Statement of Retraction: MicroRNA-592 serves as a novel tumor suppressor in Uveal melanoma: bioinformatics analysis and in vitro cell function verification

Statement of Retraction We, the Editors and Publisher of the journal Bioengineered, have retracted the following article from publication. Lei, P., Xue, L., Wu, Y., & Zhong, J. (2022). MicroRNA-592 serves as a novel tumor suppressor in Uveal melanoma: bioinformatics analysis and in vitro cell function verification. Bioengineered, 13(7–12), 15033–15044. https://doi.org/10.1080/21655979.2023.2184317 Since publication, significant concerns have been raised about the integrity of the data and reported results in the article. When approached for an explanation, the authors provided their original data and answered our queries, but these do not sufficiently address the concerns. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The authors have been informed of this decision. The authors do not agree with the retraction. We have been informed in our decision-making by our policy on publishing ethics and integrity and COPE guidelines. The retracted article will remain online to maintain the scholarly record and will be digitally watermarked on each page as ‘Retracted’.

MicroRNA-32 (miR-32) has been shown to be dysregulated in some human malignancies and this has been found to be correlated with tumor progression. However, its role in uveal melanoma formation and progression remains largely unknown. Thus, the aim of this study was to explore the expression and function of miR-32 in human uveal melanoma. Using quantitative reverse transcription-polymerase chain reaction, we detected miR-32 expression in uveal melanoma tumor tissues and cell lines. The effects of miR-32 on the biological behavior of uveal melanoma cells were also investigated. Finally, the potential regulatory function of miR-32 on EZH2 expression was confirmed. miR-32 expression levels were significantly downregulated in uveal melanoma samples and cell lines (both P < 0.01). Ectopic expression of miR-32 could inhibit uveal melanoma cell proliferation, migration, and invasion, and promote cell apoptosis in vitro. Further, EZH2 was confirmed as a direct target of miR-32 by using the luciferase reporter assay. These findings indicate that miR-32 may function as a novel tumor suppressor in uveal melanoma and could be a potential therapeutic target for this disease.

El trabajo realizado a continuacion trata de poner a prueba mediante experimentacion, el metodo de “dibujar con el lado derecho del cerebro” de la Dra. BETTY EDWARDS, con ninos de 5, 6,7, anos de edad dentro de una institucion educativa. Dentro de la ensenanza de artes en las escuelas, podemos notar la falta de procesos que lleven a un verdadero aprendizaje de dibujo, pintura, etc. debido a que vemos el arte en un papel muy secundario, incluso es tomado como momento de recreacion, siendo el aprendizaje del arte en ninos pequenos una antesala al de la escritura y el entendimiento del mundo que nos rodea , ya que este esta basado en imagenes y formas , teniendo en cuenta esto, hemos realizado el trabajo con este metodo: “dibujar con el lado derecho del cerebro” El cual tiene como objetivo principal ensenar a tener una vision real del mundo en el que vivimos y no a tener una pre concepcion de los objetos que nos rodean , asi por ejemplo cuando ponemos una mesa al frente , y pedimos a un nino que nos dibuje lo que ve, el al saber que es una mesa y cotejar la palabra mesa con lo que aprendio del concepto mesa ,ni siquiera mira lo que tiene al frente sino que directamente dibuja un cuadrado con cuatro patas lo cual es lo que esta ya dentro de su cabeza, la cual se interpreta directo al papel sin pasar por la observacion del modelo .

Background MicroRNAs (miRNAs) contribute to tumorigenesis by acting as either oncogenes or tumor suppressor genes. In this study, we investigated the role of miR-145 in the pathogenesis of uveal melanoma. Methods Expression profiles of miRNAs in uveal melanoma were performed using Agilent miRNA array. Quantitative real-time polymerase chain reaction was used to screen the expression levels of miR-145 in normal uveal tissue, uveal melanoma tissue, and uveal melanoma cell lines. Lenti-virus expression system was used to construct MUM-2B and OCM-1 cell lines with stable overexpression of miR-145. Cell proliferation, cell cycle, and cell apoptosis of these miR-145 overexpression cell lines were examined by MTT assay and flow cytometry respectively. The target genes of miR-145 were predicted by bioinformatics and confirmed using a luciferase reporter assay. The expression of insulin-like growth factor-1 receptor (IGF-1R), insulin receptor substrate-1 (IRS-1) proteins was determined by Western blotting analysis. IRS-1 was knocked down in OCM-1 cells. TUNEL, BrdU, and flow cytometry assay were performed in IRS-1 knocked down OCM-1 cell lines to analyze its function. Results Forty-seven miRNAs were up regulated in uveal melanoma and 61 were down regulated. miR-145 expression was significantly lower in uveal melanoma sample and the cell lines were compared with normal uveal sample. Overexpression of miR-145 suppressed cell proliferation by blocking the G1 phase entering S phase in uveal melanoma cells, and promoted uveal melanoma cell apoptosis. IRS-1 was identified as a potential target of miR-145 by dual luciferase reporter assay. Knocking down of IRS-1 had similar effect as overexpression of miR-145. Conclusion miR-145 might act as a tumor suppressor in uveal melanoma, and downregulation of the target IRS-1 might be a potential mechanism.

MiR-216a-5p/Hexokinase 2 axis regulates uveal melanoma growth through modulation of Warburg effect

To identify the spectrum of somatic mutations in an Asian Indian patient with uveal melanoma (UM) without metastasis using exome sequencing. A 49-year-old man from India was diagnosed as having cilio-choroidal (uveal) melanoma (UM), without metastasis, in his right eye with the help of magnetic resonance imaging. This was later confirmed by histopathological evaluation. Two individuals from India with non-neoplastic blind eyes were recruited as controls. The affected eyes from the UM patient and the two control individuals were enucleated, and uveal tissues were collected. DNA was extracted from uveal tissue, and the matched blood sample from each of the three individuals was followed by exome sequencing. Statistical and bioinformatic analyses were done to identify somatic mutations and their putative associations with UM. Thirty-one somatic mutations (25 amino acid altering) in protein-coding (exonic) regions were detected in the UM patient. Of the amino acid-altering somatic mutations, 16 mutations were predicted to be candidate mutations relevant to UM. Somatic mutations, putatively causal for UM, were identified in GNAQ, SF3B1, and SOX10. Somatic mutations in GNAQ and SF3B1 genes were probable drivers of UM in the Indian patient; these were also reported earlier in some White patients. In addition, a frameshift deletion of 20 base pairs has been identified in SOX10 in the UM patient. Somatic mutations in SOX10, a transcription factor, which acts upstream of microphthalmia-associated transcription factor and synergizes with microphthalmia-associated transcription factor, was identified in some melanoma cell lines. The transcription factor SOX10 was found to have an essential role in melanocyte development and pigmentation. Our finding of the frameshift deletion (p.H387fs) in exon 4 of SOX10 in UM provides an important insight and complements earlier findings of mutations in GNAQ and SF3B1 on the genomic basis of UM.

Genetic Study of Familial Uveal Melanoma: Association of Uveal and Cutaneous Melanoma with Cutaneous and Ocular Nevi

Introduction: Much has been learned about the molecular basis of melanoma in recent years. However, the role of epigenetic alterations in melanoma genesis is poorly understood. Here we report the identification and characterization of MLL2, which encodes a histone lysine methyltransferase, as a novel tumor suppressor in melanoma. Methods: We performed an in vivo shRNA screen using 475 shRNAs targeting 95 epigenetic enzymes to identify novel tumor suppressors of melanoma genesis. Immortalized human melanocytic cell lines expressing BrafV600E (HMEL/PMEL) were transduced with pooled shRNAs and injected subcutaneously in nude mice. Candidate genes were identified from orthotopic tumors formed using PCR and Sanger sequencing and independently validated using multiple independent shRNAs and human cell lines. Results: Among 11 candidate genes identified from tumors formed in the in vivo shRNA screen, MLL2 knockdown was associated with the shortest time to tumor appearance (6 weeks) and highest penetrance (tumor formation at 80% of sites injected). In validation experiments, loss of MLL2 in human melanocytic and melanoma cell lines resulted in worse tumor-free survival when injected orthotopically in mice. Analysis of human melanoma data from The Cancer Genome Atlas (TCGA) project revealed that MLL2 is mutated in 15% of TCGA cases and is not associated with either BRAF or NRAS mutations. We found that MLL2 knockdown in human cell lines was associated with decreased expression of transcription factor TCF3 by qRT-PCR as well as decreased expression of TCF3 gene targets by gene set enrichment analysis (GSEA) of microarray data. Furthermore, GSEA analysis of data from TCGA samples with MLL2 mutations across tumor types revealed decreased expression of genes with TCF3 binding sites. Finally, we found that MLL2 knockdown in a human melanocytic cell line resulted in decreased H3K4 di- and tri-methylation at the promoter region of the TCF3 gene as well as at transcriptional start sites of TCF3 gene targets in ChIP-Seq experiments, suggesting a possible mechanism by which MLL2 loss may contribute to melanoma genesis and progression through dysregulation of the transcription factor TCF3. Conclusions: MLL2 is a novel tumor suppressor in melanoma identified through an in vivo shRNA tumorigenesis screen targeting 95 epigenetic enzymes. MLL2, which encodes for an epigenetic enzyme (a histone methyltransferase), is significantly mutated in human melanoma as represented in the TCGA and loss of MLL2 results in enhanced tumorigenesis in vivo. Studies to elucidate the mechanisms by which MLL2 loss contributes to melanoma genesis and progression and which focus on the transcription factor TCF3 are ongoing. Citation Format: Emily Z. Keung, Kunal Rai, Kadir C. Akdemir, Liren Li, Sneha Sharma, Bryce Axelrad, Lynda Chin. The identification and characterization of MLL2, an epigenetic enzyme, as a novel tumor suppressor in melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-134. doi:10.1158/1538-7445.AM2014-LB-134

MicroRNAs (miRNAs) are a group endogenous small non-coding RNAs that inhibit protein translation through binding to specific target mRNAs. Recent studies have demonstrated that miRNAs are implicated in the development of cancer. However, the role of miR-144 in uveal melanoma metastasis remains largely unknown. MiR-144 was downregulated in both uveal melanoma cells and tissues. Transfection of miR-144 mimic into uveal melanoma cells led to a decrease in cell growth and invasion. After identification of two putative miR-144 binding sites within the 3' UTR of the human c-Met mRNA, miR-144 was proved to inhibit the luciferase activity inMUM-2B cells with a luciferase reporter construct containing the binding sites. In addition, the expression of c-Met protein was inhibited by miR-144. Furthermore, c-Met-mediated cell proliferation and invasion were inhibited by restoration of miR-144 in uveal melanoma cells. In conclusion, miR-144 acts as a tumor suppressor in uveal melanoma, through inhibiting cell proliferation and migration. miR-144 might serve as a potential therapeutic target in uveal melanoma patients.

&lt;div&gt;Abstract&lt;p&gt;Malignant melanoma is a common and frequently lethal disease. Current therapeutic interventions have little effect on survival, emphasizing the need for a better understanding of the genetic, epigenetic, and phenotypic changes in melanoma formation and progression. We identified 17 genes that were not previously known to be silenced by methylation in melanoma using a microarray-based screen following treatment of melanoma cell lines with the DNA methylation inhibitor 5-Aza-2′-deoxycytidine. Eight of these genes have not been previously shown to undergo DNA methylation in any form of cancer. Three of the genes, &lt;i&gt;QPCT, CYP1B1&lt;/i&gt;, and &lt;i&gt;LXN&lt;/i&gt;, are densely methylated in &gt;95% of uncultured melanoma tumor samples. Reexpression of either of two of the silenced genes, &lt;i&gt;HOXB13&lt;/i&gt; and &lt;i&gt;SYK&lt;/i&gt;, resulted in reduced colony formation &lt;i&gt;in vitro&lt;/i&gt; and diminished tumor formation &lt;i&gt;in vivo&lt;/i&gt;, indicating that these genes function as tumor suppressors in melanoma. (Cancer Res 2006; 66(23): 11187-93)&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;Malignant melanoma is a common and frequently lethal disease. Current therapeutic interventions have little effect on survival, emphasizing the need for a better understanding of the genetic, epigenetic, and phenotypic changes in melanoma formation and progression. We identified 17 genes that were not previously known to be silenced by methylation in melanoma using a microarray-based screen following treatment of melanoma cell lines with the DNA methylation inhibitor 5-Aza-2′-deoxycytidine. Eight of these genes have not been previously shown to undergo DNA methylation in any form of cancer. Three of the genes, &lt;i&gt;QPCT, CYP1B1&lt;/i&gt;, and &lt;i&gt;LXN&lt;/i&gt;, are densely methylated in &gt;95% of uncultured melanoma tumor samples. Reexpression of either of two of the silenced genes, &lt;i&gt;HOXB13&lt;/i&gt; and &lt;i&gt;SYK&lt;/i&gt;, resulted in reduced colony formation &lt;i&gt;in vitro&lt;/i&gt; and diminished tumor formation &lt;i&gt;in vivo&lt;/i&gt;, indicating that these genes function as tumor suppressors in melanoma. (Cancer Res 2006; 66(23): 11187-93)&lt;/p&gt;&lt;/div&gt;

Uveal melanoma (UM) is an aggressive intraocular malignant tumour that is closely related to autophagic dysfunction. We aimed to identify autophagy-related long noncoding RNAs (lncRNAs) to elucidate the molecular mechanism of UM. Here, we show that LINC01278 is a new potential biomarker with clinical prognostic value in UM through bioinformatics analysis. Application of an autophagy inhibitor (3-MA) and an autophagy agonist (MG-132) indicated that LINC01278 can inhibit UM cell proliferation, migration, and invasion by inducing autophagy. A xenograft nude mouse model was used to examine the tumorigenesis of UM cells in vivo. Mechanistically, LINC01278 can inhibit the mTOR signalling pathway to activate autophagy, as shown by experiments with an mTOR agonist (MHY1485) and mTOR inhibitor (rapamycin) treatment. Our findings indicate that LINC01278 functions as a tumour suppressor by inhibiting the mTOR signalling pathway to induce autophagy. Targeting the LINC01278-mTOR axis might be a novel and promising therapeutic approach for UM.

BackgroundMicroRNAs (miRNAs) have been shown to function in many different cellular processes, including proliferation, apoptosis, differentiation and development. miR-181a, -181b, -181c and -181d are miR-181 members of the family, which has been rarely studied, especially uveal melanoma.MethodsThe expression level of miR-181 family in human uveal melanoma cell lines was measured via real-time PCR (RT-PCR). The function of miR-181 on cell cycle was detected through Flow Cytometry assay. Microarray assay and Bioinformatics analysis were used to find the potential target of miR-181b, and dual-luciferase reporter assays further identified the target gene.ResultsMiR-181 family members were found to be highly homologous across different species and their upregulation significantly induces UM cell cycle progression. Of the family members, miR-181b was significantly overexpressed in UM tissues and most UM cells. Bioinformatics and dual luciferase reporter assay confirmed CTDSPL as a target of miR-181b. miR-181b over-expression inhibited CTDSPL expression, which in turn led to the phosphorylation of RB and an accumulation of the downstream cell cycle effector E2F1, promoting cell cycle progression in UM cells. Knockdown CTDSPL using siRNAs showing the same effect, including increase of E2F1 and the progression of cell cycle.ConclusionsMiR-181 family members are key negative regulators of CTDSPL-mediated cell cycle progression. These results highlight that miR-181 family members, especially miR-181b, may be useful in the development of miRNA-based therapies and may serve as novel diagnostic and therapeutic candidate for UM.

10521 Background: Uveal melanoma (UM) is a rare malignancy with a poor prognosis. Familial predisposition to UM is rare and accounts for only a few percent of all cases. The genetic background of hereditary UM is unknown and the aim of our project was to identify susceptibility gene(s) for UM. Methods: We identified a family with hereditary predisposition for UM – the proband of which is a young female diagnosed with UM at age 16 who within 6 months developed liver metastases. We also identified two older paternal relatives who were diagnosed with UM at 39 and 44 years of age, respectively. We performed massively parallel sequencing using the Illumina Hiseq2000 technology on germline DNA from the proband, her parents and a healthy sibling. After QC and mapping against the human reference genome the average coverage across the exome was between 35 and 86 for the four sequenced samples. Results: Out of more than 260,000 single nucleotide variants (SNVs) and small insertion / deletion variants (indels), 51 gene variants were filtered out by being novel, shared by the affected proband and her father (considered an obligate mutation carrier), but not by the healthy mother, of predicted functional importance and /or located within strongly conserved regions. The strongest candidate among these was a loss of function-variant in the BAP1 gene, since BAP1 has been suggested as a tumor suppressor in several cancer-related syndromes, including cases of UM. The sequence data indicated an insertion of one base-pair in exon 3 of the BAP1 genecausing a frame-shift and subsequently a truncated protein lacking all its functional domains. The mutation was also present in UM tumor tissue from the two deceased paternal relatives and was found to segregate with the UM phenotype in the family. We also detected loss of heterozygosity in the tumor of the proband, supporting BAP1 as the causative gene in this family. Conclusions: The identification of BAP1 as the gene responsible for this syndrome is the first demonstration of a germline mutation causing UM. This enables us to identify and monitor risk individuals belonging to mutation positive families with predisposition to UM, and possibly other cancer syndromes. We are continuously screening other cases of familial UM for mutations in BAP1.

Ce travail a pour theme la generation automatique de textes. Nous proposons une nouvelle approche de l'organisation textuelle dans un cadre de generation de textes. Le modele est applique a la production d'explications causales, dans un contexte de modelisation qualitative de systemes physiques. Le modele conceptuel dans lequel sont decrits les systemes physiques, est fonde sur la theorie des processus qualitatifs de forbus. Le processus de generation proprement dit vise a satisfaire un but communicatif initial. Il commence par developper un plan de communication par decomposition hierarchique du but initial en buts plus elementaires. Puis, la structure du texte est determinee a un niveau d'abstraction intermediaire entre le plan de communication prealablement etabli et le texte en surface. A ce niveau, les mecanismes de structuration procedent a la construction d'unites globales d'organisation et determinent non seulement l'articulation interne de ces unites globales en termes de relations de cohesion textuelle, mais aussi l'enchainement lineaire de ces unites. Nous decrivons dans ce rapport l'ensemble du modele de generation en nous attardant plus particulierement sur la definition des concepts manipules dans l'approche integree de l'organisation textuelle developpee, et sur les mecanismes d'elaboration des structures de textes