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da Silva Zanzarini I, Henrique Kita D, Scheiffer G, Karoline Dos Santos K, de Paula Dutra J, Augusto Pastore M, Gomes de Moraes Rego F, Picheth G, Ambudkar SV, Pulvirenti L, Cardullo N, Rotuno Moure V, Muccilli V, Tringali C, Valdameri G. Magnolol derivatives as specific and noncytotoxic inhibitors of breast cancer resistance protein (BCRP/ABCG2). Bioorg Chem 2024; 146:107283. [PMID: 38513324 PMCID: PMC11069345 DOI: 10.1016/j.bioorg.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/20/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
The breast cancer resistance protein (BCRP/ABCG2) transporter mediates the efflux of numerous antineoplastic drugs, playing a central role in multidrug resistance related to cancer. The absence of successful clinical trials using specific ABCG2 inhibitors reveals the urge to identify new compounds to attend this critical demand. In this work, a series of 13 magnolol derivatives was tested as ABCG2 inhibitors. Only two compounds, derivatives 10 and 11, showed partial and complete ABCG2 inhibitory effect, respectively. This inhibition was selective toward ABCG2, since none of the 13 compounds inhibited neither P-glycoprotein nor MRP1. Both inhibitors (10 and 11) were not transported by ABCG2 and demonstrated a low cytotoxic profile even at high concentrations (up to 100 µM). 11 emerged as the most promising compound of the series, considering the ratio between cytotoxicity (IG50) and ABCG2 inhibition potency (IC50), showing a therapeutic ratio (TR) higher than observed for 10 (10.5 versus 1.6, respectively). This derivative showed a substrate-independent and a mixed type of inhibition. The effect of compound 11 on the ABCG2 ATPase activity and thermostability revealed allosteric protein changes. This compound did not affect the expression levels of ABCG2 and increased the binding of the conformational-sensitive antibody 5D3. A docking study showed that 11 did not share the same binding site with ABCG2 substrate mitoxantrone. Finally, 11 could revert the chemoresistance to SN-38 mediated by ABCG2.
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Affiliation(s)
- Isadora da Silva Zanzarini
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Diogo Henrique Kita
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gustavo Scheiffer
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Kelly Karoline Dos Santos
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Matteo Augusto Pastore
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | | | - Geraldo Picheth
- Department of Clinical Analysis, Federal University of Parana, Curitiba, Brazil
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Luana Pulvirenti
- Istituto di Chimica Biomolecolare del Consiglio Nazionale delle Ricerche (ICB-CNR), Catania, Italy
| | - Nunzio Cardullo
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil
| | - Vera Muccilli
- Department of Chemical Sciences, University of Catania, Catania, Italy.
| | - Corrado Tringali
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, Brazil.
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Gupta DG, Varma N, Abdulkadir SA, Singh P, Sachdeva MUS, Naseem S, Siddiqui MR, Bose P, Binota J, Malhotra P, Khadwal A, Varma S. Identification and validation of the optimal reference genes for standardizing the gene expression profiling diagnostic panel of Ph-like B-lineage acute lymphoblastic leukemia. Clin Exp Med 2023; 23:4539-4551. [PMID: 37470909 DOI: 10.1007/s10238-023-01131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/25/2023] [Indexed: 07/21/2023]
Abstract
Gene expression profiling is the criterion standard for recognizing Ph-like ALL signatures among B-ALLs. The prerequisite of GEP is the accurate normalization of target genes with stable expression of housekeeping genes in a quantitative PCR. HKGs exhibit differential expression in the different experimental conditions and affect the target genes' expression, leading to imprecise qPCR results. The selection of stable HKGs is crucial in GEP experiments, especially in identifying high-risk Ph-like ALL cases. We have evaluated the expression stability of nine HKGs (GAPDH, ACTB, GUSB, RNA18S, EEF2, PGK1, B2M, TBP and ABL1) in identified Ph-like ALLs and Ph-negative (n = 23 each) using six algorithms, 4 traditional softwares; geNorm, BestKeeper, NormFinder, Delta Cq value method, and two algorithms, RefFinderTM and ComprFinder. Further, we have validated the expression of 8 overexpressed normalized genes in Ph-like ALL cases (JCHAIN, CA6, MUC4, SPATS2L, BMPR1B, CRLF2, ADGRF1 and NRXN3). GeNorm, BestKeeper, NormFinder, Delta Cq value method, RefFinderTM and ComprFinder algorithm analysis revealed that EEF2, GAPDH, and PGK1 form the best representative HKGs in Ph-like ALL cases, while RNA18s, ß-actin, and ABL1 in Ph-negative ALLs. Lastly, we performed a correlation analysis and found that the combination of EEF2, GAPDH, and PGK1 represents the best combination with a very high correlation in Ph-like ALL cases. This is the first report that shows EEF2, GAPDH, and PGK1 are the best HKG genes and can be used in the diagnostic panel of Ph-like ALL cases using qPCR at baseline diagnosis.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Sarki Abba Abdulkadir
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Parmod Singh
- Department of Anatomy, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Mohammad Rizwan Siddiqui
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Alka Khadwal
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Subhash Varma
- Department of Clinical Hematology and Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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Dutra JDP, Scheiffer G, Kronenberger T, Gomes LJC, Zanzarini I, dos Santos KK, Tonduru AK, Poso A, Rego FGDM, Picheth G, Valdameri G, Moure VR. Structural and molecular characterization of lopinavir and ivermectin as breast cancer resistance protein (BCRP/ABCG2) inhibitors. EXCLI JOURNAL 2023; 22:1155-1172. [PMID: 38204967 PMCID: PMC10776880 DOI: 10.17179/excli2023-6427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 01/12/2024]
Abstract
A current clinical challenge in cancer is multidrug resistance (MDR) mediated by ABC transporters. Breast cancer resistance protein (BCRP) or ABCG2 transporter is one of the most important ABC transporters implicated in MDR and the use of inhibitors is a promising approach to overcome the resistance in cancer. This study aimed to characterize the molecular mechanism of ABCG2 inhibitors identified by a repurposing drug strategy using antiviral, anti-inflammatory and antiparasitic agents. Lopinavir and ivermectin can be considered as pan-inhibitors of ABC transporters, since both compounds inhibited ABCG2, P-glycoprotein and MRP1. They inhibited ABCG2 activity showing IC50 values of 25.5 and 23.4 µM, respectively. These drugs were highly cytotoxic and not transported by ABCG2. Additionally, these drugs increased the 5D3 antibody binding and did not affect the mRNA and protein expression levels. Cell-based analysis of the type of inhibition suggested a non-competitive inhibition, which was further corroborated by in silico approaches of molecular docking and molecular dynamics simulations. These results showed an overlap of the lopinavir and ivermectin binding sites on ABCG2, mainly interacting with E446 residue. However, the substrate mitoxantrone occupies a different site, binding to the F436 region, closer to the L554/L555 plug. In conclusion, these results revealed the mechanistic basis of lopinavir and ivermectin interaction with ABCG2. See also the Graphical abstract(Fig. 1).
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Affiliation(s)
- Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Gustavo Scheiffer
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Lucas Julian Cruz Gomes
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Isadora Zanzarini
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Kelly Karoline dos Santos
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Arun K. Tonduru
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | | | - Geraldo Picheth
- Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba, PR, Brazil
| | - Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
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Toro TB, Skripnikova EV, Bornes KE, Zhang K, Watt TJ. Endogenous expression of inactive lysine deacetylases reveals deacetylation-dependent cellular mechanisms. PLoS One 2023; 18:e0291779. [PMID: 37721967 PMCID: PMC10506724 DOI: 10.1371/journal.pone.0291779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
Acetylation of lysine residues is an important and common post-translational regulatory mechanism occurring on thousands of non-histone proteins. Lysine deacetylases (KDACs or HDACs) are a family of enzymes responsible for removing acetylation. To identify the biological mechanisms regulated by individual KDACs, we created HT1080 cell lines containing chromosomal point mutations, which endogenously express either KDAC6 or KDAC8 having single inactivated catalytic domain. Engineered HT1080 cells expressing inactive KDA6 or KDAC8 domains remained viable and exhibited enhanced acetylation on known substrate proteins. RNA-seq analysis revealed that many changes in gene expression were observed when KDACs were inactivated, and that these gene sets differed significantly from knockdown and knockout cell lines. Using GO ontology, we identified several critical biological processes associated specifically with catalytic activity and others attributable to non-catalytic interactions. Treatment of wild-type cells with KDAC-specific inhibitors Tubastatin A and PCI-34051 resulted in gene expression changes distinct from those of the engineered cell lines, validating this approach as a tool for evaluating in-cell inhibitor specificity and identifying off-target effects of KDAC inhibitors. Probing the functions of specific KDAC domains using these cell lines is not equivalent to doing so using previously existing methods and provides novel insight into the catalytic functions of individual KDACs by investigating the molecular and cellular changes upon genetic inactivation.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Elena V. Skripnikova
- Division of Basic and Pharmaceutical Sciences, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kiara E. Bornes
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kun Zhang
- Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, United States of America
- Bioinformatics Core, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
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Tsochantaridis I, Roupas A, Mohlin S, Pappa A, Voulgaridou GP. The Concept of Cancer Stem Cells: Elaborating on ALDH1B1 as an Emerging Marker of Cancer Progression. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010197. [PMID: 36676146 PMCID: PMC9863106 DOI: 10.3390/life13010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
Cancer is a multifactorial, complex disease exhibiting extraordinary phenotypic plasticity and diversity. One of the greatest challenges in cancer treatment is intratumoral heterogeneity, which obstructs the efficient eradication of the tumor. Tumor heterogeneity is often associated with the presence of cancer stem cells (CSCs), a cancer cell sub-population possessing a panel of stem-like properties, such as a self-renewal ability and multipotency potential. CSCs are associated with enhanced chemoresistance due to the enhanced efflux of chemotherapeutic agents and the existence of powerful antioxidant and DNA damage repair mechanisms. The distinctive characteristics of CSCs make them ideal targets for clinical therapeutic approaches, and the identification of efficient and specific CSCs biomarkers is of utmost importance. Aldehyde dehydrogenases (ALDHs) comprise a wide superfamily of metabolic enzymes that, over the last years, have gained increasing attention due to their association with stem-related features in a wide panel of hematopoietic malignancies and solid cancers. Aldehyde dehydrogenase 1B1 (ALDH1B1) is an isoform that has been characterized as a marker of colon cancer progression, while various studies suggest its importance in additional malignancies. Here, we review the basic concepts related to CSCs and discuss the potential role of ALDH1B1 in cancer development and its contribution to the CSC phenotype.
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Affiliation(s)
- Ilias Tsochantaridis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Angelos Roupas
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Sofie Mohlin
- Division of Pediatrics, Clinical Sciences, Lund Stem Cell Center, Lund University Cancer Center, 22384 Lund, Sweden
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Georgia-Persephoni Voulgaridou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence:
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Janvier AJ, Pendleton EG, Mortensen LJ, Green DC, Henstock JR, Canty-Laird EG. Multimodal analysis of the differential effects of cyclic strain on collagen isoform composition, fibril architecture and biomechanics of tissue engineered tendon. J Tissue Eng 2022; 13:20417314221130486. [PMID: 36339372 PMCID: PMC9629721 DOI: 10.1177/20417314221130486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/18/2022] [Indexed: 11/07/2022] Open
Abstract
Tendon is predominantly composed of aligned type I collagen, but additional isoforms are known to influence fibril architecture and maturation, which contribute to the tendon’s overall biomechanical performance. The role of the less well-studied collagen isoforms on fibrillogenesis in tissue engineered tendons is currently unknown, and correlating their relative abundance with biomechanical changes in response to cyclic strain is a promising method for characterising optimised bioengineered tendon grafts. In this study, human mesenchymal stem cells (MSCs) were cultured in a fibrin scaffold with 3%, 5% or 10% cyclic strain at 0.5 Hz for 3 weeks, and a comprehensive multimodal analysis comprising qPCR, western blotting, histology, mechanical testing, fluorescent probe CLSM, TEM and label-free second-harmonic imaging was performed. Molecular data indicated complex transcriptional and translational regulation of collagen isoforms I, II, III, V XI, XII and XIV in response to cyclic strain. Isoforms (XII and XIV) associated with embryonic tenogenesis were deposited in the formation of neo-tendons from hMSCs, suggesting that these engineered tendons form through some recapitulation of a developmental pathway. Tendons cultured with 3% strain had the smallest median fibril diameter but highest resistance to stress, whilst at 10% strain tendons had the highest median fibril diameter and the highest rate of stress relaxation. Second harmonic generation exposed distinct structural arrangements of collagen fibres in each strain group. Fluorescent probe images correlated increasing cyclic strain with increased fibril alignment from 40% (static strain) to 61.5% alignment (10% cyclic strain). These results indicate that cyclic strain rates stimulate differential cell responses via complex regulation of collagen isoforms which influence the structural organisation of developing fibril architectures.
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Affiliation(s)
- Adam J Janvier
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Emily G Pendleton
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Luke J Mortensen
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Daniel C Green
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK,The Medical Research Council Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Liverpool, UK
| | - James R Henstock
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK,The Medical Research Council Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA), Liverpool, UK,Elizabeth G Canty-Laird, Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Elizabeth G Canty-Laird
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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8
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Han JM, Jung HJ. Cyclophilin A/CD147 Interaction: A Promising Target for Anticancer Therapy. Int J Mol Sci 2022; 23:ijms23169341. [PMID: 36012604 PMCID: PMC9408992 DOI: 10.3390/ijms23169341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Cyclophilin A (CypA), which has peptidyl-prolyl cis-trans isomerase (PPIase) activity, regulates multiple functions of cells by binding to its extracellular receptor CD147. The CypA/CD147 interaction plays a crucial role in the progression of several diseases, including inflammatory diseases, coronavirus infection, and cancer, by activating CD147-mediated intracellular downstream signaling pathways. Many studies have identified CypA and CD147 as potential therapeutic targets for cancer. Their overexpression promotes growth, metastasis, therapeutic resistance, and the stem-like properties of cancer cells and is related to the poor prognosis of patients with cancer. This review aims to understand the biology and interaction of CypA and CD147 and to review the roles of the CypA/CD147 interaction in cancer pathology and the therapeutic potential of targeting the CypA/CD147 axis. To validate the clinical significance of the CypA/CD147 interaction, we analyzed the expression levels of PPIA and BSG genes encoding CypA and CD147, respectively, in a wide range of tumor types using The Cancer Genome Atlas (TCGA) database. We observed a significant association between PPIA/BSG overexpression and poor prognosis, such as a low survival rate and high cancer stage, in several tumor types. Furthermore, the expression of PPIA and BSG was positively correlated in many cancers. Therefore, this review supports the hypothesis that targeting the CypA/CD147 interaction may improve treatment outcomes for patients with cancer.
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Affiliation(s)
- Jang Mi Han
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
| | - Hye Jin Jung
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan 31460, Korea
- Genome-Based BioIT Convergence Institute, Sun Moon University, Asan 31460, Korea
- Correspondence: ; Tel.: +82-41-530-2354; Fax: +82-41-530-2939
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Gupta DG, Varma N, Kumar A, Naseem S, Sachdeva MUS, Bose P, Binota J, Gupta M, Sonam P, Rana P, Malhotra P, Varma S. Identification and validation of suitable housekeeping genes for gene expression studies in BCR-ABL1 positive B-lineage acute lymphoblastic leukemia. Mol Biol Rep 2022; 49:4841-4848. [PMID: 35344115 DOI: 10.1007/s11033-022-07337-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The stability of the housekeeping gene (HKG) expression is an absolute prerequisite for accurate normalization of target gene expression in a quantitative real-time polymerase chain reaction (RQ-PCR). In RQ-PCR, the widely used normalization approach involves the standardization of target genes to the most stable HKG control genes. According to the recent literature, in different experimental conditions the HKGs exhibit either up or down-regulation and thus affecting the gene expression profiles of target genes which leads to erroneous results. This implies that it is very important to select the appropriate HKG and verify the expression stability of the HKG before quantification of the target gene. METHODS AND RESULTS The present study aims to analyze six different HKGs for their expression profiles and stability in BCR-ABL1 negative cases and validate them in BCR-ABL1 positive cases, detected by multiplex reverse transcribed polymerase chain reaction (RT-PCR). Six commonly used reference genes (GAPDH, ABL1, RNA18S, ACTB, GUSB, and EEF2) were selected in this study. RQ-PCR was performed on 24 BCR-ABL1 negative cases and the outcomes were validated on 24 BCR-ABL1 positive cases. RefFinder™, a web-based composite software was used to check the stability of HKG genes by different algorithms and comprehensive ranking of each HKG gene in BCR-ABL1 negative cases and finally validated in BCR-ABL1 positive cases. CONCLUSIONS It was found that RNA18S, ABL1 and GUSB are good stable HKG genes, which showed minimum variability in gene expression compared to GAPDH, EEF2, and ACTB, the most commonly used HKG.
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Affiliation(s)
- Dikshat Gopal Gupta
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India.
| | - Ashish Kumar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shano Naseem
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Jogeshwar Binota
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Minakshi Gupta
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Priti Sonam
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Palak Rana
- Department of Hematology, Post Graduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, 160012, India
| | - Pankaj Malhotra
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Subhash Varma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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10
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O'Callaghan P, Engberg A, Eriksson O, Fatsis-Kavalopoulos N, Stelzl C, Sanchez G, Idevall-Hagren O, Kreuger J. Piezo1 activation attenuates thrombin-induced blebbing in breast cancer cells. J Cell Sci 2022; 135:274949. [PMID: 35274124 PMCID: PMC9016622 DOI: 10.1242/jcs.258809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cancer cells exploit a variety of migration modes to leave primary tumors and establish metastases, including amoeboid cell migration, which is typically reliant on bleb formation. Here we demonstrate that thrombin induces dynamic blebbing in the MDA-MB-231 breast cancer cell line and confirm that protease-activated receptor 1 (PAR1) activation is sufficient to induce this effect. Cell confinement has been implicated as a driving force in bleb-based migration. Unexpectedly, we found that gentle contact compression, exerted using a custom built ‘cell press’ to mechanically stimulate cells, reduced thrombin-induced blebbing. Thrombin-induced blebbing was similarly attenuated using the small molecule Yoda1, an agonist of the mechanosensitive Ca2+ channel Piezo1, and this attenuation was impaired in Piezo1-depleted cells. Additionally, Piezo1 activation suppressed thrombin-induced phosphorylation of ezrin, radixin and moesin (ERM) proteins, which are implicated in the blebbing process. Our results provide mechanistic insights into Piezo1 activation as a suppressor of dynamic blebbing, specifically that which is induced by thrombin. Summary: Thrombin and protease-activated receptor agonists induce dynamic blebbing in breast cancer cells, which can be attenuated by contact-mediated compression, and activation of the mechanosensitive ion channel Piezo1.
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Affiliation(s)
- Paul O'Callaghan
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Adam Engberg
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Olle Eriksson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | | | - Christina Stelzl
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Gonzalo Sanchez
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | | | - Johan Kreuger
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
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11
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da Conceição Braga L, Gonçalves BÔP, Coelho PL, da Silva Filho AL, Silva LM. Identification of best housekeeping genes for the normalization of RT-qPCR in human cell lines. Acta Histochem 2022; 124:151821. [PMID: 34861601 DOI: 10.1016/j.acthis.2021.151821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/01/2022]
Abstract
The identification of the best reference gene is a critical step to evaluate the relative change in mRNA expression of a target gene by RT-qPCR. In this work, we evaluated nineteen genes of different functional classes using Real Time Human Reference Gene Panel (Roche Applied Sciences), to identify the internal housekeeping genes (HKGs) most suitable for gene expression normalization data in human cell lines. Normal cell lines CCD-19LU (lung fibroblast), HEK-293 (epithelial cell of embryonic kidney), WI-26 VA4 (lung fibroblast), and human cancer cells, BT-549 (breast cancer), Hs 578T (breast cancer), MACL-1 (breast cancer), HeLa (cervical carcinoma), U-87 MG (glioblastoma/astrocytoma), RKO-AS45-1 (colorectal carcinoma), and TOV-21G (ovarian adenocarcinoma) were cultivated according to manufacturer's protocol. Twelve candidate reference genes were commonly expressed in five cell lines (CCD-19Lu, HEK-293, RKO-AS45-1, TOV-21G, and U-87 MG). To verify the expression stability, we used the RefFinder web tool, which integrates data from the computational programs Normfinder, BestKeeper, geNorm, and the comparative Delta-Ct method. The ACTB was the most stable reference gene to the CCD-19Lu and HEK-293 cells. The best combination of HKGs for the RKO-AS45-1 and TOV-21G cell lines were B2M/GAPDH and PBGD/B2M, respectively. For the U-87 MG cells, GAPDH and IPO8 were the most suitable HKGs. Thus, our findings showed that it is crucial to use the right HKGs to precise normalize gene expression levels in cancer studies, once a suitable HKG for one cell type cannot be to the other.
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12
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Verma AH, Ganesh S, Venkatakrishnan K, Tan B. Self-functional gold nanoprobes for intra-nuclear epigenomic monitoring of cancer stem-like cells. Biosens Bioelectron 2022; 195:113644. [PMID: 34571478 DOI: 10.1016/j.bios.2021.113644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/02/2022]
Abstract
Cancer epigenomic-environment is a core center of a tumor's genetic and epigenetic configuration. Surveying epigenomic-environment of cancer stem-like cells (CSC) is vital for developing novel diagnostic methods and improving current therapies since CSCs are among the most challenging clinical hurdles. To date, there exists no technique which can successfully monitor the epigenomics of CSC. Here, we have developed unique sub-10 nm Self-functional Gold Nanoprobes (GNP) as a CSC epigenomic monitoring platform that can easily maneuver into the nucleus while not producing any conformal changes to the genomic DNA. The GNP was synthesized using physical synthesis method of pulsed laser multiphoton ionization, which enabled the shrinking of GNP to 2.69 nm which helped us achieve two critical parameters for epigenomics monitoring: efficient nuclear uptake (98%) without complex functionalization and no conformational nuclear changes. The GNP efficiently generated SERS for structural, functional, molecular epigenetics, and nuclear proteomics in preclinical models of breast and lung CSCs. To the best of knowledge, this study is first to utilize the intranuclear epigenomic signal to distinguish between CSC from different tissues with >99% accuracy and specificity. Our findings are anticipated to help advance real-time epigenomics surveillance technologies such as nucleus-targeted drug surveillance and epigenomic prognosis and diagnostics.
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Affiliation(s)
- Anish Hiresha Verma
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada; Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership Between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada; Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada; Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
| | - Swarna Ganesh
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada; Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership Between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada; Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada; Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada; Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership Between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada; Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada; Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada.
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada; Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership Between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada; Nano-characterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3, Canada; Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
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13
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Sánchez-Botet A, Quandt E, Masip N, Escribá R, Novellasdemunt L, Gasa L, Li VSW, Raya Á, Clotet J, Ribeiro MPC. Atypical cyclin P regulates cancer cell stemness through activation of the WNT pathway. Cell Oncol (Dordr) 2021; 44:1273-1286. [PMID: 34604945 PMCID: PMC8648692 DOI: 10.1007/s13402-021-00636-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Cancer stem cells represent a cancer cell subpopulation that has been found to be associated with metastasis and chemoresistance. Therefore, it is vital to identify mechanisms regulating cancer stemness. Previously, we have shown that the atypical cyclin P (CCNP), also known as CNTD2, is upregulated in lung and colorectal cancers and is associated with a worse clinical prognosis. Given that other cyclins have been implicated in pluripotency regulation, we hypothesized that CCNP may also play a role in cancer stemness. METHODS Cell line-derived spheroids, ex vivo intestinal organoid cultures and induced-pluripotent stem cells (iPSCs) were used to investigate the role of CCNP in stemness. The effects of CCNP on cancer cell stemness and the expression of pluripotency markers and ATP-binding cassette (ABC) transporters were evaluated using Western blotting and RT-qPCR assays. Cell viability was assessed using a MTT assay. The effects of CCNP on WNT targets were monitored by RNA-seq analysis. Data from publicly available web-based resources were also analyzed. RESULTS We found that CCNP increases spheroid formation in breast, lung and colorectal cancers, and upregulates the expression of stemness (CD44, CD133) and pluripotency (SOX2, OCT4, NANOG) markers. In addition, we found that CCNP promotes resistance to anticancer drugs and induces the expression of multidrug resistance ABC transporters. Our RNA-seq data indicate that CCNP activates the WNT pathway, and that inhibition of this pathway abrogates the increase in spheroid formation promoted by CCNP. Finally, we found that CCNP knockout decreases OCT4 expression in iPSCs, further supporting the notion that CCNP is involved in stemness regulation. CONCLUSION Our results reveal CCNP as a novel player in stemness and as a potential therapeutic target in cancer.
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Affiliation(s)
- Abril Sánchez-Botet
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Eva Quandt
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Núria Masip
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Rubén Escribá
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain
- Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Laura Novellasdemunt
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | - Laura Gasa
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | - Ángel Raya
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain
- Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Josep Clotet
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain.
| | - Mariana P C Ribeiro
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain.
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14
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Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line. Genes (Basel) 2021; 12:genes12101631. [PMID: 34681026 PMCID: PMC8535678 DOI: 10.3390/genes12101631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stable expression. Additionally, thirteen RGs from the literature were analyzed. The expression variations of the candidate genes were studied over five successive passages (p) in two parallel cultures S1 and S2 and in acute and chronic hypoxia using various algorithms. Finally, the most stable RGs were selected and validated for normalization of the expression of three genes of interest (GOIs) in normoxia and hypoxia. Our results indicate that HSP90AB1, DAD1, PFN1 and PUM1 can be used in any combination of three (triplets) for optimizing intra- and inter-assay gene expression differences in the SK-BR-3 cell line. Additionally, we discourage the use of conventional RGs (ACTB, GAPDH, RPL13A, RNA18S and RNA28S) as internal controls for RT-qPCR in SK-BR-3 cell line.
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15
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Lucero M, Thind J, Sandoval J, Senaati S, Jimenez B, Kandpal RP. Stem-like Cells from Invasive Breast Carcinoma Cell Line MDA-MB-231 Express a Distinct Set of Eph Receptors and Ephrin Ligands. Cancer Genomics Proteomics 2021; 17:729-738. [PMID: 33099474 DOI: 10.21873/cgp.20227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND/AIM Breast cancer cell lines consist of bulk tumor cells and a small proportion of stem-like cells. While the bulk cells are known to express a distinct combination of Eph receptors and ephrin ligands, the transcript profiles of stem-like cells in these cell lines have not been adequately characterized. The aim of this study was to determine Eph receptor/ephrin ligand profiles of cancer stem cells specific to a triple negative breast carcinoma cell line. MATERIALS AND METHODS The normal breast cell line MCF10A and the invasive breast carcinoma cell line MDA-MB-231 were used to isolate CD24+/CD24- cell populations. The profiles of Eph receptors and ephrin ligands were determined by real-time PCR and the relative abundance in bulk and stem cells were compared. RESULTS Based on the mean ΔCT values, the descending order of abundance was as follows. Ephrin-A5 > EPHA2 > (EPHA8, EPHB2) > ephrin-B2 > (EPHA7, EPHB4, ephrin-A4) > ephrin-A3 > ephrin-A1 > (EPHB3, ephrin-B1) > EPHA4 > EPHA1 > EPHA10. EPHA6 and ephrin-A2 transcripts were not detectable in stem cells from either cell line. The expression of EPHA4, EPHA7, EPHA8, and ephrin-A5 in MDA-MB-231 stem cells was up-regulated by 12, 20, ~500, and 6.5-fold respectively. CONCLUSION The up-regulation of transcripts for EPHA8 and its cognate ligand, ephrin-A5, in the stem cells isolated from MDA-MB-231, suggest their involvement in the invasiveness of this cell line. Based on literature reports, we propose the role of EPHA8 and ephrin-A5 in MDA-MB-231 stem cells via the PI3K-AKT-mTOR pathway.
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Affiliation(s)
- Mariana Lucero
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A
| | - Jaspreet Thind
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A
| | - Jacqueline Sandoval
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A
| | - Shayan Senaati
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A
| | - Belinda Jimenez
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A
| | - Raj P Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A.
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16
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Establishment and Characterization of a Sclerosing Spindle Cell Rhabdomyosarcoma Cell Line with a Complex Genomic Profile. Cells 2020; 9:cells9122668. [PMID: 33322555 PMCID: PMC7763666 DOI: 10.3390/cells9122668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
Sclerosing spindle cell rhabdomyosarcoma (SSRMS) is a rare rhabdomyosarcomas (RMS) subtype. Especially cases bearing a myogenic differentiation 1 (MYOD1) mutation are characterized by a high recurrence and metastasis rate, often leading to a fatal outcome. SSRMS cell lines are valuable in vitro models for studying disease mechanisms and for the preclinical evaluation of new therapeutic approaches. In this study, a cell line established from a primary SSRMS tumor of a 24-year-old female after multimodal chemotherapeutic pretreatment has been characterized in detail, including immunohistochemistry, growth characteristics, cytogenetic analysis, mutation analysis, evaluation of stem cell marker expression, differentiation potential, and tumorigenicity in mice. The cell line which was designated SRH exhibited a complex genomic profile, including several translocations and deletions. Array-comparative genomic hybridization (CGH) revealed an overall predominating loss of gene loci. The mesenchymal tumor origin was underlined by the expression of mesenchymal markers and potential to undergo adipogenic and osteogenic differentiation. Despite myogenic marker expression, terminal myogenic differentiation was inhibited, which might be elicited by the MYOD1 hotspot mutation. In vivo tumorigenicity could be confirmed after subcutaneous injection into NOD/SCID/γcnull mice. Summarized, the SRH cell line is the first adult SSRMS cell line available for preclinical research on this rare RMS subtype.
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Okamoto K, Saito Y, Narumi K, Furugen A, Iseki K, Kobayashi M. Different mechanisms of cisplatin resistance development in human lung cancer cells. Biochem Biophys Res Commun 2020; 530:745-750. [PMID: 32782152 DOI: 10.1016/j.bbrc.2020.07.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Cisplatin (CDDP) is a highly potent and important anticancer drug in lung cancer treatment. Long-term use of an anticancer agent causes resistance in cancer cells, and CDDP resistance involves multiple mechanisms. As the mechanism of resistance development differs depending on the cancer cell types, we aimed to evaluate the detailed mechanism of resistance to CDDP in two types of lung cancer cells: SBC-3 and A549 cells. The CDDP-resistant SBC-3/DDP and A549/DDP cells were established through continuous treatment with a gradually increasing dose of CDDP. The viability of SBC-3/DDP and A549/DDP cells treated with CDDP was 3.68 and 2.08 times higher than that of the respective parental cells. Moreover, SBC-3/DDP cells showed significantly increased cystine/glutamate transporter (xCT) mRNA level, and A549/DDP cells showed markedly increased sex determining region Y-box 2 (SOX2) mRNA level. Moreover, the uptake of cystine, a substrate of xCT, was higher in SBC-3/DDP cells than in SBC-3 cells, and cystine uptake in A549/DDP cells was not different from that in A549 cells. In addition, co-treatment with CDDP and sulfasalazine, an xCT inhibitor, showed lower the concentration of 50% inhibition for cell viability than CDDP alone in SBC-3 and SBC-3/DDP cells, but not in A549 and A549/DDP cells. Furthermore, SBC-3 cells transiently overexpressing xCT were resistant to CDDP, and xCT knockdown in A549/DDP cells did not significantly change the level of SOX2 mRNA and viability of cells upon CDDP treatment. In conclusion, the two lung cancer cell lines showed different mechanisms of resistance to CDDP.
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Affiliation(s)
- Keisuke Okamoto
- Laboratory of Clinical Pharmaceutics & Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Yoshitaka Saito
- Department of Pharmacy, Hokkaido University Hospital, Kita-14-jo, Nishi-5-chome, Kita-ku, Sapporo, 060-8648, Japan
| | - Katsuya Narumi
- Laboratory of Clinical Pharmaceutics & Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Ayako Furugen
- Laboratory of Clinical Pharmaceutics & Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Ken Iseki
- Laboratory of Clinical Pharmaceutics & Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Masaki Kobayashi
- Laboratory of Clinical Pharmaceutics & Therapeutics, Division of Pharmasciences, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12-jo, Nishi-6-chome, Kita-ku, Sapporo, 060-0812, Japan.
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18
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Ambrosini G, Dalla Pozza E, Fanelli G, Di Carlo C, Vettori A, Cannino G, Cavallini C, Carmona-Carmona CA, Brandi J, Rinalducci S, Scupoli MT, Rasola A, Cecconi D, Palmieri M, Dando I. Progressively De-Differentiated Pancreatic Cancer Cells Shift from Glycolysis to Oxidative Metabolism and Gain a Quiescent Stem State. Cells 2020; 9:cells9071572. [PMID: 32605166 PMCID: PMC7408749 DOI: 10.3390/cells9071572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is typically characterized by high chemoresistance and metastatic spread, features mainly attributable to cancer stem cells (CSCs). It is of central interest the characterization of CSCs and, in particular, the study of their metabolic features in order to selectively identify their peculiarities for an efficient therapeutic approach. In this study, CSCs have been obtained by culturing different PDAC cell lines with a specific growth medium. Cells were characterized for the typical stem/mesenchymal properties at short-, medium-, and long-term culture. Metabolomics, proteomics, analysis of oxygen consumption rate in live cells, and the effect of the inhibition of lactate transporter on cell proliferation have been performed to delineate the metabolism of CSCs. We show that gradually de-differentiated pancreatic cancer cells progressively increase the expression of both stem and epithelial-to-mesenchymal transition markers, shift their metabolism from a glycolytic to an oxidative one, and lastly gain a quiescent state. These quiescent stem cells are characterized by high chemo-resistance, clonogenic ability, and metastatic potential. Re-differentiation reverts these features, re-activating their proliferative capacity and glycolytic metabolism, which generally correlates with high aggressiveness. These observations add an important piece of knowledge to the comprehension of the biology of CSCs, whose metabolic plasticity could be exploited for the generation of promising and selective therapeutic approaches for PDAC patients.
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Affiliation(s)
- Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
| | - Elisa Dalla Pozza
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
| | - Giuseppina Fanelli
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (S.R.)
| | - Claudia Di Carlo
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.D.C.); (A.V.); (J.B.); (D.C.)
| | - Andrea Vettori
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.D.C.); (A.V.); (J.B.); (D.C.)
| | - Giuseppe Cannino
- Department of Biomedical Sciences, University of Padova, 35122 Padova, Italy; (G.C.); (A.R.)
| | - Chiara Cavallini
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, 37134 Verona, Italy;
| | - Cristian Andres Carmona-Carmona
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
| | - Jessica Brandi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.D.C.); (A.V.); (J.B.); (D.C.)
| | - Sara Rinalducci
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (S.R.)
| | - Maria Teresa Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
- Research Center LURM (Interdepartmental Laboratory of Medical Research), University of Verona, 37134 Verona, Italy;
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, 35122 Padova, Italy; (G.C.); (A.R.)
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.D.C.); (A.V.); (J.B.); (D.C.)
| | - Marta Palmieri
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
| | - Ilaria Dando
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.D.P.); (C.A.C.-C.); (M.T.S.); (M.P.)
- Correspondence: ; Tel.: +39-045-8027174
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19
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Al Matari N, Deeb G, Mshiek H, Sinjab A, Kadara H, Abou-Kheir W, Mhanna R. Anti-Tumor Effects of Biomimetic Sulfated Glycosaminoglycans on Lung Adenocarcinoma Cells in 2D and 3D In Vitro Models. Molecules 2020; 25:E2595. [PMID: 32503108 PMCID: PMC7321182 DOI: 10.3390/molecules25112595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022] Open
Abstract
Lung cancer development relies on cell proliferation and migration, which in turn requires interaction with extracellular matrix (ECM) components such as glycosaminoglycans (GAGs). The mechanisms through which GAGs regulate cancer cell functions are not fully understood but they are, in part, mediated by controlled interactions with cytokines and growth factors (GFs). In order to mechanistically understand the effect of the degree of sulfation (DS) of GAGs on lung adenocarcinoma (LUAD) cells, we synthesized sulfated alginate (AlgSulf) as sulfated GAG mimics with DS = 0.0, 0.8, 2.0, and 2.7. Human (H1792) and mouse (MDA-F471) LUAD cell lines were treated with AlgSulf of various DSs at two concentrations 10 and 100 µg/mL and their anti-tumor properties were assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), trypan blue exclusion, and wound healing assays for 2D models and sphere formation assay for the 3D model. The proliferation and number of live MDA-F471 cells at the concentration of 100 µg/mL decreased significantly with the increase in the DS of biomimetic GAGs. In addition, the increase in the DS of biomimetic GAGs decreased cell migration (p < 0.001 for DS = 2.0 and 2.7 compared to control) and decreased the diameter and number of spheres formed (p < 0.001). The increased DS of biomimetic GAGs attenuated the expression of cancer stem cell (CSC)/progenitor markers in the 3D cultures. In conclusion, GAG-mimetic AlgSulf with increased DS exhibit enhanced anti-proliferative and migratory properties while also reducing growth of KRAS-mutant LUAD spheres in vitro. We suggest that these anti-tumor effects by GAG-mimetic AlgSulf are possibly due to differential binding to GFs and consequential decreased cell stemness. AlgSulf may be suitable for applications in cancer therapy after further in vivo validation.
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Affiliation(s)
- Nada Al Matari
- Department of Biomedical Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (N.A.M.); (G.D.)
| | - George Deeb
- Department of Biomedical Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (N.A.M.); (G.D.)
| | - Hiba Mshiek
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon;
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (H.K.)
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (H.K.)
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon;
| | - Rami Mhanna
- Department of Biomedical Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (N.A.M.); (G.D.)
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20
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Molecular Chaperones in Cancer Stem Cells: Determinants of Stemness and Potential Targets for Antitumor Therapy. Cells 2020; 9:cells9040892. [PMID: 32268506 PMCID: PMC7226806 DOI: 10.3390/cells9040892] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer stem cells (CSCs) are a great challenge in the fight against cancer because these self-renewing tumorigenic cell fractions are thought to be responsible for metastasis dissemination and cases of tumor recurrence. In comparison with non-stem cancer cells, CSCs are known to be more resistant to chemotherapy, radiotherapy, and immunotherapy. Elucidation of mechanisms and factors that promote the emergence and existence of CSCs and their high resistance to cytotoxic treatments would help to develop effective CSC-targeting therapeutics. The present review is dedicated to the implication of molecular chaperones (protein regulators of polypeptide chain folding) in both the formation/maintenance of the CSC phenotype and cytoprotective machinery allowing CSCs to survive after drug or radiation exposure and evade immune attack. The major cellular chaperones, namely heat shock proteins (HSP90, HSP70, HSP40, HSP27), glucose-regulated proteins (GRP94, GRP78, GRP75), tumor necrosis factor receptor-associated protein 1 (TRAP1), peptidyl-prolyl isomerases, protein disulfide isomerases, calreticulin, and also a transcription heat shock factor 1 (HSF1) initiating HSP gene expression are here considered as determinants of the cancer cell stemness and potential targets for a therapeutic attack on CSCs. Various approaches and agents are discussed that may be used for inhibiting the chaperone-dependent development/manifestations of cancer cell stemness.
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21
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Bond C, Johnson J, Chaudhary V, McCarthy E, McWhorter M, Woehrle N. Perinatal fluoxetine exposure results in social deficits and reduced monoamine oxidase gene expression in mice. Brain Res 2020; 1727:146282. [DOI: 10.1016/j.brainres.2019.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/28/2019] [Accepted: 06/01/2019] [Indexed: 12/27/2022]
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22
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Selection of reference genes suitable for normalization of RT-qPCR data in glioma stem cells. Biotechniques 2019; 68:130-137. [PMID: 31870167 DOI: 10.2144/btn-2019-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Considering the importance of gene expression studies for understanding the biology of glioma stem cells (GSCs), we aimed to identify the reliable reference genes in GSCs that were derived from the glioma cell lines T98G, LN229, 090116 and 091214. Quantitative real-time reverse-transcription PCR was employed using 11 reference genes identified through a PubMed literature search, and the assessment of stability through the geNorm, Normfinder and coefficient of variation methods was performed to select suitable reference genes. We found that HPRT1 and RPL13A were the most suitable reference genes, and validated the geometric mean of these genes to normalize the expression of stemness genes by GSCs. Therefore, it is necessary to select novel cell-specific reference genes with greater expression stability for gene expression studies in GSCs.
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23
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Romswinkel A, Infanger M, Dietz C, Strube F, Kraus A. The Role of C-X-C Chemokine Receptor Type 4 (CXCR4) in Cell Adherence and Spheroid Formation of Human Ewing's Sarcoma Cells under Simulated Microgravity. Int J Mol Sci 2019; 20:ijms20236073. [PMID: 31810195 PMCID: PMC6929163 DOI: 10.3390/ijms20236073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
We studied the behavior of Ewing's Sarcoma cells of the line A673 under simulated microgravity (s-µg). These cells express two prominent markers-the oncogene EWS/FLI1 and the chemokine receptor CXCR4, which is used as a target of treatment in several types of cancer. The cells were exposed to s-µg in a random-positioning machine (RPM) for 24 h in the absence and presence of the CXCR4 inhibitor AMD3100. Then, their morphology and cytoskeleton were examined. The expression of selected mutually interacting genes was measured by qRT-PCR and protein accumulation was determined by western blotting. After 24 h incubation on the RPM, a splitting of the A673 cell population in adherent and spheroid cells was observed. Compared to 1 g control cells, EWS/FLI1 was significantly upregulated in the adherent cells and in the spheroids, while CXCR4 and CD44 expression were significantly enhanced in spheroids only. Transcription of CAV-1 was upregulated and DKK2 and VEGF-A were down-regulated in both, adherent in spheroid cells, respectively. Regarding, protein accumulation EWS/FLI1 was enhanced in adherent cells only, but CD44 decreased in spheroids and adherent cells. Inhibition of CXCR4 did not change spheroid count, or structure. Under s-µg, the tumor marker EWS/FLI1 is intensified, while targeting CXCR4, which influences adhesion proteins, did not affect spheroid formation.
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Affiliation(s)
| | | | | | | | - Armin Kraus
- Correspondence: ; Tel.: +49-391-67-15599; Fax: +49-391-67-15588
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24
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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25
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Pavlou M, Shah M, Gikas P, Briggs T, Roberts S, Cheema U. Osteomimetic matrix components alter cell migration and drug response in a 3D tumour-engineered osteosarcoma model. Acta Biomater 2019; 96:247-257. [PMID: 31302294 DOI: 10.1016/j.actbio.2019.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Osteosarcoma management continues to lack the appropriate prognostic tools to assign personalised treatment. This leaves non-responders to standard care vulnerable to recurring disease and pulmonary metastases. Developing 3D in vitro disease models to serve as a test bed for personalised treatment is a promising approach to address this issue. This study describes the generation of 3D osteosarcoma models termed "tumouroids", which are geometrically compartmentalised to reproduce the bone cancer mass and its surrounding. Although the tumour microenvironment impacts osteosarcoma in many ways, this model focussed on interrogating the influence of a biomimetic matrix on tumour cell behaviour. The 3D matrix was supplemented with the bone-marrow proteins laminin, fibronectin and NuOss® bone granules. This led to increased invasion of osteosarcoma cell aggregates from within the bone-like matrix into the surrounding acellular bone marrow-like ECM. The presence of bone granules also yielded an atypical molecular profile of osteosarcoma cells, suggesting malignant metabolic reprogramming. Changes include decreased MMP-9 (p < 0.05) and increased PTEN (p < 0.05), MCP-1 (p < 0.01) and MCT-4 (p < 0.05) gene expression. This complex 3D biomimetic composition also changed cellular responses to doxorubicin, a common chemotherapeutic agent used to treat osteosarcoma, and reproduced key issues of in vivo treatment like drug penetrance and doxorubicin-induced bone toxicity. This work highlights the importance of a biomimetic matrix in 3D osteosarcoma models for both basic and translational research. STATEMENT OF SIGNIFICANCE: This study describes the generation of 3D osteosarcoma models termed "tumouroids", which are geometrically compartmentalised to reproduce the bone cancer mass and its environment. Utilising this novel model, specific parameters of osteosarcoma growth and invasion were investigated. Osteosarcoma cell lines proliferate at a slower rate, exhibit malignant metabolic reprogramming, and respond to drug intervention at lower concentrations of doxorubicin hydrochloride in matrix-complex compared to basic tumouroids. As such, this study provides evidence that the tumour microenvironment impacts osteosarcoma in many ways. The osteosarcoma tumouroid described herein may form the basis of a personalised-medicine strategy, which will allow the testing of drug effectiveness similar to that used for antibiotic selection for pathogenic bacteria.
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26
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de Lázaro I, Kostarelos K. Exposure to graphene oxide sheets alters the expression of reference genes used for real-time RT-qPCR normalization. Sci Rep 2019; 9:12520. [PMID: 31467336 PMCID: PMC6715796 DOI: 10.1038/s41598-019-48970-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 08/07/2019] [Indexed: 11/19/2022] Open
Abstract
Studies unraveling the interactions between graphene oxide (GO) and the biological milieu, including cells and tissues, are multiplying quickly as the biomedical applications of this and other 2D materials continue to be explored. Many of such studies rely on real-time RT-qPCR as a powerful yet simple technique to assess gene expression. However, a systematic investigation of potential GO-induced changes in the expression of reference genes, crucial for appropriate qPCR data normalization, is still lacking. We aimed to cover this gap investigating the stability of the expression of ten candidate reference genes upon exposure to increasing, but subtoxic, GO concentrations, with two established algorithms (Bestkeeper and NormFinder). The study was performed in a human cancer cell line (MCF7) and in mouse, non-cancerous, primary cells (mouse embryonic fibroblasts, MEFs), to assess different behaviors between cell types. Both algorithms evidenced significant deviations in the expression of various reference genes. Ribosomal proteins scored among the most significantly dysregulated in both cell types. ACTB and GAPDH, the most frequent calibrators in real-time RT-qPCR, were also affected, although differences existed between cell lines. This study illustrates the need to validate reference genes for appropriate real-time RT-qPCR normalization, according to specific experimental conditions, when GO-cell interactions occur.
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Affiliation(s)
- Irene de Lázaro
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, AV Hill Building, The University of Manchester, Manchester, M13 9PT, UK. .,National Graphene Institute, The University of Manchester, Booth Street E, Manchester, M13 9PL, UK. .,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| | - Kostas Kostarelos
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, AV Hill Building, The University of Manchester, Manchester, M13 9PT, UK.,National Graphene Institute, The University of Manchester, Booth Street E, Manchester, M13 9PL, UK
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27
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Bag AK, Mandloi S, Jarmalavicius S, Mondal S, Kumar K, Mandal C, Walden P, Chakrabarti S, Mandal C. Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PLoS Comput Biol 2019; 15:e1007090. [PMID: 31386654 PMCID: PMC6684045 DOI: 10.1371/journal.pcbi.1007090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
As malignant transformation requires synchronization of growth-driving signaling (S) and metabolic (M) pathways, defining cancer-specific S-M interconnected networks (SMINs) could lead to better understanding of oncogenic processes. In a systems-biology approach, we developed a mathematical model for SMINs in mutated EGF receptor (EGFRvIII) compared to wild-type EGF receptor (EGFRwt) expressing glioblastoma multiforme (GBM). Starting with experimentally validated human protein-protein interactome data for S-M pathways, and incorporating proteomic data for EGFRvIII and EGFRwt GBM cells and patient transcriptomic data, we designed a dynamic model for EGFR-driven GBM-specific information flow. Key nodes and paths identified by in silico perturbation were validated experimentally when inhibition of signaling pathway proteins altered expression of metabolic proteins as predicted by the model. This demonstrated capacity of the model to identify unknown connections between signaling and metabolic pathways, explain the robustness of oncogenic SMINs, predict drug escape, and assist identification of drug targets and the development of combination therapies. Complex and highly dynamic interconnected networks allow cancer to take different routes and circumvent chemotherapy. Therefore, understanding these context-specific networks and their dynamics of molecular interactions driven by different oncogenic signaling and metabolic pathways is very much needed to predict drug targets and the effect of therapeutics. We incorporated high-throughput transcriptome and proteome data into mathematical models to deduce properties of cancer cells through systems biology approach. Here we report the development, testing and validation of an integrated systems biology model of information flow between signaling and metabolic pathways to understand the regulation of the interconnection between them in cancer. Our model efficiently identified unique connections and key nodes important in signaling-metabolic information flow. We predicted some potential novel targets before performing actual drug tests. We have successfully applied this model to identify the interconnections altered in the constitutive signaling of the mutated EGFR by comparing EGF-dependent and wild-type EGFR signaling in glioblastoma multiforme.
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Affiliation(s)
- Arup K. Bag
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Sapan Mandloi
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Saulius Jarmalavicius
- Department of Dermatology, Venerology and Allergology, Charité– Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susmita Mondal
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Krishna Kumar
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Chhabinath Mandal
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Peter Walden
- Department of Dermatology, Venerology and Allergology, Charité– Universitätsmedizin Berlin corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- * E-mail: (PW); , (SC); , (CM)
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Kolkata, India
- * E-mail: (PW); , (SC); , (CM)
| | - Chitra Mandal
- Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
- * E-mail: (PW); , (SC); , (CM)
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28
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Improving characterisation of human Multipotent Stromal Cells cultured in 2D and 3D: Design and evaluation of primer sets for accurate gene expression normalisation. PLoS One 2018; 13:e0209772. [PMID: 30596738 PMCID: PMC6312307 DOI: 10.1371/journal.pone.0209772] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023] Open
Abstract
Human Multipotent Stromal Cells (MSCs) are a valuable resource for regenerative medicine and are widely studied. They can be isolated from a variety of tissues and differentiate into multiple cell types (multi-potent). Many reports have been published using human MSCs and to be able to compare outcome, or be able to identify differences between MSCs, several cell surface markers have been proposed. Nevertheless, still many differences remain. Gene expression is known to be different between cell stage and origin. Furthermore, cells cultured on a culture dish (2D) show different gene expression profiles as compared to cells grown on scaffolds (3D). Even the RNA extraction method and the selection of genes used for normalisation have a role in gene expression profiling. To be able to compare gene expression data from samples cultured in different dimensions and RNA extracted using a variety of protocols we set out to define a set of reference genes suitable to normalise qPCR data from a very heterogeneous sample set. Hereto, Trizol was used to extract RNA from human MSCs cultured in 3D and 2D to validate newly designed and previously published primer sets. Subsequently, RNA from fresh human MSC samples and samples stored in RLT-buffer, Trizol or RNAlater was extracted using RNeasy and Trizol methods. All samples have been used to rank the candidate reference genes according to their stability after qPCR enabling identification of the most suitable reference gene(s) for normalisation of a heterogeneous sample set. The most stably expressed reference genes indicated superior normalisation of MSC marker gene expression over the least stable reference genes.
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29
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Zhang Q, Zhang M, Li J, Xiao H, Wu D, Guo Q, Zhang Y, Wang H, Li S, Liao S. Selection and Validation of Reference Genes for RT-PCR Expression Analysis of Candidate Genes Involved in Morphine-Induced Conditioned Place Preference Mice. J Mol Neurosci 2018; 66:587-594. [PMID: 30386959 DOI: 10.1007/s12031-018-1198-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022]
Abstract
The expression of reference genes should be constitutively stable under the experimental conditions, so determining stable reference genes is critical for obtaining reliable results in gene expression studies. Morphine addiction persistently influences neurotransmitters and signal transduction systems, which may negatively alter behavioral responses at the cellular levels and interfere the expression of reference genes. In order to research morphine dependence, animal models are commonly used in physiology, pathology, and therapeutics field since human trials have many limitations. Therefore, it is necessary to select stable reference genes in standardized animal model. The objective of this study is to find out a set of optimal reference genes to standardize the gene expression of morphine-induced conditioned place preference (CPP) mice. During the process, eight reference genes were chosen. Then, the stability of their expression in two different brain tissues (Caudate Putamen and Hippocampus) was tested in two developmental stages (puberty and adult) under two treatments (physiological saline as control and morphine). Based on two algorithm-based methods (geNorm and NormFinder), which can rank and assess the stability of expression of eight reference genes, thereby quantifying the transcriptional levels of these genes by high sensitive, specific, and accurate real-time quantitative reverse transcription PCR (RT-qPCR) assays.
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Affiliation(s)
- Qian Zhang
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mengting Zhang
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Jiaqi Li
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hai Xiao
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Dong Wu
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Qiannan Guo
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Yuwei Zhang
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Hongdan Wang
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Zhengzhou University People's Hospital, Zhengzhou, Henan, China. .,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Shengbin Li
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Shixiu Liao
- Henan Provincial Key Medical Laboratory of Genetics, Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.
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30
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Validation of Suitable Housekeeping Genes for the Normalization of mRNA Expression for Studying Tumor Acidosis. Int J Mol Sci 2018; 19:ijms19102930. [PMID: 30261649 PMCID: PMC6213411 DOI: 10.3390/ijms19102930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Similar to other types of cancer, acidification of tumor microenvironment is an important feature of osteosarcoma, and a major source of cellular stress that triggers cancer aggressiveness, drug resistance, and progression. Among the different effects of low extracellular pH on tumor cells, we have recently found that short-term exposure to acidosis strongly affects gene expression. This alteration might also occur for the most commonly used housekeeping genes (HKG), thereby causing erroneous interpretation of RT-qPCR data. On this basis, by using osteosarcoma cells cultured at different pH values, we aimed to identify the ideal HKG to be considered in studies on tumor-associated acidosis. We verified the stability of 15 commonly used HKG through five algorithms (NormFinder, geNorm, BestKeeper, ΔCT, coefficient of variation) and found that no universal HKG is suitable, since at least four HKG are necessary for proper normalization. Furthermore, according to the acceptable range of values, YWHAZ, GAPDH, GUSB, and 18S rRNA were the most stable reference genes at different pH. Our results will be helpful for future investigations focusing on the effect of altered microenvironment on cancer behavior, particularly on the effectiveness of anticancer therapies in acid conditions.
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Jiménez G, Hackenberg M, Catalina P, Boulaiz H, Griñán-Lisón C, García MÁ, Perán M, López-Ruiz E, Ramírez A, Morata-Tarifa C, Carrasco E, Aguilera M, Marchal JA. Mesenchymal stem cell's secretome promotes selective enrichment of cancer stem-like cells with specific cytogenetic profile. Cancer Lett 2018; 429:78-88. [DOI: 10.1016/j.canlet.2018.04.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/15/2022]
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de Campos RP, Schultz IC, de Andrade Mello P, Davies S, Gasparin MS, Bertoni APS, Buffon A, Wink MR. Cervical cancer stem-like cells: systematic review and identification of reference genes for gene expression. Cell Biol Int 2018; 42:139-152. [PMID: 28949053 DOI: 10.1002/cbin.10878] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/24/2017] [Indexed: 12/21/2022]
Abstract
Cervical cancer is the fourth most common cancer affecting women worldwide. Among many factors, the presence of cancer stem cells, a subpopulation of cells inside the tumor, has been associated with a worse prognosis. Considering the importance of gene expression studies to understand the biology of cervical cancer stem cells (CCSC), this work identifies stable reference genes for cervical cancer cell lines SiHa, HeLa, and ME180 as well as their respective cancer stem-like cells. A literature review was performed to identify validated reference genes currently used to normalize RT-qPCR data in cervical cancer cell lines. Then, cell lines were cultured in regular monolayer or in a condition that favors tumor sphere formation. RT-qPCR was performed using five reference genes: ACTB, B2M, GAPDH, HPRT1, and TBP. Stability was assessed to validate the selected genes as suitable reference genes. The evaluation validated B2M, GAPDH, HPRT1, and TBP in these experimental conditions. Among them, GAPDH and TBP presented the lowest variability according to the analysis by Normfinder, Bestkeeper, and ΔCq methods, being therefore the most adequate genes to normalize the combination of all samples. These results suggest that B2M, GAPDH, HPRT1, and TBP are suitable reference genes to normalize RT-qPCR data of established cervical cancer cell lines SiHa, HeLa, and ME180 as well as their derived cancer stem-like cells. Indeed, GAPDH and TBP seem to be the most convenient choices for studying gene expression in these cells in monolayers or spheres.
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Affiliation(s)
- Rafael P de Campos
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
| | - Iago C Schultz
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
| | - Paola de Andrade Mello
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
- Laboratório de Análises Bioquímicas e Citológicas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90610-000, Rio Grande do Sul, Brazil
| | - Samuel Davies
- Laboratório de Análises Bioquímicas e Citológicas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90610-000, Rio Grande do Sul, Brazil
| | - Manuela S Gasparin
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
- Laboratório de Análises Bioquímicas e Citológicas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90610-000, Rio Grande do Sul, Brazil
| | - Ana P S Bertoni
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
| | - Andréia Buffon
- Laboratório de Análises Bioquímicas e Citológicas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90610-000, Rio Grande do Sul, Brazil
| | - Márcia R Wink
- Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, Rio Grande do Sul, Brazil
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Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Human Stem Cell Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1119:151-168. [PMID: 30267307 DOI: 10.1007/5584_2018_277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely utilized method for evaluating the gene expressions in stem cell research. This method enables researchers to obtain fast and precise results, but the accuracy of the data depends on certain factors, such as those associated with biological sample preparation and PCR efficiency. In order to achieve accurate and reliable results, it is of utmost importance to designate the reference genes, the expressions of which are suitable to all kinds of experimental conditions. Hence it is vital to normalize the qRT-PCR data by using the reference genes. In recent years, it has been found that the expression levels of reference genes widely used in stem cell research present a substantial amount of variation and are not necessarily suitable for normalization. This chapter at hand stresses the significance of selecting suitable reference genes from the point view of human stem cell research.
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Picot T, Kesr S, Wu Y, Aanei CM, Flandrin-Gresta P, Tondeur S, Tavernier E, Wattel E, Guyotat D, Campos L. Potential Role of OCT4 in Leukemogenesis. Stem Cells Dev 2017; 26:1637-1647. [DOI: 10.1089/scd.2017.0134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Tiphanie Picot
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Sanae Kesr
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Yuenv Wu
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Carmen Mariana Aanei
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Pascale Flandrin-Gresta
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Sylvie Tondeur
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Emmanuelle Tavernier
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
- Département d'Hématologie et Thérapie Cellulaire, Institut de Cancérologie Lucien Neuwirth, Saint-Etienne, France
| | - Eric Wattel
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
| | - Denis Guyotat
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
- Département d'Hématologie et Thérapie Cellulaire, Institut de Cancérologie Lucien Neuwirth, Saint-Etienne, France
| | - Lydia Campos
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire de Saint-Etienne, Saint-Etienne, France
- Laboratoire de Biologie et Modélisation de la Cellule, UMR 5239, Lyon, France
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Lemma S, Di Pompo G, Porporato PE, Sboarina M, Russell S, Gillies RJ, Baldini N, Sonveaux P, Avnet S. MDA-MB-231 breast cancer cells fuel osteoclast metabolism and activity: A new rationale for the pathogenesis of osteolytic bone metastases. Biochim Biophys Acta Mol Basis Dis 2017; 1863:3254-3264. [PMID: 28866133 DOI: 10.1016/j.bbadis.2017.08.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 12/19/2022]
Abstract
Recent progress in dissecting the molecular paracrine circuits of cancer and stromal cells in bone metastases (BM) are offering new options to improve current merely palliative approach. The study of tumor-stroma metabolic interplay may further ameliorate this scenario. In this context, we demonstrated that highly glycolytic MDA-MB-231 cancer cells, that form osteolytic BM in vivo, release a large amount of lactate at a significantly higher level than MCF7 cells. Thus, we speculated that lactate released from carcinoma cells is uptaken and metabolically used by osteoclasts, the key players of osteolysis associated with BM. First, we demonstrated that the release of lactate at the bone site is mediated by monocarboxylate transporter 4 (MCT4), as revealed by immunostaining and MCT4 localization at the plasma membrane of tumor cells in mouse model of BM and in human tissue sections of BM. Then, we showed that in vitro lactate is uptaken by osteoclasts to be used as a fuel for the oxidative metabolism of osteoclasts, ultimately enhancing Type I collagen resorption. The passive transport of lactate into osteoclasts was mediated by MCT1: MCT1 expression is significantly upregulated during osteoclast differentiation and Type I collagen resorption is significantly impaired when osteoclasts are treated with 7-(N-benzyl-N-methylamino)-2-oxo-2H-chromene-3-carboxylic acid, an MCT-1 inhibitor. Together, these data demonstrate that lactate released by glycolytic breast carcinoma cells in the bone microenvironment promotes the formation of osteolytic lesions, and provide the rationale for further studies on the use of MCT1 targeting as a novel therapeutic approach in advanced cancer patients with BM.
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Affiliation(s)
- Silvia Lemma
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Gemma Di Pompo
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo E Porporato
- Pole of Pharmacology, Institute of Experimental and Clinical Research (IREC), Université catholique de Louvain (UCL), Brussels, Belgium
| | - Martina Sboarina
- Pole of Pharmacology, Institute of Experimental and Clinical Research (IREC), Université catholique de Louvain (UCL), Brussels, Belgium
| | - Shonagh Russell
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States
| | - Robert J Gillies
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States
| | - Nicola Baldini
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pierre Sonveaux
- Pole of Pharmacology, Institute of Experimental and Clinical Research (IREC), Université catholique de Louvain (UCL), Brussels, Belgium
| | - Sofia Avnet
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy.
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Carmona R, Arroyo M, Jiménez-Quesada MJ, Seoane P, Zafra A, Larrosa R, Alché JDD, Claros MG. Automated identification of reference genes based on RNA-seq data. Biomed Eng Online 2017; 16:65. [PMID: 28830520 PMCID: PMC5568602 DOI: 10.1186/s12938-017-0356-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. Results An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. Conclusion Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs. Electronic supplementary material The online version of this article (doi:10.1186/s12938-017-0356-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosario Carmona
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Macarena Arroyo
- Servicio de Neumología, Hospital Regional Universitario de Málaga, Avda Carlos Haya s/n, Malaga, Spain
| | - María José Jiménez-Quesada
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain
| | - Adoración Zafra
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Rafael Larrosa
- Departamento de Arquitectura de Computadores, Universidad de Málaga, Malaga, Spain
| | - Juan de Dios Alché
- Plant Reproductive Biology Laboratory, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Malaga, Spain.
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Picot T, Aanei CM, Fayard A, Flandrin-Gresta P, Tondeur S, Gouttenoire M, Tavernier-Tardy E, Wattel E, Guyotat D, Campos L. Expression of embryonic stem cell markers in acute myeloid leukemia. Tumour Biol 2017; 39:1010428317716629. [PMID: 28718379 DOI: 10.1177/1010428317716629] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Acute myeloid leukemia is driven by leukemic stem cells which can be identified by cross lineage expression or arrest of differentiation compared to normal hematopoietic stem cells. Self-renewal and lack of differentiation are also features of stem cells and have been associated with the expression of embryonic genes. The aim of our study was to evaluate the expression of embryonic antigens (OCT4, NANOG, SOX2, SSEA1, SSEA3) in hematopoietic stem cell subsets (CD34+CD38- and CD34+CD38+) from normal bone marrows and in samples from acute myeloid leukemia patients. We observed an upregulation of the transcription factors OCT4 and SOX2 in leukemic cells as compared to normal cells. Conversely, SSEA1 protein was downregulated in leukemic cells. The expression of OCT4, SOX2, and SSEA3 was higher in CD34+CD38- than in CD34+CD38+ subsets in leukemic cells. There was no correlation with biological characteristics of the leukemia. We evaluated the prognostic value of marker expression in 69 patients who received an intensive treatment. The rate of complete remission was not influenced by the level of expression of markers. Overall survival was significantly better for patients with high SOX2 levels, which was unexpected because of the inverse correlation with favorable genetic subtypes. These results prompt us to evaluate the potential role of these markers in leukemogenesis and to test their relevance for better leukemic stem cell identification.
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Affiliation(s)
- Tiphanie Picot
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Carmen Mariana Aanei
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Amandine Fayard
- 3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Pascale Flandrin-Gresta
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Sylvie Tondeur
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Marina Gouttenoire
- 3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Emmanuelle Tavernier-Tardy
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.,3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Eric Wattel
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Denis Guyotat
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.,3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Lydia Campos
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
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Identification of reference genes for qPCR analysis during hASC long culture maintenance. PLoS One 2017; 12:e0170918. [PMID: 28182697 PMCID: PMC5300122 DOI: 10.1371/journal.pone.0170918] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/12/2017] [Indexed: 01/15/2023] Open
Abstract
Up to now quantitative PCR based assay is the most common method for characterizing or confirming gene expression patterns and comparing mRNA levels in different sample populations. Since this technique is relative easy and low cost compared to other methods of characterization, e.g. flow cytometry, we used it to typify human adipose-derived stem cells (hASCs). hASCs possess several characteristics that make them attractive for scientific research and clinical applications. Accurate normalization of gene expression relies on good selection of reference genes and the best way to choose them appropriately is to follow the common rule of the “Best 3”, at least three reference genes, three different validation software and three sample replicates. Analysis was performed on hASCs cultivated until the eleventh cell confluence using twelve candidate reference genes, initially selected from literature, whose stability was evaluated by the algorithms NormFinder, BestKeeper, RefFinder and IdealRef, a home-made version of GeNorm. The best gene panel (RPL13A, RPS18, GAPDH, B2M, PPIA and ACTB), determined in one patient by IdealRef calculation, was then investigated in other four donors. Although patients demonstrated a certain gene expression variability, we can assert that ACTB is the most unreliable gene whereas ribosomal proteins (RPL13A and RPS18) show minor inconstancy in their mRNA expression. This work underlines the importance of validating reference genes before conducting each experiment and proposes a free software as alternative to those existing.
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Normann KR, Øystese KAB, Berg JP, Lekva T, Berg-Johnsen J, Bollerslev J, Olarescu NC. Selection and validation of reliable reference genes for RT-qPCR analysis in a large cohort of pituitary adenomas. Mol Cell Endocrinol 2016; 437:183-189. [PMID: 27561203 DOI: 10.1016/j.mce.2016.08.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/11/2016] [Accepted: 08/20/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Real-time reverse transcription quantitative PCR (RT-qPCR) has become the method of choice for quantification of gene expression changes. The most important limitations of RT-qPCR are inappropriate data normalization and inconsistent data analyses. Pituitary adenomas are common tumours, and the appropriate interpretation of increasingly published data within this field is prevented by the lack of a proper selection and validation of stably expressed reference genes. AIM To find and validate the optimal reference gene or gene combination for reliable RT-qPCR gene expression in both non-functioning (NFPA) and hormone secreting (GH and ACTH) pituitary adenomas. MATERIAL AND METHODS Thirty commonly used reference genes (PCR array reference gene panel, BioRad, Hercules, CA) were quantified by RT-qPCR in 24 pituitary adenomas (12 NFPA, 8 GH and 4 ACTH). The data was analysed using three programs: geNorm (Qbase+), Normfinder and BestKeeper having different algorithms to identify the most stable reference gene or combination of reference genes. Three reference genes ALAS1, PSMC4 and GAPDH, were selected for further validation in a larger cohort of 223 adenomas (141 NFPA, 63 GH and 19 ACTH). RESULTS In all adenomas, ALAS1 and PSMC4 were the most stable reference genes as estimated by geNorm and Normfinder, whereas Bestkeeper ranked RPLP0 and ACTB as the two most stable out of 10 carefully selected genes. The best gene combination was PSMC4 and ALAS1 (geNorm) or PSMC4 and GAPDH (Normfinder). The validation experiment (geNorm) showed that the most stable gene combinations were ALAS1 and GAPDH in NFPA, and PSMC4 and GAPDH in hormone secreting adenomas. CONCLUSIONS Several of the reference genes expressed good stability yielding several candidate genes. PSMC4 and ALAS1 were overall the most stably expressed genes in pituitary adenoma merely differing in ranking order. PSMC4 and ALAS1 have so far not been reported as reference genes in pituitary adenomas. The various reference gene algorithms showed a mixed selection of top ranked genes, thus suggesting a need for an individualised and rational choice of reference genes.
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Affiliation(s)
- Kjersti Ringvoll Normann
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Research Institute for Internal Medicine, Oslo University Hospital, Oslo, Norway.
| | - Kristin Astrid Berland Øystese
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Petter Berg
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Tove Lekva
- Research Institute for Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Jon Berg-Johnsen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
| | - Jens Bollerslev
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nicoleta Cristina Olarescu
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway; Research Institute for Internal Medicine, Oslo University Hospital, Oslo, Norway
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Cortini M, Massa A, Avnet S, Bonuccelli G, Baldini N. Tumor-Activated Mesenchymal Stromal Cells Promote Osteosarcoma Stemness and Migratory Potential via IL-6 Secretion. PLoS One 2016; 11:e0166500. [PMID: 27851822 PMCID: PMC5112800 DOI: 10.1371/journal.pone.0166500] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/28/2016] [Indexed: 12/20/2022] Open
Abstract
Osteosarcoma (OS) is an aggressive bone malignancy with a high relapse rate despite combined treatment with surgery and multiagent chemotherapy. As for other cancers, OS-associated microenvironment may contribute to tumor initiation, growth, and metastasis. We consider mesenchymal stromal cells (MSC) as a relevant cellular component of OS microenvironment, and have previously found that the interaction between MSC and tumor cells is bidirectional: tumor cells can modulate their peripheral environment that in turn becomes more favorable to tumor growth through metabolic reprogramming. Here, we determined the effects of MSC on OS stemness and migration, two major features associated with recurrence and chemoresistance. The presence of stromal cells enhanced the number of floating spheres enriched in cancer stem cells (CSC) of the OS cell population. Furthermore, the co-culturing with MSC stimulated the migratory capacity of OS via TGFβ1 and IL-6 secretion, and the neutralizing antibody anti-IL-6 impaired this effect. Thus, stromal cells in combination with OS spheres exploit a vicious cycle where the presence of CSC stimulates mesenchymal cytokine secretion, which in turn increases stemness, proliferation, migration, and metastatic potential of CSC, also through the increase of expression of adhesion molecules like ICAM-1. Altogether, our data corroborate the concept that a comprehensive knowledge of the interplay between tumor and stroma that also includes the stem-like fraction of tumor cells is needed to develop novel and effective anti-cancer therapies.
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Affiliation(s)
- Margherita Cortini
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli (IOR), 40136, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126, Bologna, Italy
| | - Annamaria Massa
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli (IOR), 40136, Bologna, Italy
| | - Sofia Avnet
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli (IOR), 40136, Bologna, Italy
| | - Gloria Bonuccelli
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli (IOR), 40136, Bologna, Italy
| | - Nicola Baldini
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli (IOR), 40136, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126, Bologna, Italy
- * E-mail:
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Krzystek-Korpacka M, Hotowy K, Czapinska E, Podkowik M, Bania J, Gamian A, Bednarz-Misa I. Serum availability affects expression of common house-keeping genes in colon adenocarcinoma cell lines: implications for quantitative real-time PCR studies. Cytotechnology 2016; 68:2503-2517. [PMID: 27339468 PMCID: PMC5101321 DOI: 10.1007/s10616-016-9971-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/18/2016] [Indexed: 11/29/2022] Open
Abstract
Careful selection of housekeeping genes (HKG) is prerequisite to yield sound qPCR results. HKG expression varies in response to hypoxia but the effect of manipulations of serum availability, a common experimental procedure, remains unknown. Also, no data on HKG expression stability across colon adenocarcinoma lines that would aid selection of normalizers suitable for studies involving several lines are available. Thus, we evaluated the effect of serum availability on the expression of commonly used HKG (ACTB, B2M, GAPDH, GUSB, HPRT1, IPO8, MRPL19, PGK1, PPIA, RPLP0, RPS23, SDHA, TBP, UBC, and YWHAZ) in seven colon adenocarcinoma cell lines (Caco-2, DLD-1, HCT116, HT29, Lovo, SW480, and SW620). Sets of stably expressed line-specific and pan-line HKG were validated against absolutely quantified CDKN1A, TP53, and MDK transcripts. Both serum availability and line type affected HKG expression. UBC was fourfold down-regulated and HPRT1 1.75-fold up-regulated in re-fed HT29 cultures. Line-to-line variability in HKG expression was more pronounced than that caused by altering serum availability and could be found even between isogenic cell lines. PPIA, RPLP0, YWHAZ, and IPO8 were repeatedly highly ranked while ACTB, B2M, UBC, and PGK1 were ranked poorly. Normalization against PPIA/RPLP0/SDHA was found optimal for studies involving various colon adenocarcinoma cell lines subjected to manipulations of serum availability. We found HKG expression to vary, more pronouncedly by line type than growth conditions with significant differences also between isogenic cell lines. Although using line-specific normalizers remains optimal, a set of pan-line HKG that yields good estimation of relative expression of target genes was proposed.
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Affiliation(s)
| | - Katarzyna Hotowy
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
| | - Elzbieta Czapinska
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
| | - Magdalena Podkowik
- Department of Food Hygiene and Consumer Health, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Andrzej Gamian
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland.,Wroclaw Research Center EIT+, Wroclaw, Poland
| | - Iwona Bednarz-Misa
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
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42
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Cancer Stem Cell Quiescence and Plasticity as Major Challenges in Cancer Therapy. Stem Cells Int 2016; 2016:1740936. [PMID: 27418931 PMCID: PMC4932171 DOI: 10.1155/2016/1740936] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/15/2016] [Indexed: 02/06/2023] Open
Abstract
Cells with stem-like properties, tumorigenic potential, and treatment-resistant phenotypes have been identified in many human malignancies. Based on the properties they share with nonneoplastic stem cells or their ability to initiate and propagate tumors in vivo, such cells were designated as cancer stem (stem-like) or tumor initiating/propagating cells. Owing to their implication in treatment resistance, cancer stem cells (CSCs) have been the subject of intense investigation in past years. Comprehension of CSCs' intrinsic properties and mechanisms they develop to survive and even enhance their aggressive phenotype within the hostile conditions of the tumor microenvironment has reoriented therapeutic strategies to fight cancer. This report provides selected examples of malignancies in which the presence of CSCs has been evidenced and briefly discusses methods to identify, isolate, and functionally characterize the CSC subpopulation of cancer cells. Relevant biological targets in CSCs, their link to treatment resistance, proposed targeting strategies, and limitations of these approaches are presented. Two major aspects of CSC physiopathology, namely, relative in vivo quiescence and plasticity in response to microenvironmental cues or treatment, are highlighted. Implications of these findings in the context of the development of new therapies are discussed.
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43
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Arun PVPS, Miryala SK, Chattopadhyay S, Thiyyagura K, Bawa P, Bhattacharjee M, Yellaboina S. Identification and functional analysis of essential, conserved, housekeeping and duplicated genes. FEBS Lett 2016; 590:1428-37. [PMID: 27129600 DOI: 10.1002/1873-3468.12192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 01/09/2023]
Abstract
Gene conservation, duplication and constitutive expression are intricately linked and strong predictors of essentiality. Here, we introduce metrics based on diversity indices to measure gene conservation, duplication and constitutive expression and validate them by measuring their performance in prediction of essential genes. Conservation and duplication were measured using the diversity indices on the bit score profile of Escherichia coli K12 orthologues, across the genomes, and paralogues, within the genome respectively. Constitutive expression was measured using expression diversity of E. coli K12 genes across different conditions. In addition, we developed a systematic method for enrichment analysis of gene-sets in a given ranked list of genes. The method was used to identify genome-wide functions of essential, conserved, constitutively expressed and duplicated genes. Furthermore, we also ranked various operons, complexes and pathways according to their essentiality, conservation, constitutive expression and duplication.
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Affiliation(s)
- P V Parvati Sai Arun
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | - Sravan Kumar Miryala
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.,National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Subhayan Chattopadhyay
- School of Mathematics and Statistics, University of Hyderabad, Hyderabad, Telangana, India
| | - Kranthi Thiyyagura
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | - Payal Bawa
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | | | - Sailu Yellaboina
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
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