Wild-type Promoter Research Articles

Integrated Analysis of Altered lncRNA, circRNA, microRNA, and mRNA Expression in Hepatocellular Carcinoma Carrying TERT Promoter Mutations.

Telomerase reverse transcriptase (TERT) promoter mutations are one of the most common mutations responsible for the development of hepatocellular carcinoma (HCC). Noncoding RNAs (ncRNAs) play a regulatory role in different cancers through the long noncoding RNA (lncRNA)/circular RNA (circRNA)-microRNA (miRNA)-mRNA axis. The aim of the study was to explore the influence of TERT promoter mutations on the ncRNA regulatory network in HCC. Four tumor samples with a wildtype TERT promoter and four tumor samples with TERT promoter mutations (sequencing cohort) were collected from HCC patients for high-throughput next-generation sequencing. Selected ncRNAs and mRNAs were validated by qPCR in 15 HCC tumors with a wildtype TERT promoter and seven HCC tumors with TERT promoter mutations (validation cohort, including the sequencing cohort). In the mutant TERT promoter group, 536 lncRNAs, 21 circRNAs, 41 miRNAs, and 266 mRNAs were significantly up-regulated, while 1745 lncRNAs, 23 circRNAs, 32 miRNAs, and 1117 mRNAs were significantly down-regulated (P < 0.05) compared with the findings in wildtype group. AL360169.3-201, LINC02672-203, hsa_circ_0021412, hsa-miR-29b-1-5p, hsa-miR-4699-5p, hsa-miR-199a-5p, REG3A, SFRP5, and GSTM1 were verified at the RNA expression level to validate the sequencing results. A differentially expressed lncRNA/circRNA-miRNA-mRNA network was constructed to explore the effects of TERT promoter mutations on ncRNA regulation. Two ncRNA regulatory axes associated with TERT promoter mutations (hsa_circ_0003154/hsa_circ_0008952/IGLL5-AS1/LINC576/LINC575-hsa-miR-1260b -CLPTM1L/GSTM1 and hsa_circ_0031584/LINC2101-hsa-miR-214-3p-CD151) had carcinogenic potential. This study provides novel insights into the role of TERT promoter mutations on ncRNAs regulatory network in HCC progression.

Identification and functional analysis of genetic variants of ISL1 gene promoter in human atrial septal defects.

Atrial septal defect (ASD) is a common type of congenital heart disease. A gene promoter plays pivotal role in the disease development. This study was designed to investigate the pathological role of variants of the ISL1 gene promoter region in ASD patients. Total DNA extracted from 625 subjects, including 332 ASD patients and 293 healthy controls, was sequenced to identify variants in the promoter region of ISL1 gene. Further functional analyses of the variants were performed with dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). All possible binding sites of transcription factor affected by the identified variants were predicted using the JASPAR database. Four variants in the ISL1 gene promoter were found only in patients with ASD by sequencing. Three of the four variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] significantly decreased the transcriptional activities compared with the wild-type ISL1 gene promoter (p < 0.05). The EMSA revealed that these variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] in the ISL1 gene promoter affected the number and affinity of binding sites of transcription factors. Further analysis with the online JASPAR database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants. These sequence variants identified from the promoter region of ISL1 gene in ASD patients are probably involved in the development of ASD by affecting the transcriptional activity and altering ISL1 levels. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of ASD.

C-Jun-mediated miR-19b expression induces endothelial barrier dysfunction in an in vitro model of hemorrhagic shock

BackgroundOur previous data demonstrated that miR-19b expression was increased in human lung microvascular endothelial cells in-vitro-, in-vivo and in patients with hemorrhagic shock, leading to a decrease in syndecan-1 mRNA and protein and resulting in loss of endothelial barrier function. However, the mechanism underlying increased miR-19b expression remains unclear. The objective of the current study was to determine if c-Jun mediates the early responsive microRNA, miR-19b, to cause endothelial barrier dysfunction.MethodHuman lung microvascular endothelial cells (HLMEC) or HEK293T cells were transfected with c-Jun overexpressing vector, c-Jun siRNA, miR-19b promoter vector, miR-19b mutated promoter vector, miR-19b oligo inhibitor, then subjected to hypoxia/reoxygenation as in-vitro model of hemorrhagic shock. Levels of protein, miRNA, and luciferase activity were measured. Transwell permeability of endothelial monolayers were also determined. Plasma levels of c-Jun were measured in injured patients with hemorrhagic shock.ResultHypoxia/reoxygenation induced primary (pri-)miR-19b, mature miR-19b, and c-Jun expression over time in a comparable timeframe. c-Jun silencing by transfection with its specific siRNA reduced both pri-miR-19b and mature miR-19b levels. Conversely, c-Jun overexpression enhanced H/R-induced pri-miR-19b. Studies using a luciferase reporter assay revealed that in cells transfected with vectors containing the wild-type miR-19b promoter and luciferase reporter, c-Jun overexpression or hypoxia/ reoxygenation significantly increased luciferase activity. c-Jun knockdown reduced the luciferase activity in these cells, suggesting that the miR-19b promoter is directly activated by c-Jun. Further, chromatin immunoprecipitation assay confirmed that c-Jun directly bound to the promoter DNA of miR-19b and hypoxia/reoxygenation significantly increased this interaction. Additionally, c-Jun silencing prevented cell surface syndecan-1 loss and endothelial barrier dysfunction in HLMECs after hypoxia/reoxygenation. Lastly, c-Jun was significantly elevated in patients with hemorrhagic shock compared to healthy controls.ConclusionTranscription factor c-Jun is inducible by hypoxia/reoxygenation, binds to and activates the miR-19b promoter. Using an in-vitro model of hemorrhagic shock, our findings identified a novel cellular mechanism whereby hypoxia/ reoxygenation increases miR-19b transcription by inducing c-Jun and leads to syndecan-1 decrease and endothelial cell barrier dysfunction. This finding supports that miR-19b could be a potential therapeutic target for hemorrhage shock.

Nonclassic Adrenal Hyperplasia (NCAH) due to 21-hydroxylase deficiency: A cohort of 78 patients

Diagnosis of nonclassic adrenal hyperplasia (NCAH) due to 21-hydroxylase deficiency (21-OHD) may be challenging due to its occult manifestations. To characterize clinical and molecular features of NCAH patients due to 21-hydroxylase deficiency, we retrospectively included 78 NCAH patients. Their phenotype and genotype were presented and compared. The transcription activities of novel CYP21A2 promoter variants were investigated using a dual-reporter luciferase assay system. This cohort included 53 females (68 %) and 25 males (32 %). The median of onset age was 13 years old (female: 13 range from 7 to 38; male: 11 range from 6 to 71). Menstrual cycle disorder was the most common complaint in females (62 %, n = 33) and for males, it was adrenal incidentalomas (52 %, n = 13). A total of 17 (22 %) patients complained of infertility. The most frequently variant was p.Ile173Asn (20 %, n = 31). Importantly, five variants in the promoter region including − 103/− 126 and − 196/− 296 were found in 21 (27 %) patients. Patients with promoter variants showed older onset age and less impaired hormone levels of 17-hydroxyprogesterone, ACTH, progesterone, and androstenedione. Compared with the wild-type promoter, the basic transcription activity of − 103/− 126 and − 196/− 296 promoter variants were reduced by 57% and 25%, respectively. Therefore, females with menstrual cycle disorders or infertility and males with adrenal incidentaloma should be considered of NCAH due to 21-OHD. When genotyping patients with NCAH, the promoter region of the CYP21A2 gene should be also investigated.

P16.03.A Epithelioid gliobastoma requires rapid treatment and BRAF inhibitors should be made readily available for their treatment

Abstract Background Epithelioid glioblastoma is a rare subtype of Glioblastoma. We examine two cases who presented acutely with symptoms of headache, neck stiffness and an eye squint. The purpose of this case review is to look at their management, the spread of the disease and propose the availability of BRAF inhibiting agents be made readily available for this subtype. Material and Methods The clinical records including pathology and surgical reports, multi-disciplinary team meeting documents, oncology plans and inpatient notes have all been reviewed alongside the literature on epithelioid GBM and BRAF V600e mutations and inhibitors. Results Patients were females aged 25 and 32 presenting with acute onset headache and neck stiffness to emergency Department. The 25 year old had developed a right eye squint within seven days of the other symptoms, her tumour was right frontal with midline shift. The 32 year old had symptoms for 10 days prior to presentation, the tumour was right temporal. They both underwent craniotomies. The frontal tumour was totally resected, while the temporal lobe tumour was haemorrhagic in nature and minimally de-bulked. Pre-operative stealth imaging showed that there had been an increase in the size of the temporal lesion in the fourteen days since presentation. Histology proved these to be epithelioid GBM’s with BRAF V600e mutations, IDH wild-type and TERT promoter mutant. Full pathology reports with molecular markers were available within ten days. The frontal lobe patient began chemo-radiation sixteen days from her surgical date. On day two she was admitted with severe headache and nausea. She became agitated, confused, and transferred back to the neurosurgery unit for management of hydrocephalus. She was diagnosed with PRES and simultaneously treated for this and hydrocephalus. Clinically she suffered storming, passing away exactly eight weeks from presentation. Seven days after surgery the temporal lobe tumour patient suffered a seizure and admitted for symptom management and expedite oncology treatment. She passed away six days later suffering continual neurological deterioration and the tumour progression with leptomeningeal spread. This was exactly four weeks from initial presentation. Conclusion The prognosis for epithelioid Glioblastoma is limited to weeks to short months. Extent of resection in these case studies demonstrates benefit in delaying progression though it is clear that time is of the essence from presentation, to surgery, to adjuvant treatment. Neither of these tumours were methylated meaning the standard treatment for glioblastoma is likely to lack efficacy. BRAF inhibitors should be made readily available for this rare sub-type to commence treatment expediently. Both patients suffered distressing neurological symptoms in their final days which require expert management and are best managed in a neurosurgical centre.

VIPR1 promoter methylation promotes transcription factor AP-2α binding to inhibit VIPR1 expression and promote hepatocellular carcinoma cell growth in vitro

To explore the transcriptional regulation mechanism and biological function of low expression of vasoactive intestinal peptide receptor 1 (VIPR1) in hepatocellular carcinoma (HCC). We constructed plasmids carrying wild-type VIPR1 promoter or two mutant VIPR1 promoter sequences for transfection of the HCC cell lines Hep3B and Huh7, and examined the effect of AP-2α expression on VIPR1 promoter activity using dual-luciferase reporter assay. Pyrosequencing was performed to detect the changes in VIPR1 promoter methylation level in HCC cells treated with a DNA methyltransferase inhibitor (DAC). Chromatin immunoprecipitation was used to evaluate the binding ability of AP-2α to VIPR1 promoter. Western blotting was used to assess the effect of AP-2α knockdown on VIPR1 expression and examine the differential expression of VIPR1 in the two cell lines. The effects of VIPR1 overexpression and knockdown on the proliferation, cell cycle and apoptosis of HCC cells were analyzed using CCK8 assay and flow cytometry. We also observed the growth of HCC xenograft with lentivirus-mediated over-expression of VIPR1 in nude mice. Compared with the wild-type VIPR1 promoter group, co-transfection with the vector carrying two promoter mutations and the AP-2α-over-expressing plasmid obviously restored the luciferase activity in HCC cells (P < 0.05). DAC treatment of the cells significantly decreased the methylation level of VIPR1 promoter and inhibited the binding of AP-2α to VIPR1 promoter (P < 0.01). The HCC cells with AP-2α knockdown showed increased VIPR1 expression, which was lower in Huh7 cells than in Hep3B cells. VIPR1 overexpression in HCC cells caused significant cell cycle arrest in G2/M phase (P < 0.01), promoted cell apoptosis (P < 0.001), and inhibited cell proliferation (P < 0.001), while VIPR1 knockdown produced the opposite effects. In the tumor-bearing nude mice, VIPR1 overexpression in the HCC cells significantly suppressed the increase of tumor volume (P < 0.001) and weight (P < 0.05). VIPR1 promoter methylation in HCC promotes the binding of AP-2α and inhibits VIPR1 expression, while VIPR1 overexpression causes cell cycle arrest, promotes cell apoptosis, and inhibits cell proliferation and tumor growth.

Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans.

In Drosophila, pairing of maternal and paternal homologs can permit trans-interactions between enhancers on one homolog and promoters on another, an example of a phenomenon called transvection. When chromosomes are paired, promoters in cis and in trans to an enhancer can compete for the enhancer's activity, but the parameters that govern this competition are as yet poorly understood. To assess how the linear spacing between an enhancer and promoter can influence promoter competition in Drosophila, we employed transgenic constructs wherein the eye-specific enhancer GMR is placed at varying distances from a heterologous hsp70 promoter driving a fluorescent reporter. While GMR activates the reporter to a high degree when the enhancer and promoter are spaced by a few hundred base pairs, activation is strongly attenuated when the enhancer is moved 3kb away. By examining transcription of endogenous genes near the point of transgene insertion, we show that linear spacing of 3 kb between GMR and the hsp70 promoter results in elevated transcription of neighboring promoters, suggesting a loss of specificity between the enhancer and its intended transgenic target promoter. Furthermore, increasing spacing between GMR and hsp70 by just 100 bp can enhance transvection, resulting in increased activation of a promoter on a paired homolog at the expense of a promoter in cis to the enhancer. Finally, cis-/trans-promoter competition assays in which one promoter carries mutations to key core promoter elements show that GMR will skew its activity toward a wild-type promoter, suggesting that an enhancer is in a balanced competition between its potential target promoters in cis and in trans.

An IDH Wildtype, EGFR Amplified and TERT Promoter Mutated Astrocytoma that is Clinically and Molecularly Incompatible with the Diagnosis of Glioblastoma, IDH Wildtype. (P13-9.001)

An IDH Wildtype, EGFR Amplified and TERT Promoter Mutated Astrocytoma that is Clinically and Molecularly Incompatible with the Diagnosis of Glioblastoma, IDH Wildtype. (P13-9.001)

Identification and functional analysis of variants in ISL1 promoter from patients with isolated atrial septal defects

ObjectiveAtrial septal defect (ASD) is one of the most common types of congenital heart disease (CHD). As a transcription factor, ISL1 is expressed specifically in second heart field during embryogenesis and plays a crucial role in heart development and cardiovascular morphogenesis. Studies have shown association of ISL1 multiple variants with diverse type of CHD including ASD, whereas the variants of ISL1 gene promoter region in ASD patients have not been reported. We hypothesized that variants in ISL1 promoter may be involved in the formation of ASD.MethodsBlood samples from 593 subjects, including 300 patients with isolated ASD and 293 healthy controls were studied. Total DNA from all subjects was extracted and the PCR combined with Sanger sequencing was used to identify ISL1 gene promoter variants. Functional analysis of DNA sequence variants was performed using a dual luciferase reporter assay. Electrophoretic mobility shift assay (EMSA) was selected to examine the influence of the variants in ISL1 gene promoter on binding of transcription factors. All possible binding sites of transcription factor influenced by the identified variants were predicted by the PROMO database.ResultsFour variants in ISL1 gene promoter were found only in patients with ASD by sequencing. Three of the 4 variations [g.4923 G&gt;C (rs541081886), g.5079 A&gt;G (rs1371835943), g.5309 G&gt;A (rs116222082)] significantly decreased the transcriptional activities compared with the wild‐type ISL1 gene promoter (P &lt; 0.05). The EMSA revealed that these variants [g.4923 G&gt;C (rs541081886), g.5079 A&gt;G (rs1371835943), g.5309 G&gt;A (rs116222082)] in ISL1 promoter affected the number and affinity of binding sites of transcription factors. Further analysis with the online PROMO database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants.ConclusionThese sequence variants identified from the promoter region of ISL1 gene in ASD patients are likely involved in the development of ASD by affecting the transcriptional activity and altering ISL1 levels. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of ASD.

Long non-coding RNA MIR4435-2HG/microRNA-125a-5p axis is involved in myocardial ischemic injuries

ABSTRACT This study aimed to investigate whether and how long non-coding RNA (lncRNA) MIR4435-2 host gene (MIR4435-2HG) involved in acute myocardial ischemia/reperfusion (I/R). Blood samples were collected from acute myocardial infarction (AMI) patients to detect MIR4435-2HG expression. In vivo myocardial I/R mice model and in vitro H2O2-induced oxidative stress model were established. Echocardiography, TUNEL assay and lactate dehydrogenase (LDH) detection were performed to assess heart infarction and myocardium apoptosis. Relationship among microRNA-125a-5p (miR-125a-5p), MIR4435-2HG and Mitochondrial fission protein 1 (MTFP1) was predicted by Targetscan and verified by luciferase reporter assay. MIR4435-2HG was notably upregulated in AMI patients, myocardial I/R mice and H2O2-treated cells. Knockdown of MIR4435-2HG notably alleviated infraction volume, ejection fraction (EF) and fractional shortening (FS) levels, cell apoptosis portion and pro-apoptotic cleaved-caspase-3 and Cyt c expression caused by myocardial I/R and oxidative stress, as well as improved cardiomyocytes viability. Transfection with miR-125a-5p alleviated MIR4435-2HG-caused cardiomyocytes apoptosis during oxidative stress. MiR-125a-5p overexpression decreased luciferase activity of the wild-type MIR4435-2HG compared with the mutated MIR4435-2HG. The expression levels of MTFP1 were elevated in myocardium from MI mice model and H2O2-treated AC16 cardiomyocytes. In addition, miR-125a-5p overexpression inhibited MTFP1 expression, and could stimulate the wild-type MTFP1 promoter luciferase activity but not the mutated one. Our findings revealed the role of MIR4435-2HG in MI-induced myocardium injury and cardiomyocytes apoptosis, disclosed a novel MIR4435-2HG/miR-125a-5p regulatory axis during myocardial I/R, and thus identified a potential target for the therapy of myocardial IR injury.

Paradoxical Association Between Relative Cerebral Blood Volume Dynamics Following Chemoradiation and Increased Progression-Free Survival in Newly Diagnosed IDH Wild-Type MGMT Promoter Methylated Glioblastoma With Measurable Disease.

Background and PurposeWhile relative cerebral blood volume (rCBV) may be diagnostic and prognostic for survival in glioblastoma (GBM), changes in rCBV during chemoradiation in the subset of newly diagnosed GBM with subtotal resection and the impact of MGMT promoter methylation status on survival have not been explored. This study aimed to investigate the association between rCBV response, MGMT methylation status, and progression-free (PFS) and overall survival (OS) in newly diagnosed GBM with measurable enhancing lesions.Methods1,153 newly diagnosed IDH wild-type GBM patients were screened and 53 patients (4.6%) had measurable post-surgical tumor (>1mL). rCBV was measured before and after patients underwent chemoradiation. Patients with a decrease in rCBV >10% were considered rCBV Responders, while patients with an increase or a decrease in rCBV <10% were considered rCBV Non-Responders. The association between change in enhancing tumor volume, change in rCBV, MGMT promotor methylation status, and PFS or OS were explored.ResultsA decrease in tumor volume following chemoradiation trended towards longer OS (p=0.12; median OS=26.8 vs. 16.3 months). Paradoxically, rCBV Non-Responders had a significantly improved PFS compared to Responders (p=0.047; median PFS=9.6 vs. 7.2 months). MGMT methylated rCBV Non-Responders exhibited a significantly longer PFS compared to MGMT unmethylated rCBV Non-Responders (p<0.001; median PFS=0.5 vs. 7.1 months), and MGMT methylated rCBV Non-Responders trended towards longer PFS compared to methylated rCBV Responders (p=0.089; median PFS=20.5 vs. 13.8 months).ConclusionsThis preliminary report demonstrates that in newly diagnosed IDH wild-type GBM with measurable enhancing disease after surgery (5% of patients), an enigmatic non-response in rCBV was associated with longer PFS, particularly in MGMT methylated patients.

Construction and application of a synthetic promoter library for Corynebacterium glutamicum

Promoter is an important genetic tool for fine-tuning of gene expression and has been widely used for metabolic engineering. Corynebacterium glutamicum is an important chassis for industrial biotechnology. However, promoter libraries that are applicable to C. glutamicum have been rarely reported, except for a few developed based on synthetic sequences containing random mutations. In this study, we constructed a promoter library based on the native promoter of odhA gene by mutating the -10 region and the bystanders. Using a red fluorescent protein (RFP) as the reporter, 57 promoter mutants were screened by fluorescence imaging technology in a high-throughput manner. These mutants spanned a strength range between 2.4-fold and 19.6-fold improvements of the wild-type promoter. The strongest mutant exhibited a 2.3-fold higher strength than the widely used strong inducible promoter Ptrc. Sequencing of all 57 mutants revealed that 55 mutants share a 1-4 bases shift (4 bases shift for 68% mutants) of the conserved -10 motif "TANNNT" to the 3' end of the promoter, compared to the wild-type promoter. Conserved T or G bases at different positions were observed for strong, moderate, and weak promoter mutants. Finally, five promoter mutants with different strength were employed to fine-tune the expression of γ-glutamyl kinase (ProB) for L-proline biosynthesis. Increased promoter strength led to enhanced L-proline production and the highest L-proline titer of 6.4 g/L was obtained when a promoter mutant with a 9.8-fold higher strength compared to the wild-type promoter was used for ProB expression. The use of stronger promoter variants did not further improve L-proline production. In conclusion, a promoter library was constructed based on a native C. glutamicum promoter PodhA. The new promoter library should be useful for systems metabolic engineering of C. glutamicum. The strategy of mutating native promoter may also guide the construction of promoter libraries for other microorganisms.

Interaction between CASP8AP2 and ZEB2-CtBP2 Regulates the Expression of LEF1

Low expression of CTBP2 and CASP8AP2 correlated with poor outcome and predicted risk of relapse in pediatric B-cell acute lymphoblastic leukemia (B-ALL). This study aimed to investigate the molecular mechanism by which CASP8AP2 regulates LEF1 expression by interacting with CtBP2 and ZEB2 in Acute lymphoblastic lymphoma (ALL). There was an interaction between CASP8AP2, ZEB2, and CtBP2, and then the interaction between CtBP2 and ZEB2 was observed after downregulating the expression of CASP8AP2. The wild type (containing the ZEB2 binding site) or mutant (containing a mutant binding site) LEF1 gene promoter sequence was inserted into the pGL3-basic plasmid, and a dual-luciferase reporter gene detection system was used to observe how CASP8AP2, ZEB2, and CtBP2 regulate the transcription of the LEF1 gene. We conclude that CASP8AP2, CtBP2, and ZEB2 can all bind to the LEF1 gene promoter region and reduce the luciferase activity of the LEF1 promoter. Meanwhile, the interaction of ZEB2 and the LEF1 promoter was significantly weakened after downregulation of CASP8AP2. Knockdown of CASP8AP2 in the 697 cell lines resulted in the significant upregulation of the mRNA expression levels of the stemness-related genes CD44, JAG1, and SALL4. In conclusion, CASP8AP2 is vital for the interaction between CtBP2 and ZEB2, inhibiting LEF1 and stemness-related genes expression ALL. Supplemental data for this article is available online at https://doi.org/10.1080/08880018.2022.2033369 .

Correlation of Human Leukocyte Antigen-E Genomic Polymorphism with Leukemia and Functional Study of Human Leukocyte Antigen-E Different Type Promoters.

Human leukocyte antigen (HLA)-E is one of the least polymorphic nonclassical major histocompatibility complex (MHC) I genes; its nucleotide variability can affect immune response. In this study, we assess the correlation between HLA-E polymorphism and leukemia and further study the transcriptional activity of promoter variation at nucleotide position-26. A total of 142 healthy blood donors and 111 leukemia patients were collected. The genomic sequence of HLA-E was amplified by high-fidelity reaction system and identified by Sanger and cloning sequencing. The dual luciferase reporter gene assay was used to detect the transcription activity of promoter variation at nucleotide position-26. In the HLA-E genomic sequence results, a total of 16 alleles and 32 genotypes were detected; the HLA-E*01:01:01:06 allele had a significantly lower frequency in leukemia patients than in healthy participants (p = 0.026 < 0.05). And the HLA-E*01:03:02:01, *01:03:02:01 genotype showed the greatest difference in frequency between the two groups of participants (p = 0.028 < 0.05). Eight HLA-E alleles were first reported worldwide in Chinese individuals. The results of the dual luciferase reporter gene experiment showed that the transcription activity of the mutant-type promoter (HLA-E*01:01:01:06 with "T" allele at nucleotide position-26) was significantly lower compared with the wild-type promoter (HLA-E*01:01:01:01 with "G" allele at nucleotide position-26) (p = 0.0242 < 0.05). HLA-E*01:01:01:06 allele has a protective effect against leukemia through decreasing transcription activity by "T" variation at nucleotide position-26.

Molecular Analysis of Colorectal Cancers Suggests a High Frequency of Lynch Syndrome in Indonesia.

Simple SummaryThe incidence of young people <50 years old who are diagnosed with colorectal cancer (CRC), termed as early onset colorectal cancer (EOCRC), accounted for nearly 30% of the total CRC patients in Indonesia, which is about three times higher than what is being reported in Europe, the UK and USA. Lynch syndrome (LS) is a hereditary type of CRC that is associated with a younger age of onset. Detecting LS has been long reported to be a cost-effective strategy to provide aid in the diagnosis or management of the individual or at-risk family members. The aim of this retrospective study was to screen for Lynch Syndrome in Indonesian CRC patients using simple and robust polymerase chain reaction (PCR)-based molecular testing, known as N_LyST (Nottingham Lynch Syndrome Test). To our knowledge, we are the first to study and observe a potentially higher frequency of LS (13.85%) among CRC patients in Indonesia (n = 231). This may partially contribute to the reported much higher rate of EOCRC found in the country.There is about three times higher incidence of young patients <50 years old with colorectal cancer, termed EOCRC, in Indonesia as compared to Europe, the UK and USA. The aim of this study was to investigate the frequency of Lynch Syndrome (LS) in Indonesian CRC patients. The previously described Nottingham Lynch Syndrome Test (N_LyST) was used in this project. N_LyST is a robust high-resolution melting (HRM)-based test that has shown 100% concordance with standard reference methods, including capillary electrophoresis and Sanger sequencing. The test consisted of five mononucleotide microsatellite markers (BAT25, BAT26, BCAT25, MYB, EWSR1), BRAF V600E mutation and MLH1 region C promoter for methylation (using bisulphite-modified DNA). A total of 231 archival (2016–2019) formalin-fixed, paraffin-embedded (FFPE) tumour tissues from CRC patients collected from Dr. Sardjito General Hospital Yogyakarta, Indonesia, were successfully tested and analysed. Among those, 44/231 (19.05%) were MSI, 25/231 (10.82%) were harbouring BRAF V600E mutation and 6/231 (2.60%) had MLH1 promoter methylation. Almost all—186/197 (99.45%)—MSS cases were MLH1 promoter unmethylated, while there were only 5/44 (11.36%) MSI cases with MLH1 promoter methylation. Similarly, only 9/44 (20.45%) of MSI cases were BRAF mutant. There were 50/231 (21.65%) EOCRC cases, with 15/50 (30%) regarded as MSI, as opposed to 29/181 (16.02%) within the older group. In total, 32/231 patients (13.85%) were classified as “Probable Lynch” (MSI, BRAF wildtype and MLH1 promoter unmethylated), which were enriched in EOCRC as compared to older patients (24% vs. 11.05%, p = 0.035). Nonetheless, 30/50 (76.00%) cases among the EOCRC cases were non-LS (sporadic) and were significantly associated with a left-sided tumour. The overall survival of both “Probable Lynch” and non-LS (sporadic) groups (n = 227) was comparable (p = 0.59), with follow up period of 0–1845 days/61.5 months. Stage, node status, histological grading and ECOG score were significantly associated with patient overall survival (p < 0.005), yet only ECOG was an independent factor for OS (HR: 4.38; 95% CI: 1.72–11.2; p = 0.002). In summary, this study is the first to reveal a potentially higher frequency of LS among CRC patients in Indonesia, which may partially contribute to the reported much higher number of EOCRC as compared to the incidence in the West.

Chemoradiotherapy with temozolomide vs. radiotherapy alone in patients with IDH wild-type and TERT promoter mutation WHO grade II/III gliomas: A prospective randomized study

PurposePatients with grade II/III diffuse glioma (lower grade glioma, LGG) with isocitrate dehydrogenase wild-type (IDH-wt) and telomerase reverse-transcriptase promoter mutation (TERTp-mut) experience shorter overall survival (OS) time than IDH mutant patients. The optimal treatment strategy for these patients is unclear. We compared the effects of radiotherapy (RT) alone vs. RT concurrent with temozolomide (TMZ) followed by adjuvant TMZ in these LGG patients. Patients and methodsThirty-seven LGG patients with IDH-wt and TERTp-mut were randomly allocated to either RT alone treatment (RT group, n = 18; 60 Gy in 30 daily fractions) or RT concurrent with TMZ (75 mg/m2/d, 7 d/week) followed by adjuvant TMZ (CRT group, n = 19). The median follow-up duration was 17 months. Log-rank test was used for OS and PFS comparisons. ResultsThe 1-year OS rate was 94.1% [95% confidence interval (CI) 82.9–100] in the CRT group and 74.6% (95% CI, 52.9–96.4) in the RT group. The median OS values in the CRT and RT groups were statistically different [25 vs. 17 months, respectively; hazard ratio (HR) 0.271; 95% CI, 0.092–0.793; P = 0.017], while PFS values were not (16 vs. 7 months, respectively; HR, 0.917; 95% CI, 0.397–2.120; P = 0.840). Multivariate analysis indicated that CRT treatment and female sex were associated with significantly longer OS (P = 0.001, P = 0.016, respectively). ConclusionCRT treatment for IDH-wt/TERTp-mut grade II/III gliomas resulted in significantly longer OS than RT alone. Female sex was a significant favorable prognostic factor.

TERT Promoter Mutations Increase Sense and Antisense Transcription from the TERT Promoter.

Background: Chief among mechanisms of telomerase reverse transcriptase (TERT) reactivation is the appearance of mutations in the TERT promoter. The two main TERT promoter mutations are C>T transitions located −146C>T and −124C>T upstream from the translational start site. They generate a novel Ets/TCF binding site. Both mutations are mutually exclusive and −124C>T is strikingly overrepresented in most cancers. We investigated whether this mutational bias and mutual exclusion could be due to transcriptional constraints. Methods: We compared sense and antisense transcription of a panel of TERT promoter-luciferase vectors harboring the −124C>T and -146C>T mutations alone or together. lncRNA TAPAS levels were measured by RT-PCR. Results: Both mutations generally increased TERT transcription by 2–4-fold regardless of upstream and downstream regulatory elements. The double mutant increased transcription in an additive fashion, arguing against a direct transcriptional constraint. The −146C>T mutation, alone or in combination with −124C>T, also unleashed antisense transcription. In line with this finding, lncRNA TAPAS was higher in cells with mutated TERT promoter (T98G and U87) than in cells with wild-type promoter, suggesting that lncRNA TAPAS may balance the effect of TERT promoter mutations. Conclusions: −146C>T and −124C>T TERT promoter mutations increase TERT sense and antisense transcription, and the double mutant features higher transcription levels. Increased antisense transcription may contain TERT expression within sustainable levels.

Splicing Factor SRSF1 Promotes Tumorigenesis Via Oncogenic Splice-Switching and Predicts Poor Prognosis in Multiple Myeloma

ObjectiveDysregulation of alternative splicing (AS) triggers many tumors, yet its contribution to multiple myeloma (MM) has not been elucidated. Our study aims to reveal the role of AS in MM progression, and to explore the molecular mechanisms of the candidate splicing factor (SF), thus valuates its feasibility as a treatment target and prognostic factor.Design and results 1.Gene set enrichment analysis (GSEA) revealed a significant difference in the expression pattern of the alternative splicing pathway genes, notably enriched in MM patients (Figure 1A). And, the splicing factor SRFS1 expression showed concordant differential expression in MM versus normal donors in two datasets (GSE6477, GSE13591). Kaplan-Meier analysis showed that high SRSF1 expression in CD138 + MM cells was associated with decreased PFS and poor OS (GSE9782) (Figure 1B). Moreover, the SRSF1 levels appeared a progressive increase in the progression of plasma cell dyscrasias (MGUS, SMM, MM and PCL) (Figure 1C). A cohort of 57 newly diagnosed MM patients was uniformly treated and followed. Univariate and multivariate analyses indicated that high SRSF1 expression was correlated with decreased PFS and OS. The c-indices of the Cox model fit with the combination of RISS and SRSF1 were higher than those of models fit without SRSF1, suggesting that SRSF1 improved the prognostic stratification of patients with MM.2.In vitro, SRSF1 downregulation in MM cells resulted in decreased proliferation, increased apoptosis and cell cycle arrest in G1 phase. In orthotopic MM xenograft models, bioluminescent imaging monitoring revealed a decreased burden of disease and a prolongation in overall survival in mice injected with SRSF1-shRNA cells versus the control (Figure 1D-F).3.Pearson correlation analysis suggested that the expression of TF YY1 was positively correlated with SRSF1 in five sets of GEO (Figure 1G). CHIP-seq BigWig files were downloaded from GSE31477 and Integrative Genomics Viewer (IGV) tracks displayed the binding site of YY1 at SRSF1 promoter locus from chr17: 56084421 to 56084751 (Figure 1H). CHIP-qPCR assay confirmed that endogenous YY1 directly interacted with the core element of the SRSF1 promoter in myeloma cells. Silencing of YY1 expression decreased the luciferase activity of the reporter construct carrying wild-type SRSF1 promoter region but not mutant in the YY1 binding site. Consistent with the effects of SRSF1, downregulation YY1 displayed anticancer activity in myeloma cells. Kaplan-Meier analysis showed that high YY1 expression in CD138 + myeloma cells was associated with decreased PFS and poor OS.4.RNA-seq analysis revealed a total of 7678 SRSF1-regulated AS events in LP-1 cell with an FDR cut-off of <0.05. Among them, the index of percent spliced in percentage-spliced-in (PSI) was upregulated in 4098 AS events and downregulated in 3580 AS via the downregulation of SRSF1. Changes in alternative splicing events were analyzed by replicate multivariate analysis of transcript splicing (rMATS) to identify downstream key genes regulated by SRSF1. Various types of AS events, including skipped exons (SEs), alternative 5‘ ss exons (A5SSs), alternative 3‘ ss exons (A3SSs), retained introns (RIs), and mutually exclusive exons (MXEs), can be regulated by SRSF1, and of these, SE is the most common type of SRSF1-regulated AS events (Figure 1I-O). The KEGG Pathway and GO analysis revealed that SRSF1-regulated AS events were involved in spliceosome, cell cycle and cellular process. Among the most significant AS events, we noted RBBP6, which isoforms have been reported to exhibit opposite effect on oncogenic activity.5.RNA-seq and subsequent validation indicated that SRSF1 knockdown caused a significantly decreased iso1 and increased iso3 of RBBP6. An opposite effect on myeloma proliferation between iso1 and iso3 was observed upon overexpression of individual proteins. Moreover, the level of RBBP6 iso1 is associated with poor prognosis, whereas iso3 expression is associated with favorable prognosis in MM patientsConclusionOur study uncovered that SRSF1-regulated aberrant AS facilitated myeloma progression through creating reducing normal isoforms and increasing oncogenic isoforms (Figure 1P). Moreover, SRSF1 and its critical splicing target could act as an independent prognostic factor for MM patients. Thus, SRSF1 might be considered as a valuable therapeutic target and a potential prognostic biomarker for MM. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Regulating the T7 RNA polymerase expression in E. coli BL21 (DE3) to provide more host options for recombinant protein production

Escherichia coli is the most widely used bacterium in prokaryotic expression system for the production of recombinant proteins. In BL21 (DE3), the gene encoding the T7 RNA polymerase (T7 RNAP) is under control of the strong lacUV5 promoter (PlacUV5), which is leakier and more active than wild-type lac promoter (PlacWT) under certain growth conditions. These characteristics are not advantageous for the production of those recombinant proteins with toxic or growth-burdened. On the one hand, leakage expression of T7 RNAP leads to rapid production of target proteins under non-inducing period, which sucks resources away from cellular growth. Moreover, in non-inducing or inducing period, high expression of T7 RNAP production leads to the high-production of hard-to-express proteins, which may all lead to loss of the expression plasmid or the occurrence of mutations in the expressed gene. Therefore, more BL21 (DE3)-derived variant strains with rigorous expression and different expression level of T7 RNAP should be developed. Hence, we replaced PlacUV5 with other inducible promoters respectively, including arabinose promoter (ParaBAD), rhamnose promoter (PrhaBAD), tetracycline promoter (Ptet), in order to optimize the production of recombinant protein by regulating the transcription level and the leakage level of T7 RNAP. Compared with BL21 (DE3), the constructed engineered strains had higher sensitivity to inducers, among which rhamnose and tetracycline promoters had the lowest leakage ability. In the production of glucose dehydrogenase (GDH), a protein that causes host autolysis, the engineered strain BL21 (DE3::ara) exhibited higher biomass, cell survival rate and foreign protein expression level than that of BL21 (DE3). In addition, these engineered strains had been successfully applied to improve the production of membrane proteins, including E. coli cytosine transporter protein (CodB), the E. coli membrane protein insertase/foldase (YidC), and the E. coli F-ATPase subunit b (Ecb). The engineered strains constructed in this paper provided more host choices for the production of recombinant proteins.

An emerging and variant viral promoter of HIV-1 subtype C exhibits low-level gene expression noise

BackgroundWe observe the emergence of several promoter-variant viral strains in India during recent years. The variant viral promoters contain additional copies of transcription factor binding sites present in the viral modulatory region or enhancer, including RBEIII, LEF-1, Ap-1 and/or NF-κB. These sites are crucial for governing viral gene expression and latency. Here, we infer that one variant viral promoter R2N3-LTR containing two copies of RBF-2 binding sites (an RBEIII site duplication) and three copies of NF-κB motifs may demonstrate low levels of gene expression noise as compared to the canonical RN3-LTR or a different variant R2N4-LTR (a duplication of an RBEIII site and an NF-κB motif). To demonstrate this, we constructed a panel of sub-genomic viral vectors of promoter-variant LTRs co-expressing two reporter proteins (mScarlet and Gaussia luciferase) under the dual-control of Tat and Rev. We established stable pools of CEM.NKR-CCR5 cells (CEM-CCR5RL reporter cells) and evaluated reporter gene expression under different conditions of cell activation.ResultsThe R2N3-LTR established stringent latency that was highly resistant to reversal by potent cell activators such as TNF-α or PMA, or even to a cocktail of activators, compared to the canonical RN3- or the variant R2N4-LTR. The R2N3-LTR exhibited low-level basal gene expression in the absence of cell activation that enhanced marginally but significantly when activated. In the presence of Tat and Rev, trans-complemented in the form of an infectious virus, the R2N3-LTR demonstrated gene expression at levels comparable to the wild-type viral promoter. The R2N3-LTR is responsive to Tat and Rev factors derived from viral strains representing diverse genetic subtypes.ConclusionWith extremely low-level transcriptional noise, the R2N3-LTR can serve as an excellent model to examine the establishment, maintenance, and reversal of HIV-1 latency. The R2N3-LTR would also be an ideal viral promoter to develop high-throughput screening assays to identify potent latency-reversing agents since the LTR is not affected by the usual background noise of the cell.