scholarly journals Pax-5 Protein Expression Is Regulated by Transcriptional 3′UTR Editing

Cells ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 76
Author(s):  
Annie-Pier Beauregard ◽  
Brandon Hannay ◽  
Ehsan Gharib ◽  
Nicolas Crapoulet ◽  
Nicholas Finn ◽  
...  
Keyword(s):  
Protein Expression ◽  
Molecular Mechanisms ◽  
Alternative Polyadenylation ◽  
Regulatory Elements ◽  
Genetic Alterations ◽  
Leukemic Cells ◽  
Aberrant Expression ◽  
Rapid Amplification ◽  
Cell Commitment ◽  
And Function

The Pax-5 gene encodes a transcription factor that is essential for B-cell commitment and maturation. However, Pax-5 deregulation is associated with various cancer lesions, notably hematopoietic cancers. Mechanistically, studies have characterized genetic alterations within the Pax-5 locus that result in either dominant oncogenic function or haploinsufficiency-inducing mutations leading to oncogenesis. Apart from these mutations, some examples of aberrant Pax-5 expression cannot be associated with genetic alterations. In the present study, we set out to elucidate potential alterations in post-transcriptional regulation of Pax-5 expression and establish that Pax-5 transcript editing represents an important means to aberrant expression. Upon the profiling of Pax-5 mRNA in leukemic cells, we found that the 3′end of the Pax-5 transcript is submitted to alternative polyadenylation (APA) and alternative splicing events. Using rapid amplification of cDNA ends (3′RACE) from polysomal fractions, we found that Pax-5 3′ untranslated region (UTR) shortening correlates with increased ribosomal occupancy for translation. These observations were also validated using reporter gene assays with truncated 3′UTR regions cloned downstream of a luciferase gene. We also showed that Pax-5 3′UTR editing has direct repercussions on regulatory elements such as miRNAs, which in turn impact Pax-5 protein expression. More importantly, we found that advanced staging of various hematopoietic cancer lesions relates to shorter Pax-5 3′UTRs. Altogether, our findings identify novel molecular mechanisms that account for aberrant expression and function of the Pax-5 oncogene in cancer cells. These findings also present new avenues for strategic intervention in Pax-5-mediated cancers.

scholarly journals Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

2020 ◽  
Author(s):  
Konstantin Okonechnikov ◽  
Aylin Camgoz ◽  
Donglim Esther Park ◽  
Owen Chapman ◽  
Jens-Martin Hübner ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Chromosomal Rearrangements ◽  
Regulatory Elements ◽  
Genetic Alterations ◽  
Aberrant Expression ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Disease Subtype ◽  
Expression Of Genes ◽  
Novel Therapeutic

Abstract Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial RELA-fusion associated group and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment1. Although the molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF (insulators) and H3K27ac (active enhancers) ChIP-seq as well as gene expression and whole-genome DNA methylation profiling in primary and relapsed ependymoma tumors and cell lines to identify chromosomal rearrangements and regulatory mechanisms underlying aberrant expression of genes that are essential for ependymoma tumorigenesis. In particular, we observe the formation of new topologically associating domains (‘neo-TADs’) by intra- and inter-chromosomal structural variants, tumor-specific 3D chromatin complexes of regulatory elements, and the replacement of CTCF insulators by DNA hyper-methylation as novel oncogenic mechanisms in ependymoma. Through inhibition experiments we validated that the newly identified genes, including RCOR2, ITGA6, LAMC1, and ARL4C, are highly essential for the survival of patient-derived ependymoma models in a disease subtype-specific manner. Thus, this study identifies potential novel therapeutic vulnerabilities in ependymoma and extends our ability to reveal tumor-dependency genes and pathways by oncogenic 3D genome conformations even in tumors that lack known genetic alterations.

scholarly journals Transcription of the Human 5-Hydroxytryptamine Receptor 2B (HTR2B) Gene Is under the Regulatory Influence of the Transcription Factors NFI and RUNX1 in Human Uveal Melanoma

2018 ◽  
Vol 19 (10) ◽  
pp. 3272 ◽  
Author(s):  
Manel Benhassine ◽  
Sylvain Guérin
Keyword(s):  
Transcription Factors ◽  
Uveal Melanoma ◽  
Serotonin Receptor ◽  
Molecular Mechanisms ◽  
Regulatory Region ◽  
Gene Signature ◽  
Regulatory Elements ◽  
Gene Encoding ◽  
Aberrant Expression ◽  
Factor I

Because it accounts for 70% of all eye cancers, uveal melanoma (UM) is therefore the most common primary ocular malignancy. In this study, we investigated the molecular mechanisms leading to the aberrant expression of the gene encoding the serotonin receptor 2B (HTR2B), one of the most discriminating among the candidates from the class II gene signature, in metastatic and non-metastatic UM cell lines. Transfection analyses revealed that the upstream regulatory region of the HTR2B gene contains a combination of alternative positive and negative regulatory elements functional in HTR2B− but not in HTR23B+ UM cells. We demonstrated that both the transcription factors nuclear factor I (NFI) and Runt-related transcription factor I (RUNX1) interact with regulatory elements from the HTR2B gene to either activate (NFI) or repress (RUNX1) HTR2B expression in UM cells. The results of this study will help understand better the molecular mechanisms accounting for the abnormal expression of the HTR2B gene in uveal melanoma.

scholarly journals Human erythroleukemia genetics and transcriptomes identify master transcription factors as functional disease drivers

Blood ◽  
2020 ◽  
Vol 136 (6) ◽  
pp. 698-714 ◽  
Author(s):  
Alexandre Fagnan ◽  
Frederik Otzen Bagger ◽  
Maria-Riera Piqué-Borràs ◽  
Cathy Ignacimouttou ◽  
Alexis Caulier ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Hematologic Malignancy ◽  
Ectopic Expression ◽  
Leukemic Cells ◽  
Erythroid Progenitors ◽  
Molecular Subgroup ◽  
Aberrant Expression ◽  
In Vivo Models ◽  
Hematopoietic Stem

Abstract Acute erythroleukemia (AEL or acute myeloid leukemia [AML]-M6) is a rare but aggressive hematologic malignancy. Previous studies showed that AEL leukemic cells often carry complex karyotypes and mutations in known AML-associated oncogenes. To better define the underlying molecular mechanisms driving the erythroid phenotype, we studied a series of 33 AEL samples representing 3 genetic AEL subgroups including TP53-mutated, epigenetic regulator-mutated (eg, DNMT3A, TET2, or IDH2), and undefined cases with low mutational burden. We established an erythroid vs myeloid transcriptome-based space in which, independently of the molecular subgroup, the majority of the AEL samples exhibited a unique mapping different from both non-M6 AML and myelodysplastic syndrome samples. Notably, >25% of AEL patients, including in the genetically undefined subgroup, showed aberrant expression of key transcriptional regulators, including SKI, ERG, and ETO2. Ectopic expression of these factors in murine erythroid progenitors blocked in vitro erythroid differentiation and led to immortalization associated with decreased chromatin accessibility at GATA1-binding sites and functional interference with GATA1 activity. In vivo models showed development of lethal erythroid, mixed erythroid/myeloid, or other malignancies depending on the cell population in which AEL-associated alterations were expressed. Collectively, our data indicate that AEL is a molecularly heterogeneous disease with an erythroid identity that results in part from the aberrant activity of key erythroid transcription factors in hematopoietic stem or progenitor cells.

scholarly journals Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

2020 ◽  
Vol 217 (9) ◽  
Author(s):  
Agata Cieslak ◽  
Guillaume Charbonnier ◽  
Melania Tesio ◽  
Eve-Lyne Mathieu ◽  
Mohamed Belhocine ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
T Cell ◽  
Molecular Mechanisms ◽  
Lymphoblastic Leukemia ◽  
Ectopic Expression ◽  
Regulatory Elements ◽  
T Cell Differentiation ◽  
Epigenetic Changes ◽  
Human T Cell ◽  
Cell Commitment

Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints.

Targeting the Hypoxic Microenvironment by mTOR Inhibitors Sensitizes ALL Cells to Chemotherapy

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 18-18 ◽  
Author(s):  
Olga Frolova ◽  
Ismael J. Samudio ◽  
Zakar H. Mnjoyan ◽  
Hongbo Lu ◽  
Sergej Konoplev ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Akt Signaling ◽  
Bone Marrow Microenvironment ◽  
Leukemic Cells ◽  
Mtor Inhibition ◽  
Hypoxic Conditions ◽  
And Function ◽  
Reh Cells

Abstract The main therapeutic challenge in the treatment of Acute Lymphocytic Leukemia (ALL) is the development of strategies aimed at overcoming resistance to chemotherapy. Interactions between leukemia cells and microenvironment promote leukemia cell survival and confer resistance to drugs commonly used to treat ALL. Recent reports indicate that the endosteum at the murine bone-bone marrow (BM) interface is hypoxic, and data in a rat model demonstrate that leukemic cells infiltrating bone marrow were markedly hypoxic compared to cells in bone marrow of healthy rats. Hypoxia-inducible factor 1α (HIF-1α) is a key regulator of the cellular response to hypoxia. To characterize expression and function of HIF-1α in the bone marrow from ALL patients, HIF-1α expression was analyzed by immunohistochemistry in the bone marrow specimens from 16 newly diagnosed patients with pre-B ALL. HIF-1α was found to be expressed in 10/16 samples tested (62.5%). Of the 16 patients, 5 patients subsequently relapsed, all of which have expressed HIF-1α at diagnosis. No relapses were seen in the 6 patients with negative HIF-1α levels at presentation. To examine the molecular mechanisms of survival of leukemic cells growing under hypoxic conditions of bone marrow microenvironment, we established a co-culture system of pre-B ALL cells with BM-derived mesenchymal stem cells (MSC). Culture of REH cells under hypoxia (1% O2) resulted in induction of HIF-1α protein which was further increased in leukemia/stroma co-culture. Exposure of cells to hypoxia resulted in robust activation of AKT phosphorylation in leukemic cells. We have recently demonstrated that rapamycin analogs inhibit AKT signaling in AML cells via inhibition of mTORC2 formation (Zeng et al., Blood 109:3509-12, 2007). Likewise, mTOR inhibition by RAD001 completely blocked HIF-1α and pAKT in REH cells. Importantly, REH cells co-cultured with MSC under hypoxia/high glucose environment exhibited significantly lower apoptotic rates (p=0.02) and growth inhibition (p=0.002) in response to vincristine, and these effects were reversed by mTOR blockade with RAD001. We have further demonstrated that inhibition of mTOR signaling reduced expression of the glucose transporter Glut-1 and diminished glucose flux, decreased glycolytic rate and ATP production, both in leukemic cell lines and in primary ALL blasts (n=8). This was associated with decreased mitochondrial membrane potential and inhibition of the hypoxia-induced hexokinase (HKII) in the mitochondrial fraction of ALL cells. In summary, data suggest that mTOR/AKT signaling critically controls HIF-1α expression and function in ALL cells studied under the hypoxic conditions characteristic of bone marrow microenvironment. Hence, mTOR inhibition or blockade of HIF-1α-mediated pro-survival signaling events may reverse microenvironment-mediated chemoresistance and improve clinical outcomes in ALL.

The frequency of a novel KANK1 and NTRK3 translocation and BRAFV600E mutation in patients diagnosed with metanephric adenoma utilizing molecular mechanisms.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 1537-1537
Author(s):  
Aida Catic ◽  
Ardis Sophian ◽  
Lech Mazur ◽  
Dinesh Rakheja ◽  
Amina Kurtovic Kozaric ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cancer Genomics ◽  
Renal Tumor ◽  
Wilms Tumor ◽  
Prognostic Significance ◽  
Genetic Alterations ◽  
Chromosome 9 ◽  
Metanephric Adenoma ◽  
Aberrant Expression

1537 Background: Renal metanephric adenoma (MA) is a very rare benign renal tumor, which is frequently misclassified when microscopic features alone are applied. Despite the classification of adenoma as a benign tumor, it is difficult to differentiate from other renal carcinomas such as malignant papillary renal cell carcinomas and in children it can be mistaken with Wilms tumor. The correct classification of a renal tumor is critical for diagnostic, prognostic, and therapeutic purposes. Despite the advancements in cancer genomics, there is limited data available regarding the genetic alterations critical to the metanephric adenoma development. Recent data suggest that 90% of MA have BRAFV600Emutations; the genetics of the remaining 10 % are unclear. Methods: This study was conducted on 13 FFPE specimens from patients who were diagnosed with renal metanephric adenoma. H&E stained slides from all cases were reviewed by study pathologist, and representative tissue blocks were further selected for BRAFV600E sequencing and fluorescent in situ hybridization was adapted to detect chromosomal rearrangement between KANK1 on chromosome 9 (9p24.3) and NTRK3 on chromosome 15 (15q25.3). Results: In this study, we identified a novel chromosomal translocation t(9;15)(p24;q24) between KANK1 and NTRK3, and provided new insights into molecular mechanisms which might identify a subset of metanephric adenomas. Such findings imply that recurrent cytogenetic aberrations may be of prognostic significance as well. Interestingly, our data suggested mutual exclusivity of BRAFV600Eand t(9;15) aberrations. Conclusions: Molecular and cytogenetic analyses have allowed us to elucidate a genetic aberration, which may be specific to metanephric adenoma. Aberrant expression of the KANK1-NTRK3 gene fusion may be one mechanism by which functionally relevant genes are altered in the development of metanephric adenoma, and thus mark a subgroup of metanephric adenomas with particular clinicopathological features. Also, our study adds KANK1 and NTRK3 to the list of candidate genes that may play a role in the 10% of renal metanephric adenomas that lack a BRAFV600E mutation.

scholarly journals Association of Bax Expression and Bcl2/Bax Ratio with Clinical and Molecular Prognostic Markers in Chronic Lymphocytic Leukemia

2016 ◽  
Vol 35 (2) ◽  
pp. 150-157 ◽  
Author(s):  
Ksenija Vucicevic ◽  
Vladimir Jakovljevic ◽  
Natasa Colovic ◽  
Natasa Tosic ◽  
Tatjana Kostic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Lymphocytic Leukemia ◽  
Mononuclear Cells ◽  
Prognostic Markers ◽  
Statistical Significance ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells ◽  
Aberrant Expression ◽  
Mutational Status

Summary Background: In chronic lymphocytic leukemia (CLL), in vivo apoptotic resistance of malignant B lymphocytes results, in part, from the intrinsic defects of their apoptotic machinery. These include genetic alterations and aberrant expression of many apoptosis regulators, among which the Bcl2 family members play a central role. Aim: The aim of this study was to investigate the association of pro-apoptotic Bax gene expression and Bcl2/Bax ratio with the clinical features of CLL patients as well as with molecular prognostic markers, namely the mutational status of rearranged immunoglobulin heavy variable (IGHV) genes and lipoprotein lipase (LPL) gene expression. Methods: We analyzed the expression of Bax mRNA and Bcl2/Bax mRNA ratio in the peripheral blood mononuclear cells of 58 unselected CLL patients and 10 healthy controls by the quantitative reverse-transcriptase polymerase chain reaction. Results: We detected significant Bax gene overexpression in CLL samples compared to non-leukemic samples (p=0.003), as well as an elevated Bcl2/Bax ratio (p=<0.001). Regarding the association with prognostic markers, the Bcl2/Bax ratio showed a negative correlation to lymphocyte doubling time (r=−0.307; p=0.0451), while high-level Bax expression was associated with LPL-positive status (p=0.035). Both the expression of Bax and Bcl2/Bax ratio were higher in patients with unmutated vs. mutated IGHV rearrangements, but this difference did not reach statistical significance. Conclusions: Our results suggest that dysregulated expression of Bcl2 and Bax, which leads to a high Bcl2/Bax ratio in leukemic cells, contributes to the pathogenesis and clinical course of CLL.

scholarly journals Pathophysiological Role of K2P Channels in Human Diseases

2021 ◽  
Vol 55 (S3) ◽  
pp. 65-86
Keyword(s):  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Expression Patterns ◽  
Ion Homeostasis ◽  
Human Diseases ◽  
Cellular Functions ◽  
Aberrant Expression ◽  
K2p Channels ◽  
And Function

The family of two-pore domain potassium (K2P) channels is critically involved in central cellular functions such as ion homeostasis, cell development, and excitability. K2P channels are widely expressed in different human cell types and organs. It is therefore not surprising that aberrant expression and function of K2P channels are related to a spectrum of human diseases, including cancer, autoimmune, CNS, cardiovascular, and urinary tract disorders. Despite homologies in structure, expression, and stimulus, the functional diversity of K2P channels leads to heterogeneous influences on human diseases. The role of individual K2P channels in different disorders depends on expression patterns and modulation in cellular functions. However, an imbalance of potassium homeostasis and action potentials contributes to most disease pathologies. In this review, we provide an overview of current knowledge on the role of K2P channels in human diseases. We look at altered channel expression and function, the potential underlying molecular mechanisms, and prospective research directions in the field of K2P channels.

P1890Pioglitazone inhibits diabetes-induced atrial mitochondrial oxidative stress and improves mitochondrial biogenesis, dynamics and function through the PGC-1 signaling pathway

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
T Liu ◽  
Z Zhang ◽  
X Zhang ◽  
L Meng ◽  
M Gong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Diabetes Mellitus ◽  
Protein Expression ◽  
Molecular Mechanisms ◽  
Mitochondrial Morphology ◽  
Atrial Remodeling ◽  
Ppar Γ ◽  
And Function ◽  
Related Proteins ◽  
Tgf Β1

Abstract Background Oxidative stress contributes to adverse atrial remodeling in diabetes mellitus. This can be prevented by the PPAR-γ agonist pioglitazone through its anti-oxidant and anti-inflammatory effects. Purpose In this study, the molecular mechanisms underlying these effects were investigated. Methods Rabbits were randomly divided into control (C), diabetic (DM), and pioglitazone-treated DM (Pio) groups. Echocardiographic, hemodynamic, electrophysiological, intracellular Ca2+ properties were measured. Serum PPAR-γ levels, serum and tissue oxidative stress and inflammatory markers, mitochondrial morphology, reactive oxygen species (ROS) production rate, respiratory function, and mitochondrial membrane potential (MMP) levels were measured. Protein expression of pro-fibrotic marker transforming growth factor β1 (TGF-β1), and the mitochondrial proteins (PGC-1α, fission and fusion-related proteins) were measured. Results Compared with controls, the DM group demonstrated larger left atrial diameter and fibrosis area associated with a higher incidence of inducible AF. Lower serum PPAR-γ level was associated with lower PGC-1α, higher NF-κB and higher TGF-β1 expression. Mn-SOD protein was not different but lower mitochondrial fission- and fusion-related proteins were detected. Mitochondrial swelling, higher mitochondrial ROS, lower respiratory control rate, lower MMP and higher intracellular Ca2+ transients were observed. In the Pio group, reversal of structural remodeling and lower inducible AF incidence were associated with higher PPAR-γ and PGC-1α. NF-κB and TGF-β1 were lower and biogenesis, fission and fusion-related protein were higher. Mitochondrial structure and function, and intracellular Ca2+ transients were improved. In HL-1 cell line, transfected with PGC-1α siRNA blunted the effect of pioglitazone on Mn-SOD protein expression and MMP collapse in H2O2-treated cells. Conclusion Diabetes mellitus induces adverse atrial structural and electrophysiological remodeling, abnormal Ca2+ handling and mitochondrial damage and dysfunction. Pioglitazone prevented these abnormalities through the PPAR-γ/PGC-1α pathway. Acknowledgement/Funding National Natural Science Foundation of China (No 81570298, 81270245, 30900618 to T.L.)

scholarly journals Molecular mechanisms of somatostatin-mediated intestinal epithelial barrier function restoration by upregulating claudin-4 in mice with DSS-induced colitis

2018 ◽  
Vol 315 (4) ◽  
pp. C527-C536 ◽  
Author(s):  
Lin Cai ◽  
Xiao Li ◽  
Chong Geng ◽  
Xuelian Lei ◽  
Chunhui Wang
Keyword(s):  
Barrier Function ◽  
Molecular Mechanisms ◽  
Intestinal Barrier ◽  
Regulatory Elements ◽  
Barrier Structure ◽  
Barrier Dysfunction ◽  
Epithelial Barrier Function ◽  
Treatment Regimens ◽  
Tnf Α ◽  
And Function

Intestinal barrier dysfunction plays a crucial role in the pathogenesis of ulcerative colitis (UC). Previous studies have shown somatostatin (SST) can protect intestinal barrier structure possibly through upregulating tight junction (TJ) protein expression, but the mechanisms of this upregulation remain undefined. This study aimed to investigate the molecular mechanisms of interaction of SST with its downstream regulatory elements in DSS-induced colitis mice. In DSS-induced colitis mice, exogenous SST supplement (octreotide) effectively ameliorated disease progression, restored colonic barrier structure and function, and stimulated claudin-4 expression. Similar effects were also observed for SST on Caco-2 cells intervened by TNF-α. SST receptor 5 (SSTR5) agonist L-817,818 upregulated the claudin-4 expression whereas the SSTR2 agonist seglitide could not reverse TNF-α-induced reduction of claudin-4. SST treatment significantly decreased the phosphorylation levels of ERK1/2 and p38 induced by TNF-α. PD-98059 (ERK1/2 pathway inhibitor) but not SB-202190 (p38 pathway inhibitor) could reverse TNF-α-induced suppression of claudin-4 expression. Both inhibitors could improve the TJ barrier function damaged by TNF-α. Our studies suggest that the protective effect of SST on intestinal barrier achieved by upregulating claudin-4 expression through activation of SSTR5 and suppression of the ERK1/2 pathways. These findings will benefit the development of novel treatment regimens for UC.

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