scholarly journals Transcription Factors and Methylation Drive Prognostic miRNA Dysregulation in Hepatocellular Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Shijie Qin ◽  
Jieyun Xu ◽  
Yunmeng Yi ◽  
Sizhu Jiang ◽  
Ping Jin ◽  
...  

Many dysregulated microRNAs (miRNAs) have been suggested to serve as oncogenes or tumor suppressors to act as diagnostic and prognostic factors for HCC patients. However, the dysregulated mechanisms of miRNAs in HCC remain largely unknown. Herein, we firstly identify 114 disordered mature miRNAs in HCC, 93 of them are caused by dysregulated transcription factors, and 10 of them are driven by the DNA methylation of their promoter regions. Secondly, we find that seven up-regulated miRNAs (miR-9-5p, miR-452-5p, miR-452-3p, miR-1180-3p, miR-4746-5p, miR-3677-3 and miR-4661-5p) can promote tumorigenesis via inhibiting multiple tumor suppressor genes participated in metabolism, which may act as oncogenes, and seven down-regulated miRNAs (miR-99-5p, miR-5589-5p, miR-5589-3p, miR-139-5p, miR-139-3p, miR-101-3p and miR-125b-5p) can suppress abnormal cell proliferation via suppressing a number of oncogenes involved in cancer-related pathways, which may serve as tumor suppressors. Thirdly, our findings reveal a mechanism that transcription factor and miRNA interplay can form various regulatory loops to synergistically control the occurrence and development of HCC. Finally, our results demonstrate that this key transcription factor FOXO1 can activate a certain number of tumor suppressor miRNAs to improve the survival of HCC patients, suggesting FOXO1 as an effective therapeutic target for HCC patients. Overall, our study not only reveals the dysregulated mechanisms of miRNAs in HCC, but provides several novel prognostic biomarkers and potential therapeutic targets for HCC patients.

Blood ◽  
1996 ◽  
Vol 87 (12) ◽  
pp. 4949-4958 ◽  
Author(s):  
A Hangaishi ◽  
S Ogawa ◽  
N Imamura ◽  
S Miyawaki ◽  
Y Miura ◽  
...  

It is now evident that the cell cycle machinery has a variety of elements negatively regulating cell cycle progression. However, among these negative regulators in cell cycle control, only 4 have been shown to be consistently involved in the development of human cancers as tumor suppressors: Rb (Retinoblastoma susceptibility protein), p53, and two recently identified cyclin-dependent kinase inhibitors, p16INK4A/MTS1 and p15INK4B/MTS2. Because there are functional interrelations among these negative regulators in the cell cycle machinery, it is particularly interesting to investigate the multiplicity of inactivations of these tumor suppressors in human cancers, including leukemias/lymphomas. To address this point, we examined inactivations of these four genes in primary lymphoid malignancies by Southern blot and polymerase chain reaction-single- strand conformation polymorphism analyses. We also analyzed Rb protein expression by Western blot analysis. The p16INK4A and p15INK4B genes were homozygously deleted in 45 and 42 of 230 lymphoid tumor specimens, respectively. Inactivations of the Rb and p53 genes were 27 of 91 and 9 of 173 specimens, respectively. Forty-one (45.1%) of 91 samples examined for inactivations of all four tumor suppressors had one or more abnormalities of these four tumor-suppressor genes, indicating that dysregulation of cell cycle control is important for tumor development. Statistical analysis of interrelations among impairments of these four genes indicated that inactivations of the individual tumor-suppressor genes might occur almost independently. In some patients, disruptions of multiple tumor-suppressor genes occurred; 4 cases with p16INK4A, p15INK4B, and Rb inactivations; 2 cases with p16INK4A, p15INK4B, and p53 inactivations; and 1 case with Rb and p53 inactivations. It is suggested that disruptions of multiple tumor suppressors in a tumor cell confer an additional growth advantage on the tumor.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2700-2700
Author(s):  
Robert K Arthur ◽  
Ningfei An ◽  
Saira Kahn ◽  
Megan E. McNerney

Abstract One third of tumor suppressor genes encode haploinsufficient transcriptional regulators, including transcription factors and chromatin remodelers. This presents a major barrier in oncology, as tumor suppressor genes and transcription factors are inherently difficult to target therapeutically. It remains unknown how a 50% reduction of a transcriptional regulator translates at the cis-regulatory level into a malignant transcriptional program. It is imperative to address this question, in order to predict and target aberrant downstream pathways. CUX1 encodes a quintessential haploinsufficient transcription factor that is recurrently mutated or deleted, monoallelically, in high-risk myeloid neoplasms and across solid tumor types. We hypothesized that the transcriptional response to changes in CUX1 level is encoded within the cis-regulatory architecture of dosage-sensitive CUX1 target genes. In this study, we determined that CUX1 primarily binds distal enhancers, in a tissue-specific manner. CUX1 binding sites are significantly enriched for co-binding with transcriptional activators and cohesin components. Haploinsufficiency of CUX1 in K562 myeloid leukemia cells led to altered expression of mitotic and apoptotic genes with concomitant increased cellular proliferation. Surprisingly, ChIP-seq of CUX1 in the haploinsufficient state revealed a unimodal decrease in CUX1 occupancy genome-wide, with no relevance to differential gene expression. Thus we used a machine-learning algorithm to identify characteristics of CUX1 binding sites at dosage-sensitive target genes and revealed a relationship with distance to the transcription start site, chromatin accessibility, and enhancer activity. Finally, we demonstrate that CUX1 binding sites at dosage-sensitive genes loop to the promoter, and those genes with an intermediate number of Hi-C loops are most responsive to changes in CUX1 abundance. Overall, these data point to a novel mechanism of transcription factor dose-responsiveness mediated by enhancer-promoter looping. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael Hamm ◽  
Pierre Sohier ◽  
Valérie Petit ◽  
Jérémy H. Raymond ◽  
Véronique Delmas ◽  
...  

AbstractWhile the major drivers of melanoma initiation, including activation of NRAS/BRAF and loss of PTEN or CDKN2A, have been identified, the role of key transcription factors that impose altered transcriptional states in response to deregulated signaling is not well understood. The POU domain transcription factor BRN2 is a key regulator of melanoma invasion, yet its role in melanoma initiation remains unknown. Here, in a BrafV600EPtenF/+ context, we show that BRN2 haplo-insufficiency promotes melanoma initiation and metastasis. However, metastatic colonization is less efficient in the absence of Brn2. Mechanistically, BRN2 directly induces PTEN expression and in consequence represses PI3K signaling. Moreover, MITF, a BRN2 target, represses PTEN transcription. Collectively, our results suggest that on a PTEN heterozygous background somatic deletion of one BRN2 allele and temporal regulation of the other allele elicits melanoma initiation and progression.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16197-e16197
Author(s):  
Oleg I. Kit ◽  
Vladimir S. Trifanov ◽  
Natalya N. Timoshkina ◽  
Dmitry Yu. Gvaldin ◽  
Milana Yu. Mesheryakova ◽  
...  

e16197 Background: Aberrant DNA methylation is a characteristic feature of cancer, affecting gene expression and tumor phenotype. In this study, we quantified the methylation of promoters of eight tumor suppressor genes in pancreatic neuroendocrine tumors (Pan-NET). Methods: The method of pyrosequencing was used to quantity level (Met,%) of methylation of gene promoters - tumor suppressors AHRR, APC1A, DAPK, MGMT, MLH1, P16, RASSF1A, RUNX3 in tumor samples from 55 patients with pancreatic NET (G1-G3) and in the blood of 10 healthy donors. Met for each sample was calculated as the median methylation of CpG sites in triplicate. Results: Hypermethylation was observed for AHRR (75%), APC1A (25%), RASSF1A (30%). In contrast, DAPK, MGMT, MLH1, P16, RUNX3 had low methylation levels ( < 20%). The median of methylation in the blood of healthy donors for AHRR was 91% (76-98); for all other loci it did not exceed 6%. A high incidence of methylation in excess of blood levels in healthy donors was identified for RASSF1A (0.96); AHRR (0.75); MGMT (0.65); RUNX3 (0.41), APC1A (0.25). For tumor suppressor P16, only one case of increased methylation was recorded (Met = 15%), despite the fact that this phenomenon is not uncommon for NETs of other localizations. In 66% of pancreatic NET cases, hypermethylation of more than two promoters of tumor suppressor genes was noted. An association tendency was found between the presence of MEN1 mutations and the RASSF1A methylation level (p = 0.08). Correlation analysis revealed a significant level of negative association between changes in methylation of MLH1 and AHRR (p < 0.01); for the latter, the prognostic value of a high methylation status and a better prognosis for many malignant neoplasms were described. Conclusions: In the present study, significant methylation of the promoters of the APC1A, DAPK, MGMT, RASSF1A, and RUNX3 genes in well-differentiated pancreatic NETs was identified with a high frequency. At the same time, isolated cases of hypermethylation were noted for the well-known tumor suppressors MLH1 and P16.


Blood ◽  
2016 ◽  
Vol 128 (13) ◽  
pp. 1735-1744 ◽  
Author(s):  
Niels Weinhold ◽  
Cody Ashby ◽  
Leo Rasche ◽  
Shweta S. Chavan ◽  
Caleb Stein ◽  
...  

Key PointsHits in driver genes and bi-allelic events affecting tumor suppressors increase apoptosis resistance and proliferation rate–driving relapse. Excessive biallelic inactivation of tumor suppressors in high-risk cases highlights the need for TP53-independent therapeutic approaches.


2017 ◽  
Vol 15 (8) ◽  
pp. 1051-1062 ◽  
Author(s):  
Kyrie Pappas ◽  
Jia Xu ◽  
Sakellarios Zairis ◽  
Lois Resnick-Silverman ◽  
Francesco Abate ◽  
...  

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1388-1388
Author(s):  
Xiaomei Chen ◽  
Fang Liu ◽  
Wei Xiong ◽  
Xiangjun Chen ◽  
Cong Lu ◽  
...  

Abstract Abstract 1388 Microvesicles(MVs) are small exosomes of endocytic origin released by normal healthy or damaged cell types, including leukemic cells. MVs have been considered as cell dust, however, recent data bring evidences that MVs generated during cell activation or apoptosis can transfer biologic messages between different cell types. MicroRNAs (miRNAs) have been demonstrated to be aberrantly expressed in leukemia and the overall miRNA expression could differentiate normal versus leukemia. The MVs expressing miRNAs were found in the primary tumors. However it is currently unknown whether miRNA content changes in MVs derived from leukemic cells. Here we compared the miRNA expression in leukemia-derived MVs to corresponding leukemia cells and analysed their roles in leukemia. K562 cells were cultured and collected. MVs derived from K562 cells were also isolated. The presence and levels of specific miRNAs from both MVs derived from K562 cells and K562 cells were determined by Agilent miRNA microarray analysis probing for 888 miRNAs. Some selected miRNAs were verified by real time qRT-PCR. Bioinformatic software tools were used to predict the target genes of identified miRNAs and define their function. Our results showed that 77 and 122 miRNAs were only expressed in MVs and K562 cells, respectively. There were significant differences in miRNA expression profiles between MVs and K562 cells. We also found that 112 miRNAs were co-expressed in MVs and K562 cells. This observaton may suggest that compartmentalization of miRNAs from cells into to MVs, for at least some miRNAs, is an active (selective) process. Among those abnormally expressed miRNAs, some have been proposed oncomiRNAs or tumor suppressors. For example, miR-155, has been proposed as oncomiRNA, was abnormally expressed only in MVs in our study, suggesting that oncomiRNA was present in MVs. Further analysis revealed that 39 potential target genes regulated by miR-155. Among them, 4 genes involed in oncogenes and the signal genes. OncomiRNAs such as miR-27a and miR-21 expressed in both MVs and corresponding cells, indicating that MVs bear miRNA characteristic of the cell origin. MVs, released into the leukemia microenvironment, play an important role in leukemia. In contrast to oncomiRNAs, if miRNA is associated with tumor suppressive activity, it is regarded as a tumor suppressor (oncosuppressor). The aberrantly expressed miR-125a-3p, miR-125-5p,miR-27b, which have implicated as tumor suppressors, appear in both cellular and MVs of leukemia in our study. MiR-125a-3p, miR-125-5p and miR-27b regulated 308 potential target genes. To our knowledge, 10 of them are tumor suppression genes. It is possible that these aberrantly expressed tumor suppressor miRNAs decreased or lost their roles of tumor suppression, which led to decrease or loss their roles of regulating their target genes including oncogenes, consequently resulted in leukemia. Since K562 cells presented t(9;22), we further examined the predicted function of the 6 expressed miRNAs located in chrosome 9 (hsa-miR-188-5p,hsa-miR-602)and 22(hsa-let-7b,hsa-miR-1249,hsa-miR-130b,hsa-miR-185), which expressed both in the MVs and K562 cells. Using the TargetScan, we found 442 predicted targets regulated by 6 miRNAs. Those miRNAs may play roles in leukemia via these 422 genes. This study is the first to identify and define miRNA expression between K562 cells presented t(9;22), derived from K562 cells and their corresponding cells. We found significant differences in miRNA expression between MVs and corresponding leukemia. K562 cells released MVs riched in miRNAs including oncomiRNAs or tumor suppressor miRNAs into leukemia microenvironment, which play a role in leukemia via regulating their targer genes including oncogenes, consequently resulted in leukemia. Disclosures: No relevant conflicts of interest to declare.


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