scholarly journals Gene expression profiling of ATL patients: compilation of disease-related genes and evidence for TCF4 involvement in BIRC5 gene expression and cell viability

Blood ◽  
2009 ◽  
Vol 113 (17) ◽  
pp. 4016-4026 ◽  
Author(s):  
Cynthia A. Pise-Masison ◽  
Michael Radonovich ◽  
Kathleen Dohoney ◽  
John C. Morris ◽  
Deirdre O'Mahony ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Viability ◽  
Cyclin B1 ◽  
Leukemic Cells ◽  
Leukemia Cells ◽  
Nuclear Antigen ◽  
Adult T Cell Leukemia ◽  
Reporter Assays ◽  
And Function ◽  
Proliferating Cell

Abstract Adult T-cell leukemia/lymphoma (ATL) is an aggressive and fatal disease. We have examined 32 patients with smoldering, chronic, lymphoma and acute leukemia using Affymetrix HG-U133A2.0 arrays. Using the BRB array program, we identified genes differentially expressed in leukemia cells compared with normal lymphocytes. Several unique genes were identified that were overexpressed in leukemic cells, including TNFSF11, RGS13, MAFb, CSPG2, C/EBP-α, and TCF4; 200 of the most highly overexpressed ATL genes were analyzed by the Pathway Studio, version 4.0 program. ATL leukemia cells were characterized by an increase in genes linked to “central” genes CDC2/cyclin B1, SYK/LYN, proliferating cell nuclear antigen, and BIRC5. Because of its potential therapeutic importance, we focused our studies on the regulation and function of BIRC5, whose expression was increased in 13 of 14 leukemia samples. TCF4 reporter assays and transfection of DN-TCF4 demonstrated that TCF4 regulates BIRC5 gene expression. Functionally, transfection of ATL cells with BIRC5 shRNA decreased BIRC5 expression and cell viability 80%. Clinical treatment of ATL patients with Zenapax or bortezomib decreased BIRC5 expression and cell viability. These experiments represent the first direct experimental evidence that BIRC5 plays an important role in ATL cell viability and provides important insight into ATL genesis and potential targeted therapies.

scholarly journals The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex

2021 ◽  
Author(s):  
Subramaniyam Ravichandran ◽  
Maria Razzaq ◽  
Nazia Parveen ◽  
Ambarnil Ghosh ◽  
Kyeong Kyu Kim
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Biological Significance ◽  
Cellular Functions ◽  
Hairpin Loops ◽  
G Quadruplex ◽  
Reporter Assays ◽  
Expression Activity ◽  
The Stability ◽  
And Function

Abstract G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

scholarly journals K6-linked SUMOylation of BAF regulates nuclear integrity and DNA replication in mammalian cells

2020 ◽  
Vol 117 (19) ◽  
pp. 10378-10387 ◽  
Author(s):  
Qiaoyu Lin ◽  
Bin Yu ◽  
Xiangyang Wang ◽  
Shicong Zhu ◽  
Gan Zhao ◽  
...  
Keyword(s):  
Dna Replication ◽  
Nuclear Localization ◽  
Proliferating Cell Nuclear Antigen ◽  
Mammalian Cells ◽  
Regulatory Mechanism ◽  
Nuclear Antigen ◽  
Multiple Functions ◽  
And Function ◽  
Proliferating Cell ◽  
Replication Failure

Barrier-to-autointegration factor (BAF) is a highly conserved protein in metazoans that has multiple functions during the cell cycle. We found that BAF is SUMOylated at K6, and that this modification is essential for its nuclear localization and function, including nuclear integrity maintenance and DNA replication. K6-linked SUMOylation of BAF promotes binding and interaction with lamin A/C to regulate nuclear integrity. K6-linked SUMOylation of BAF also supports BAF binding to DNA and proliferating cell nuclear antigen and regulates DNA replication. SENP1 and SENP2 catalyze the de-SUMOylation of BAF at K6. Disrupting the SUMOylation and de-SUMOylation cycle of BAF at K6 not only disturbs nuclear integrity, but also induces DNA replication failure. Taken together, our findings demonstrate that SUMOylation at K6 is an important regulatory mechanism that governs the nuclear functions of BAF in mammalian cells.

Gene Profiling Mechanisms of Cell Density-Dependent Growth in Myeloid and Lymphoid Leukemia Cell Lines.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4420-4420
Author(s):  
Ikuo Murohashi ◽  
Noriko Ihara
Keyword(s):  
Gene Expression ◽  
Growth Factors ◽  
Cell Density ◽  
Cell Lines ◽  
Leukemia Cell ◽  
Leukemic Cells ◽  
Leukemia Cells ◽  
Lymphoid Leukemia ◽  
Cultured Cell ◽  
Cell Densities

Abstract Abstract 4420 Normal hematopoietic stem cells have been shown to be maintained through interaction with their environmental niches, such as osteoblastic and endothelial ones. The growth of leukemic cells has been shown to be stimulated by environmental niches (paracrine growth) or by cell-to-cell interaction or excreted factors of leukemic cells (autocrine growth). The growth of myeloid (MO7-E and HL-60) and lymphoid (Raji, U-266, Daudi and RPMI-1788) leukemia cell lines cultured at various cell densities in serum free medium (Sigma H 4281) with 1% BSA was evaluated. The cells cultured at higher cell densities (cultured cell densities ≥a 105/ml) showed logarithmic linear increases in cell number, whereas those at lower cell densities (cultured cell densities □… 104/ml) ceased increasing cell number. Supernatants of myeloid leukemia cells stimulated the growth of autologous clonogenic cells, but not those of lymphoid leukemia cells. Neutralizing antibodies (Abs) against various hematopoietic growth factors failed to inhibit cell growth except for anti-VEGF, which significantly decreased HL-60 leukemia cell growth. To clarify the nature of the cultured cell density on the growth of leukemia cells, leukemia cells were cultured at higher cell density (group H, cultured cell densities of 106/ml) or at lower cell density (group L, cultured cell densities 104/ml). After culture of 3-, 6-, 10-, and 24-hr, cells were serially harvested and total cellular RNA was extracted. Gene transcript levels were determined by using Real-Time PCR. Gene transcripts examined in the present study were as follows: polycomb (Bmi1), Hox (HOXA7, HOXA9, HOXB2, HOXB4, Meis 1), Caudal-related (CDX2, 4), Mef2c, c-Myb, Wnt (Wnt 3a, Wnt 5a, β-Catenin, β-Catenin, N-Cadherin), Notch (Notch-1, -2, -3 and Jagged-1, -2), CKI (p14, p15, p16, p18, p21, p27, p57), growth factor (VEGF, IGF-1, -2, Ang-1, -2, SDF-1), growth factor receptor (Flt-1, KDR, neurophilin-1, IGF-1R, Tie-1, -2, CXCR4), and growth related (c-Myc, CyclinD1, Foxo3a) genes. p18 and p21 gene expression was higher in group L compared with group H in two and all five groups, respectively. In contrast, p14 gene expression was higher in group H compared with group L. Any of the p15, p16, p27 and p57 genes was deleted. VEGF gene expression levels at 1-3- hr culture were higher in group H compared with group L. HOX, Meis 1 and Mef2c gene expression levels at 1- to 10- hr culture were higher in group H compared with group L. At 24-hr cultures, transcripts of myeloid and lymphoid cell lines for Bmi-1, Wnt-3a, and β-Catenin were higher, and those of lymphoid cell lines for Notch 1, 2, and 3 were higher in group H compared with group L. Taken together, our present results favor the conclusions that genes related to growth factors and transcription factors are sequentially and differentially expressed through cell-to-cell interaction and excreted autocrine growth factors of leukemia cells. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Enhancer profiling identifies critical cancer genes and characterizes cell identity in adult T-cell leukemia

Blood ◽  
2017 ◽  
Vol 130 (21) ◽  
pp. 2326-2338 ◽  
Author(s):  
Regina Wan Ju Wong ◽  
Phuong Cao Thi Ngoc ◽  
Wei Zhong Leong ◽  
Alice Wei Yee Yam ◽  
Tinghu Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
T Cell Activation ◽  
Gene Expression Analysis ◽  
Cell Activation ◽  
Leukemia Cells ◽  
Cancer Genes ◽  
Cell Leukemia ◽  
Adult T Cell Leukemia ◽  
Key Points

Key Points Enhancer profiling combined with gene expression analysis identifies CCR4 and TIAM2 as critical cancer genes in ATL. Super-enhancers are enriched at genes involved in the T-cell activation pathway in ATL, reflecting the origin of leukemia cells.

scholarly journals Vitamin D regulation of a SOD1-to-SOD2 antioxidative switch to prevent osteosarcoma transformation

2020 ◽  
Author(s):  
Thomas S. Lisse
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Proliferating Cell Nuclear Antigen ◽  
Fold Increase ◽  
Nuclear Antigen ◽  
Pcr Analysis ◽  
Oxygen Species ◽  
Mitochondrial Oxidative Phosphorylation ◽  
Complex Iv ◽  
Proliferating Cell

AbstractSuperoxide, a form of reactive oxygen species (ROS), is catabolized by superoxide dismutase (SOD) and contributes to carcinogenesis via the oxidative damage it inflicts on cells. The aim of this research was to analyze the potential vitamin D-mediated regulation of the antioxidative “SOD1-to-SOD2 switch” within the human MG-63 osteosarcoma model. For this study, real-time PCR analysis was performed using MG-63 cells exposed to metabolically active 1,25(OH)2D3. Frist, a sustained statistically significant >2-fold suppression of proliferating cell nuclear antigen (PCNA) transcripts was observed after 10nM but not at 100nM of 1,25(OH)2D3 treatment, suggesting a cytostatic effect. In order to assess regulators of mitochondrial oxidative phosphorylation, gene expression of COX2 and COX4l1 of the mitochondrial complex IV and antioxidative enzymes (SOD1, SOD2 and Catalase (CAT)) were monitored. For COX2 and COX4l1, no changes in gene expression were observed. However, a concomitant decrease in CAT and SOD1 mRNA, and increase in SOD2 mRNA after 24 hours of 10nM 1,25(OH)2D3 treatment were observed. A ~8-fold increase in SOD2 mRNA was apparent after 48 hours. The significant increase in SOD2 activity in the presence of vitamin D indicates an antioxidant potential and sensitization of vitamin D during osteosarcoma transformation and mitochondrial detoxification over time.

scholarly journals Vitamin D Regulation of a SOD1-to-SOD2 Antioxidative Switch to Prevent Bone Cancer

2020 ◽  
Vol 10 (7) ◽  
pp. 2554
Author(s):  
Thomas S. Lisse
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Proliferating Cell Nuclear Antigen ◽  
Bone Cancer ◽  
Fold Increase ◽  
Nuclear Antigen ◽  
Pcr Analysis ◽  
Mitochondrial Oxidative Phosphorylation ◽  
Complex Iv ◽  
Proliferating Cell

Superoxide, a form of reactive oxygen species (ROS), is catabolized by superoxide dismutase (SOD) and contributes to carcinogenesis via the oxidative damage it inflicts on cells. The aim of this research was to analyze the potential vitamin D-mediated regulation of the antioxidative “SOD1-to-SOD2 switch” within the human MG-63 osteosarcoma model. For this study, real-time PCR analysis was performed using MG-63 cells exposed to metabolically active 1,25(OH)2D3. First, a sustained statistically significant >2-fold suppression of proliferating cell nuclear antigen (PCNA) transcripts was observed after 10 nM but not at 100 nM of 1,25(OH)2D3 treatment, suggesting a cytostatic effect. In order to assess regulators of mitochondrial oxidative phosphorylation, gene expression of COX2 and COX4l1 of the mitochondrial complex IV and antioxidative enzymes (SOD1, SOD2 and Catalase (CAT)) were monitored. For COX2 and COX4l1, no changes in gene expression were observed. However, a concomitant decrease in CAT and SOD1 mRNA, and increase in SOD2 mRNA after 24 h of 10 nM 1,25(OH)2D3 treatment were observed. A ~8-fold increase in SOD2 mRNA was apparent after 48 ours. The significant increase in SOD2 activity in the presence of vitamin D indicates an antioxidant potential and sensitization of vitamin D during osteosarcoma transformation and mitochondrial detoxification over time.

Intronic CD22 Gene Mutations as A Pathogenic Mechanism of Human B-Precursor Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 149-149
Author(s):  
Fatih M. Uckun ◽  
Patricia Goodman ◽  
Hong Ma ◽  
Ilker Dibirdik ◽  
Sanjive Qazi
Keyword(s):  
Gene Expression ◽  
Tumor Suppressor ◽  
B Cell ◽  
Tyrosine Phosphatase ◽  
Leukemic Cells ◽  
Receptor Protein ◽  
Leukemia Cells ◽  
B Lineage ◽  
Infant Leukemia ◽  
Cell Ontogeny

Abstract Abstract 149 CD22 is an inhibitory co-receptor of B-cells and B-cell precursors that acts as a negative regulator of multiple signal transduction pathways critical for B-cell homeostasis. The inhibitory and apoptosis-promoting signaling function of CD22 is dependent on recruitment of the Src homology 2 domain–containing tyrosine phosphatase (SHP)-1 to the immunoreceptor tyrosine-based inhibitory motifs (ITIMs) of its cytoplasmic domain. Collective genetic evidence from CD22-deficient or SHP-1-deficient mice shows that disruption of the CD22-SHP1 signaling network can result in development of a B-cell lymphoproliferative state associated with defective apoptosis and maturation. However, direct genetic evidence for the functional significance of CD22 in human B-cell ontogeny or its implied tumor suppressor role has been lacking. Here, we report that primary leukemic cells from infants with newly diagnosed B-precursor leukemia (BPL) express a truncated and functionally defective CD22 co-receptor protein that is unable to transmit apoptotic signals. Expression of this structurally and functionally abnormal CD22 protein is associated with a very aggressive in vivo growth of patients' primary leukemia cells causing disseminated overt leukemia in SCID mice. The abnormal CD22 co-receptor is encoded by a profoundly aberrant mRNA arising from a splicing defect that causes the deletion of exon 12 (c.2208-c.2327) (CD22DE12). CD22DE12 involves an exact splice with no other mutation at the splice junction. The deletion of exon 12 in CD22 mRNA results in a truncating frameshift mutation starting at K736 with an insertion of 15 amino acids not seen in wild-type CD22 sequence followed by a TGA termination codon. Mutant CD22DE12 protein lacks the conserved tyrosines and ITIMs that provide docking sites for the SH2 domains of the tyrosine phosphatase SHP1. It also lacks regions homologous to ITAMs, tyrosine-based activation motifs, which are docking sites for SH2 containing proteins. Thus, CD22DE12 mRNA encodes a truncated CD22 protein lacking most of the intracellular domain including the key regulatory signal transduction elements and all of the cytoplasmic tyrosine residues. The splicing defect is associated with multiple homozygous mutations within a 132-bp segment of the intronic sequence between exons 12 and 13. These mutations cause marked changes in the predicted secondary structures of the mutant CD22 pre-mRNA sequences that affect the target motifs for the splicing factors hnRNP-L, PTB, and PCBP that are up-regulated in infant leukemia cells. Forced expression of the mutant CD22DE12 protein in transgenic mice, under control of the immunoglobulin enhancer Eμ that is activated in early B-cell ontogeny prior to Ig gene rearrangements, perturbs B-cell development, as evidenced by B-precursor/B-cell hyperplasia at 6 weeks of age and corrupts the regulation of gene expression, causing reduced expression levels of several genes with a tumor suppressor function. This CD22DE12-associated unique 12-gene signature transcriptome included (i) tumor suppressor genes TP53 (as well as TP53 regulator MDM2), neurofibromatosis 2 (NF2) (as well as NF2 regulator RAC1), and the adenomatous polyposis coli (APC) gene, a tumor suppressor known to regulate the Wnt/beta-catenin signaling, (ii) genes for chromatin remodeling/global gene expression regulators with a tumor suppressor function IKZF1/IKAROS and SATB1, as well as (iii) cell cycle regulatory genes CDKN1C, CCNG1, and NOTCH4. By comparing gene expression profiles of primary leukemia cells from 31 infants vs. 30 non-infant children with ALL we found that reduced expression levels of 6 of the 9 CD22DE12 signature genes that were represented on the human cDNA arrays, including TP53 and APC as well as MDM2, SATB1, CCNG1 and GNB2 discriminated infant BPL from non-infant BPL. The documented molecular and functional abnormalities involving CD22 in primary leukemic cells from patients with newly diagnosed infant BPL uniquely implicate deficiency of this B-lineage restricted co-receptor protein in the pathogenesis of infant leukemia. This collection of experimental data is unprecedented in that it links a genetic defect involving a B-lineage specific regulatory gene to the most aggressive human B-lineage lymphoid malignancy that arises from an uncoupling of proliferation and differentiation of B-precursors during the earliest stages of B-cell ontogeny. Disclosures: No relevant conflicts of interest to declare.

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