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Dai W, Hu T, Jin B, Shi X. Incorporating grouping information into Bayesian Gaussian graphical model selection. COMMUN STAT-THEOR M 2022. [DOI: 10.1080/03610926.2022.2053864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Wei Dai
- Department of Statistics and Finance, University of Science and Technology of China, Anhui, China
| | - Taizhong Hu
- Department of Statistics and Finance, University of Science and Technology of China, Anhui, China
| | - Baisuo Jin
- Department of Statistics and Finance, University of Science and Technology of China, Anhui, China
| | - Xiaoping Shi
- Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
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Novikova S, Tikhonova O, Kurbatov L, Farafonova T, Vakhrushev I, Lupatov A, Yarygin K, Zgoda V. Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation. Biomolecules 2021; 11:907. [PMID: 34207065 PMCID: PMC8233756 DOI: 10.3390/biom11060907] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 01/01/2023] Open
Abstract
Induced granulocytic differentiation of human leukemic cells under all-trans-retinoid acid (ATRA) treatment underlies differentiation therapy of acute myeloid leukemia. Knowing the regulation of this process it is possible to identify potential targets for antileukemic drugs and develop novel approaches to differentiation therapy. In this study, we have performed transcriptomic and proteomic profiling to reveal up- and down-regulated transcripts and proteins during time-course experiments. Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation that cover both up-regulated (HIC1, NFKBIA, and CASP9) and down-regulated (PARP1, VDR, and RXRA) elements. To verify the designed network we measured HIC1 and PARP1 protein abundance during granulocytic differentiation by selected reaction monitoring (SRM) using stable isotopically labeled peptide standards. We also revealed that transcription factor CEBPB and LYN kinase were involved in differentiation onset, and evaluated their protein levels by SRM technique. Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis in a p53-independent manner. The differentially expressed transcripts and proteins, predicted transcriptional factors, and key molecules such as HIC1, CEBPB, LYN, and PARP1 may be considered as potential targets for differentiation therapy of acute myeloid leukemia.
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Affiliation(s)
| | | | | | | | | | | | | | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia; (S.N.); (O.T.); (L.K.); (T.F.); (I.V.); (A.L.); (K.Y.)
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Foroughi Pour A, Dalton LA. Optimal Bayesian Filtering for Biomarker Discovery: Performance and Robustness. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:250-263. [PMID: 30040658 DOI: 10.1109/tcbb.2018.2858814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Optimal Bayesian feature filtering (OBF) is a fast and memory-efficient algorithm that optimally identifies markers with distributional differences between treatment groups under Gaussian models. Here, we study the performance and robustness of OBF for biomarker discovery. Our contributions are twofold: (1) we examine how OBF performs on data that violates modeling assumptions, and (2) we provide guidelines on how to set input parameters for robust performance. Contribution (1) addresses an important, relevant, and commonplace problem in computational biology, where it is often impossible to validate an algorithm's core assumptions. To accomplish both tasks, we present a battery of simulations that implement OBF with different inputs and challenge each assumption made by OBF. In particular, we examine the robustness of OBF with respect to incorrect input parameters, false independence, imbalanced sample size, and we address the Gaussianity assumption by considering performance on an extensive family of non-Gaussian distributions. We address advantages and disadvantages between different priors and optimization criteria throughout. Finally, we evaluate the utility of OBF in biomarker discovery using acute myeloid leukemia (AML) and colon cancer microarray datasets, and show that OBF is successful at identifying well-known biomarkers for these diseases that rank low under moderated t-test.
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Szebeni GJ, Balog JA, Demjén A, Alföldi R, Végi VL, Fehér LZ, Mán I, Kotogány E, Gubán B, Batár P, Hackler L, Kanizsai I, Puskás LG. Imidazo[1,2- b]pyrazole-7-carboxamides Induce Apoptosis in Human Leukemia Cells at Nanomolar Concentrations. Molecules 2018; 23:E2845. [PMID: 30388846 PMCID: PMC6278434 DOI: 10.3390/molecules23112845] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Leukemia, the malignancy of the hematopoietic system accounts for 10% of cancer cases with poor overall survival rate in adults; therefore, there is a high unmet medical need for the development of novel therapeutics. Eight imidazo[1,2-b]pyrazole-7-carboxamides have been tested for cytotoxic activity against five leukemia cell lines: Acute promyelocytic leukemia (HL-60), acute monocytic leukemia (THP-1), acute T-lymphoblastic leukemia (MOLT-4), biphenotypic B myelomonocytic leukemia (MV-4-11), and erythroleukemia (K-562) cells in vitro. Imidazo[1,2-b]pyrazole-7-carboxamides hampered the viability of all five leukemia cell lines with different potential. Optimization through structure activity relationship resulted in the following IC50 values for the most effective lead compound DU385: 16.54 nM, 27.24 nM, and 32.25 nM on HL-60, MOLT-4, MV-4-11 cells, respectively. Human primary fibroblasts were much less sensitive in the applied concentration range. Both monolayer or spheroid cultures of murine 4T1 and human MCF7 breast cancer cells were less sensitive to treatment with 1.5⁻10.8 μM IC50 values. Flow cytometry confirmed the absence of necrosis and revealed 60% late apoptotic population for MV-4-11, and 50% early apoptotic population for HL-60. MOLT-4 cells showed only about 30% of total apoptotic population. Toxicogenomic study of DU385 on the most sensitive MV-4-11 cells revealed altered expression of sixteen genes as early (6 h), midterm (12 h), and late response (24 h) genes upon treatment. Changes in ALOX5AP, TXN, and SOD1 expression suggested that DU385 causes oxidative stress, which was confirmed by depletion of cellular glutathione and mitochondrial membrane depolarization induction. Imidazo[1,2-b]pyrazole-7-carboxamides reported herein induced apoptosis in human leukemia cells at nanomolar concentrations.
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Affiliation(s)
- Gábor J Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - József A Balog
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - András Demjén
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Róbert Alföldi
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Vanessza L Végi
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | | | - Imola Mán
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Edit Kotogány
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Barbara Gubán
- Department of Dermatology and Allergology, University of Szeged, Korányi fasor 6, H-6720 Szeged, Hungary.
| | - Péter Batár
- Department of Hematology, Institute of Internal Medicine, University of Debrecen, Nagyerdei Körút 98, 4032 Debrecen, Hungary.
| | - László Hackler
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Iván Kanizsai
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - László G Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
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Reikvam H, Hovland R, Forthun RB, Erdal S, Gjertsen BT, Fredly H, Bruserud Ø. Disease-stabilizing treatment based on all-trans retinoic acid and valproic acid in acute myeloid leukemia - identification of responders by gene expression profiling of pretreatment leukemic cells. BMC Cancer 2017; 17:630. [PMID: 28877686 PMCID: PMC5586053 DOI: 10.1186/s12885-017-3620-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/28/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is an aggressive malignancy only cured by intensive therapy. However, many elderly and unfit patients cannot receive such treatment due to an unacceptable risk of treatment-related morbidity and mortality. Disease-stabilizing therapy is then the only possible strategy, one alternative being treatment based on all-trans retinoic acid (ATRA) combined with the histone deacetylase inhibitor valproic acid and possibly low-toxicity conventional chemotherapy. METHODS Primary AML cells were derived from 43 patients included in two clinical studies of treatment based on ATRA, valproic acid and theophyllamine; low toxicity chemotherapy (low-dose cytarabine, hydroxyurea, 6-mercaptopurin) was also allowed. Pretreatment leukemic cells were analyzed by mutation profiling of 54 genes frequently mutated in myeloid malignancies and by global gene expression profiling before and during in vivo treatment. RESULTS Patients were classified as responders and non-responders to the treatment, however response to treatment showed no significant associations with karyotype or mutational profiles. Significance analysis of microarray (SAM) showed that responders and non-responders significantly differed with regard to the expression of 179 different genes. The differentially expressed genes encoding proteins with a known function were further classified based on the PANTHER (protein annotation through evolutionary relationship) classification system. The identified genes encoded proteins that are involved in several important biological functions, but a main subset of the genes were important for transcriptional regulation. These pretherapy differences in gene expression were largely maintained during treatment. Our analyses of primary AML cells during in vivo treatment suggest that ATRA modulates HOX activity (i.e. decreased expression of HOXA3, HOXA4 and HOXA5 and their regulator PBX3), but altered function of DNA methyl transferase 3A (DNMT3A) and G-protein coupled receptor signaling may also contribute to the effect of the overall treatment. CONCLUSIONS Responders and non-responders to AML stabilizing treatment based on ATRA and valproic acid differ in the pretreatment transcriptional regulation of their leukemic cells, and these differences may be important for the clinical effect of this treatment. TRIAL REGISTRATIONS ClinicalTrials.gov no. NCT00175812 ; EudraCT no. 2004-001663-22, registered September 9, 2005 and ClinicalTrials.gov no. NCT00995332 ; EudraCT no. 2007-2007-001995-36, registered October 14, 2009.
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Affiliation(s)
- Håkon Reikvam
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Randi Hovland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | | | - Sigrid Erdal
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Tore Gjertsen
- Section for Hematology, Institute of Clinical Science, University of Bergen, Bergen, Norway
| | - Hanne Fredly
- Section for Hematology, Institute of Clinical Science, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Section for Hematology, Institute of Clinical Science, University of Bergen, Bergen, Norway
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WANG JIN, YIN HAILIN, PANANDIKAR ASHWINI, GANDHI VARSHA, SEN SUBRATA. Elevated cyclin A associated kinase activity promotes sensitivity of metastatic human cancer cells to DNA antimetabolite drug. Int J Oncol 2015; 47:782-90. [PMID: 26058363 PMCID: PMC4501665 DOI: 10.3892/ijo.2015.3037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/04/2015] [Indexed: 11/16/2022] Open
Abstract
Drug resistance is a major obstacle in successful systemic therapy of metastatic cancer. We analyzed the involvement of cell cycle regulatory proteins in eliciting response to N (phosphonoacetyl)-L-aspartate (PALA), an inhibitor of de novo pyrimidine synthesis, in two metastatic variants of human cancer cell line MDA-MB-435 isolated from lung (L-2) and brain (Br-1) in nude mouse, respectively. L-2 and Br-l cells markedly differed in their sensitivity to PALA. While both cell types displayed an initial S phase delay/arrest, Br-l cells proliferated but most L-2 cells underwent apoptosis. There was distinct elevation in cyclin A, and phosphorylated Rb proteins concomitant with decreased expression of bcl-2 protein in the PALA treated L-2 cells undergoing apoptosis. Markedly elevated cyclin A associated and cdk2 kinase activities together with increased E2F1-DNA binding were detected in these L-2 cells. Induced ectopic cyclin A expression sensitized Br-l cells to PALA by activating an apoptotic pathway. Our findings demonstrate that elevated expression of cyclin A and associated kinase can activate an apoptotic pathway in cells exposed to DNA antimetabolites. Abrogation of this pathway can lead to resistance against these drugs in metastatic variants of human carcinoma cells.
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Affiliation(s)
- JIN WANG
- Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - HAILIN YIN
- Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - ASHWINI PANANDIKAR
- Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - VARSHA GANDHI
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - SUBRATA SEN
- Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Program in Human and Molecular Genetics, University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Wang J, Yan B, Liu SM, Sun H, Pan Y, Guan D, Zhang X, Xu J, Ma H. Transcriptomic and Functional Pathway Analysis of Human Cervical Carcinoma Cancer Cells Response to Microtubule Inhibitor. J Cancer 2015; 6:930-7. [PMID: 26316889 PMCID: PMC4543753 DOI: 10.7150/jca.12284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND There clearly is a need for effective chemotherapy for early-stage, high-risk patients with human cervical carcinoma. Vinblastine (VBL) is a key microtubule inhibitor, but unproven in its mechanisms as an important antitumor agent in cervical carcinoma. METHODS We selected the concentration of vinblastine inducing 30% cell death for analyses assessing the DNA content, gene expression and transcriptional gene regulation of VBL-treated KB-3 cells. RESULTS Transcriptomic and hierarchical clustering analysis demonstrated that treatment of KB-3 cells with VBL altered the expression of a diverse group of genes with G2/M arrest, which regulated by four oncogenic or tumor suppresser transcription factors (AP1, NFKB1, RELA, and TP53). Functional pathway analysis revealed the disease response to the biological effects of vinblastine in cervical carcinoma chemotherapy including protein ubiquitination pathway, RhoGDI signaling, integrin signaling, agranulocyte adhesion and biapedesis, and actin nucleation pathways. Northern blots also confirmed that KRT-7, FN14, IER3, and ID1 were deregulated in VBL-treated KB-3 cells. CONCLUSION Transcriptional time series profiles and a functional pathway analysis of VBL-treated KB-3 cells will provide a new strategy for improving microtubule inhibitor chemotherapy for cervical carcinoma.
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Affiliation(s)
- Jin Wang
- 1. Scientific Research Center, Shanghai Public Health Clinical Center, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
- 2. Department of Translational Molecular Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Yan
- 3. Laboratory for Food Safety and Environmental Technology, Institutes of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Song-Mei Liu
- 4. Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Huanhuan Sun
- 5. Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong 519000, China
| | - Yonglong Pan
- 3. Laboratory for Food Safety and Environmental Technology, Institutes of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Daogang Guan
- 6. Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoyan Zhang
- 1. Scientific Research Center, Shanghai Public Health Clinical Center, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Jianqing Xu
- 1. Scientific Research Center, Shanghai Public Health Clinical Center, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Haiqing Ma
- 5. Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong 519000, China
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Liu SM, Chen W, Wang J. Distinguishing between cancer cell differentiation and resistance induced by all-trans retinoic acid using transcriptional profiles and functional pathway analysis. Sci Rep 2014; 4:5577. [PMID: 24993014 PMCID: PMC4894425 DOI: 10.1038/srep05577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/18/2014] [Indexed: 11/03/2022] Open
Abstract
All-trans retinoic acid (ATRA) induces differentiation in various cell types and has been investigated extensively for its effective use in cancer prevention and treatment. Relapsed or refractory disease that is resistant to ATRA is a clinically significant problem. To identify the molecular mechanism that bridges ATRA differentiation and resistance in cancer, we selected the multidrug-resistant leukemia cell line HL-60[R] by exposing it to ATRA, followed by sequential increases of one-half log concentration. A cytotoxicity analysis revealed that HL-60[R] cells were highly resistant to ATRA, doxorubicin, and etoposide. A comparative genome hybridization analysis of HL-60[R] cells identified gains of 4q34, 9q12, and 19q13 and a loss of Yq12 compared with in the parental HL-60 cell line. Transcriptional profiles and functional pathway analyses further demonstrated that 7 genes (FEN1, RFC5, EXO1, XRCC5, PARP1, POLR2F, and GTF2H3) that were relatively up-regulated in HL-60[R] cells and repressed in cells with ATRA-induced differentiation were related to mismatch repair in eukaryotes, DNA double-strand break repair, and nucleotide excision repair pathways. Our results suggest that transcriptional time series profiles and a functional pathway analysis of drug resistance and ATRA-induced cell differentiation will be useful for identifying promyelocytic leukemia patients who are eligible for new therapeutic strategies.
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Affiliation(s)
- Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Weiping Chen
- Microarray Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Wang
- Department of Translational Molecular Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Zhang Q, Wei F, Fong CC, Yu WK, Chen Y, Koon CM, Lau KM, Leung PC, Lau CBS, Fung KP, Yang M. Transcriptional profiling of human skin fibroblast cell line Hs27 induced by herbal formula Astragali Radix and Rehmanniae Radix. JOURNAL OF ETHNOPHARMACOLOGY 2011; 138:668-675. [PMID: 22075453 DOI: 10.1016/j.jep.2011.08.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 08/17/2011] [Accepted: 08/25/2011] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The herbs Astragali Radix (AR) and Rehmanniae Radix (RR) have long been used in traditional Chinese Medicine and serve as the principal herbs in treating diabetic foot ulcer. AIM OF THE STUDY Chinese herbal formulus comprising Astragali Radix (AR) and Rehmanniae Radix (RR) have been shown to improve the healing of diabetic foot ulcer through enhancing the viability of primary fibroblasts in diabetic patients suffering insulin resistance. Our previous study demonstrated that the herbal formula NF3 comprising of AR and RR in the ratio of 2:1 was effective in promoting wound healing in diabetic rats, and in vitro data indicated that the wound healing effects of NF3 might be due to the regulation and coordination of inflammation, angiogenesis and tissue regeneration. However, the underlying molecular mechanism has not been well investigated. In this study, we investigated the cellular and molecular effects of the herbal formula NF3 on human skin fibroblast cells. MATERIALS AND METHODS Human skin fibroblast cells Hs27 were treated with NF3 ranging from 0 to 8 mg/ml for 24h, and the cells without NF3 treatment were used as control. Cell proliferation assay and cell cycle analysis were performed. Transcriptional profiles of Hs27 cells upon NF3 treatment were acquired by using a human cDNA microarray containing 10,000 genes, and the signaling pathways differentially regulated by NF3 were identified and analyzed. RESULTS NF3 promoted Hs27 cell proliferation and cell cycle progression. Microarray analysis revealed that 116 genes were differentially expressed upon NF3 treatment. Functional analysis of the genes indicated that NF3 mainly activated Wnt and angiogenesis related pathways, which are directly related to cell proliferation, angiogenesis, extracellular matrix (ECM) formation and inflammation during the process of wound healing. CONCLUSION This study provides insight into the molecular mechanism of how the herbal formula Astragali Radix and Rehmanniae Radix may serve as potential therapeutics for wound healing.
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Affiliation(s)
- Qi Zhang
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
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Jian P, Li ZW, Fang TY, Jian W, Zhuan Z, Mei LX, Yan WS, Jian N. Retinoic acid induces HL-60 cell differentiation via the upregulation of miR-663. J Hematol Oncol 2011; 4:20. [PMID: 21518431 PMCID: PMC3094392 DOI: 10.1186/1756-8722-4-20] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 04/25/2011] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Differentiation of the acute myeloid leukemia (AML) cell line HL-60 can be induced by all trans-retinoic acid (ATRA); however, the mechanism regulating this process has not been fully characterized. METHODS Using bioinformatics and in vitro experiments, we identified the microRNA gene expression profile of HL-60 cells during ATRA induced granulocytic differentiation. RESULTS Six microRNAs were upregulated by ATRA treatment, miR-663, miR-494, miR-145, miR-22, miR-363* and miR-223; and three microRNAs were downregulated, miR-10a, miR-181 and miR-612. Additionally, miR-663 expression was regulated by ATRA. We used a lentivirus (LV) backbone incorporating the spleen focus forming virus (SFFV-F) promoter to drive miR-663 expression, as the CMV (Cytomegalovirus) promoter is ineffective in some lymphocyte cells. Transfection of LV-miR-663 induced significant HL-60 cell differentiation in vitro. CONCLUSIONS Our results show miR-663 may play an important role in ATRA induced HL-60 cell differentiation. Lentivirus delivery of miR-663 could potentially be used directly as an anticancer treatment in hematological malignancies.
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Affiliation(s)
- Pan Jian
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China
| | - Zhao Wen Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Tao Yan Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Wang Jian
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Zhou Zhuan
- Hillman Cancer Center Lab, Department of Pathology, Pittsburgh University, G21 5117 Centre Ave. Pittsburgh, PA 15206 USA
| | - Liao Xin Mei
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China
| | - Wu Shui Yan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Ni Jian
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China
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Active compounds-based discoveries about the differentiation and apoptosis of leukemic cells. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11434-009-0628-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Wang J, Chan JYW, Fong CC, Tzang CH, Fung KP, Yang M. Transcriptional analysis of doxorubicin-induced cytotoxicity and resistance in human hepatocellular carcinoma cell lines. Liver Int 2009; 29:1338-47. [PMID: 19627484 DOI: 10.1111/j.1478-3231.2009.02081.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
BACKGROUND/AIMS Hepatoma is either intrinsically resistant to chemotherapy or response to it but later develop resistance. The aim of this study was to clarify the relationship of treatment with doxorubicin (Dox) in hepatoma HepG2 cells and drug resistance developed by Dox. METHODS We have analysed the bioactivities and gene expression profiles of multidrug resistant (MDR) HepG2/DR cell line and its parental HepG2 cell, which were exposure to Dox. RESULTS We confirmed that Dox-induced apoptosis of HepG2 cells in a time-dependent manner; cDNA microarray and hierarchical cluster analysis demonstrate that the features of the transcriptional programme of the later response to Dox in HepG2 cells and MDR HepG2/DR cells have a common character, which is upregulation of stress response, cytoskeleton, ubiquitin-proteasome pathway and repressed G-protein signal transduction system; differentially expressed genes in MDR HepG2/DR such as drug transporters and tumour-associated antigens were verified at the levels of mRNA by semiquantitative reverse transcriptase-polymerase chain reaction. CONCLUSIONS These results reveal novel co-ordinated changes that occurred in resistant HepG2 cells to survive from cell apoptosis elicited by Dox treatment.
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Affiliation(s)
- Jin Wang
- Department of Biology and Chemistry, and Applied Research Centre for Genomics Technology, City University of Hong Kong, Hong Kong, China
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