via promoting cell proliferation and survival, but inhibit tumor metastasis and progression; effects of p63 on tumor formation and progression depend on the context of the whole p53 family, and either amplification or loss of p63 gene locus can break the balance to cause tumorigenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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- View/download PDF
42. Regenerating human epithelia with cultured stem cells: feeder cells, organoids and beyond.
- Author
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Hynds, Robert E., Bonfanti, Paola, and Janes, Sam M.
- Abstract
Abstract: More than 40 years ago, Howard Green's laboratory developed a method for long‐term expansion of primary human epidermal keratinocytes by co‐culture with 3T3 mouse embryonic fibroblasts. This was a breakthrough for
in vitro cultivation of cells from human skin and later for other epithelia: it led to the first stem cell therapy using cultured cells and has vastly increased our understanding of epithelial stem cell biology. In recent years, new methods to expand epithelial cells as three‐dimensional organoids have provided novel means to investigate the functions of these cells in health and disease. Here, we outline the history of stratified epithelial stem cell culture and the application of cultured epithelial cells in clinical therapies. We further discuss the derivation of organoids from other types of epithelia and the challenges that remain for the translation of novel stem cell therapies toward clinical use. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
43. De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II).
- Author
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Wang, Zhengfei, Sun, Linxia, Guan, Weibing, Zhou, Chunlin, Tang, Boping, Cheng, Yongxu, Huang, Jintian, and Xuan, Fujun
- Subjects
PORTUNIDAE ,POLYMERASE chain reaction ,AQUACULTURE ,CELL proliferation ,FUNCTIONAL genomics - Abstract
Background: The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Studies are rarely conducted on the molecular regulatory mechanism underlying the development of the reproductive system during the mating embrace stage in this species. In this study, we used high-throughput sequencing to sequence all transcriptomes of the P. trituberculatus reproductive system. Results: Transcriptome sequencing of the reproductive system produced 81,688,878 raw reads (38,801,152 and 42,887,726 reads from female and male crabs, respectively). Low-quality (quality <20) reads were trimmed and removed, leaving only high-quality reads (37,020,664 and 41,021,030 from female and male crabs, respectively). A total of 126,188 (female) and 164,616 (male) transcripts were then generated by de novo transcriptome assembly using Trinity. Functional annotation of the obtained unigenes revealed that a large number of key genes and some important pathways may participate in cell proliferation and signal transduction. On the basis of our transcriptome analyses and as confirmed by quantitative real-time PCR, a number of genes potentially involved in the regulation of gonadal development and reproduction of P. trituberculatus were identified: ADRA1B, BAP1, ARL3, and TRPA1. Conclusion: This study is the first to report on the whole reproductive system transcriptome information in stage II of P. trituberculatus gonadal development and provides rich resources for further studies to elucidate the molecular basis of the development of reproductive systems and reproduction in crabs. The current study can be used to further investigate functional genomics in this species. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
44. Evaluation of the Side Effects of Antiretroviral Treatment.
- Author
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BAŞGÖNÜL, Sedef, GENÇER, Serap, and ÖZER, Serdar
- Subjects
ANTIRETROVIRAL agents ,DRUG side effects ,THERAPEUTIC use of protease inhibitors ,HYPERLIPIDEMIA ,GASTROINTESTINAL diseases - Abstract
Copyright of Mediterranean Journal of Infection, Microbes & Antimicrobials is the property of Galenos Yayinevi Tic. LTD. STI and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2018
- Full Text
- View/download PDF
45. Familial cleft tongue caused by a unique translation initiation codon variant in TP63.
- Author
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Schmidt J, Schreiber G, Altmüller J, Thiele H, Nürnberg P, Li Y, Kaulfuß S, Funke R, Wilken B, Yigit G, and Wollnik B
- Subjects
- Codon, Initiator, Humans, Male, Tongue, Transcription Factors genetics, Tumor Suppressor Proteins genetics, Cleft Lip genetics, Cleft Palate genetics, Ectodermal Dysplasia genetics
- Abstract
Variants in transcription factor p63 have been linked to several autosomal dominantly inherited malformation syndromes. These disorders show overlapping phenotypic characteristics with various combinations of the following features: ectodermal dysplasia, split-hand/foot malformation/syndactyly, lacrimal duct obstruction, hypoplastic breasts and/or nipples, ankyloblepharon filiforme adnatum, hypospadias and cleft lip/palate. We describe a family with six individuals presenting with a striking novel phenotype characterized by a furrowed or cleft tongue, a narrow face, reddish hair, freckles and various foot deformities. Whole-exome sequencing (WES) identified a novel heterozygous variant, c.3G>T, in TP63 affecting the translation initiation codon (p.1Met?). Sanger sequencing confirmed dominant inheritance of this unique variant in all six affected family members. In summary, our findings indicate that heterozygous variants in TP63 affecting the first translation initiation codon result in a novel phenotype dominated by a cleft tongue, expanding the complex genotypic and phenotypic spectrum of TP63-associated disorders., (© 2021. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
46. ASPicDB: A database resource for alternative splicing analysis
- Author
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Raffaella Rizzi, Tiziana Castrignanò, A. D'Onorio De Meo, Flavio Licciulli, Graziano Pesole, Paola Bonizzoni, Anna Maria D'Erchia, Marina Mangiulli, Flavio Mignone, Ernesto Picardi, Alberto Riva, Danilo Carrabino, Giulio Pavesi, Anna Anselmo, Mattia D'Antonio, Castrignanò, T, D'Antonio, M, Anselmo, A, Carrabino, D, D'Onorio De Meo, A, D'Erchia, A, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Riva, A, Rizzi, R, Bonizzoni, P, and Pesole, G
- Subjects
Statistics and Probability ,Molecular Sequence Data ,Information Storage and Retrieval ,UniGene ,Biology ,computer.software_genre ,Biochemistry ,Set (abstract data type) ,User-Computer Interface ,Annotation ,alternative splicing ,Databases, Genetic ,Computer Graphics ,Molecular Biology ,Base Sequence ,Database ,Alternative splicing ,Intron ,Chromosome Mapping ,INF/01 - INFORMATICA ,Sequence Analysis, DNA ,Computer Science Applications ,Computational Mathematics ,ComputingMethodologies_PATTERNRECOGNITION ,Computational Theory and Mathematics ,RNA splicing ,Proteome ,Database Management Systems ,Human genome ,RNA Splice Sites ,Sequence Alignment ,computer - Abstract
Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they provide that prevent the full exploitation of the available data. Furthermore, current resources provide limited query and download facilities. Results: ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. Splice-site detection and full-length transcript modeling have been carried out by a genome-wide application of the ASPic algorithm, based on the multiple alignments of gene-related transcripts (typically a Unigene cluster) to the genomic sequence, a strategy that greatly improves prediction accuracy compared to methods based on independent and progressive alignments. Enhanced query and download facilities for annotations and sequences allow users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB, which is regularly updated on a monthly basis, also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST sequences and their library source annotation. Availability: www.caspur.it/ASPicDB Contact: graziano.pesole@biologia.uniba.it Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2008
47. DNA damage induces expression of WWP1 to target ΔNp63α to degradation.
- Author
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Chen, Ji, Shi, Hua, Chen, Yonglong, Fan, Shijie, Liu, Dingyi, and Li, Chenghua
- Subjects
DNA damage ,CANCER chemotherapy ,CELL proliferation ,DOWNREGULATION ,PROTEOLYSIS - Abstract
ΔNp63αplays key roles in cell survival and proliferation. So its expression is always tightly controlled in cells. We previously reported that DNA damage down-regulates transcription of ΔNp63αin FaDu and HaCat cells, which contributes to cell apoptosis. In the present study, we found that DNA damage induces down-regulation of ΔNp63αvia facilitating its proteasomal degradation in cell lines such as MDA-MB-231 and MCF10A. Further investigation revealed that transcription of WWP1 is stimulated by DNA damage in these cells. Knock-down of WWP1 abrogates DNA damage-induced down-regulation of ΔNp63αand partially rescues cell apoptosis. Interestingly, DNA damage may stimulate WWP1 through different mechanisms in different cell types: it up-regulates transcription of WWP1 in a p53-dependent manner in MCF10A and HEK293 cells, while miR-452 may be involved in DNA damage-induced up-regulation of WWP1 in MDA-MB-231 cells. Our study demonstrates a novel pathway which regulates ΔNp63αupon cellular response to chemotherapeutic agents. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
48. Cardio-Renal Syndrome Type 4: The Correlation Between Cardiorenal Ultrasound Parameters.
- Author
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Lai, Silvia, Ciccariello, Mauro, Dimko, Mira, Galani, alessandro, Lucci, Silvio, Cianci, Rosario, and Mariotti, amalia
- Subjects
KIDNEY disease diagnosis ,RIGHT heart ventricle diseases ,CARDIOVASCULAR diseases ,DEATH rate ,SYSTOLIC blood pressure - Abstract
Bakground/Aims: Cardiovascular diseases represent the leading causes of morbidity and mortality in patients with cronich kidney disease (CKD). The pathogenesis includes a complex, bidirectional interaction between heart and kidney termed cardiorenal syndrome type 4. The aim of study was to evaluate the association between renal and cardiovascular ultrasonographic parameters and identify early markers of cardiovascular risk. Methods: A total of 35 patients with CKD and 25 healthy controls, were enrolled and we have evaluated inflammatory indexes, mineral metabolism, renal function, renal and cardiovascular ultrasonographic parameters. Results: Tricuspid anular plane systolic excursion (TAPSE) and estimated pulmonary artery systolic pressure (ePAPs) showed a statistically significant difference between CKD patients and healthy controls (p<0.001, p=0.05). Also 25 hydroxyvitaminD (25-OH-VitD), parathyroid hormone (iPTH), posphorus, serum uric acid, renal resistive index (RRI) and C-reactive protein (CRP) showed a significant difference between the two groups (p=0.002, p<0.001, p<0.001, p<0.001, p<0.001, p<0.001). Moreover the TAPSE correlated positively with estimated glomerula filtration rate (eGFR) and negatively with RRI (p=0.05, p=0.008), while ePAPs correlated negatively with eGFR and positively with RRI (p=0.029, p<0.001). Conclusion: CKD can contribute to the development and progression of right ventricle dysfunction with endothelial dysfunction, inflammation and mineral metabolism disorders. Accurate assessment of right ventricular function is recommended in patients with CKD. RRI and echocardiographic parameters can be an important instrument for the diagnosis, prognosis and therapeutic assessment of cardio-renal syndrome in these patients. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
49. A method for identifying discriminative isoform-specific peptides for clinical proteomics application.
- Author
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Fan Zhang and Chen, Jake Y.
- Subjects
PROTEOMICS ,BIOMARKERS ,CANCER ,SINGLE nucleotide polymorphisms ,NEOPLASTIC cell transformation - Abstract
Background: Clinical proteomics application aims at solving a specific clinical problem within the context of a clinical study. It has been growing rapidly in the field of biomarker discovery, especially in the area of cancer diagnostics. Until recently, protein isoform has not been viewed as a new class of early diagnostic biomarkers for clinical proteomics. A protein isoform is one of different forms of the same protein. Different forms of a protein may be produced from single-nucleotide polymorphisms (SNPs), alternative splicing, or post-translational modifications (PTMs). Previous studies have shown that protein isoforms play critical roles in tumorigenesis, disease diagnosis, and prognosis. Identifying and characterizing protein isoforms are essential to the study of molecular mechanisms and early detection of complex diseases such as breast cancer. However, there are limitations with traditional methods such as EST sequencing, Microarray profiling (exon array, Exon-exon junction array), mRNA next-generation sequencing used for protein isoform determination: 1) not in the protein level, 2) no connectivity about connection of nonadjacent exons, 3) no SNPs and PTMs, and 4) low reproducibility. Moreover, there exist the computational challenges of clinical proteomics studies: 1) low sensitivity of instruments, 2) high data noise, and 3) high variability and low repeatability, although recent advances in clinical proteomics technology, LC-MS/MS proteomics, have been used to identify candidate molecular biomarkers in diverse range of samples, including cells, tissues, serum/plasma, and other types of body fluids. Results: Therefore, in the paper, we presented a peptidomics method for identifying cancer-related and isoform-specific peptide for clinical proteomics application from LC-MS/MS. First, we built a Peptidomic Database of Human Protein Isoforms, then created a peptidomics approach to perform large-scale screen of breast cancer-associated alternative splicing isoform markers in clinical proteomics, and lastly performed four kinds of validations: biological validation (explainable index), exon array, statistical validation of independent samples, and extensive pathway analysis. Conclusions: Our results showed that alternative splicing isoform makers can act as independent markers of breast cancer and that the method for identifying cancer-specific protein isoform biomarkers from clinical proteomics application is an effective one for increasing the number of identified alternative splicing isoform markers in clinical proteomics. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
50. Oncogenic Intra-p53 Family Member Interactions in Human Cancers.
- Author
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Ferraiuolo, Maria, Di Agostino, Silvia, Blandino, Giovanni, and Strano, Sabrina
- Subjects
ONCOGENIC proteins ,PROTEIN structure ,TUMOR treatment ,CHARTS, diagrams, etc. - Abstract
The p53 gene family members p53, p73, and p63 display several isoforms derived from the presence of internal promoters and alternative splicing events. They are structural homologs but hold peculiar functional properties. p53, p73, and p63 are tumor suppressor genes that promote differentiation, senescence, and apoptosis. p53, unlike p73 and p63, is frequently mutated in cancer often displaying oncogenic "gain of function" activities correlated with the induction of proliferation, invasion, chemoresistance, and genomic instability in cancer cells. These oncogenic functions are promoted either by the aberrant transcriptional cooperation of mutant p53 (mutp53) with transcription cofactors (e.g., NF-Y, E2F1, Vitamin D Receptor, Ets-1, NF-kB and YAP) or by the interaction with the p53 family members, p73 and p63, determining their functional inactivation. The instauration of these aberrant transcriptional networks leads to increased cell growth, low activation of DNA damage response pathways (DNA damage response and DNA double-strand breaks response), enhanced invasion, and high chemoresistance to different conventional chemotherapeutic treatments. Several studies have clearly shown that different cancers harboring mutant p53 proteins exhibit a poor prognosis when compared to those carrying wild-type p53 (wt-p53) protein. The interference of mutantp53/p73 and/or mutantp53/p63 interactions, thereby restoring p53, p73, and p63 tumor suppression functions, could be among the potential therapeutic strategies for the treatment of mutant p53 human cancers. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
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