1
|
Tanton H, Sewastianik T, Seo HS, Remillard D, Pierre RS, Bala P, Aitymbayev D, Dennis P, Adler K, Geffken E, Yeoh Z, Vangos N, Garbicz F, Scott D, Sethi N, Bradner J, Dhe-Paganon S, Carrasco RD. A novel β-catenin/BCL9 complex inhibitor blocks oncogenic Wnt signaling and disrupts cholesterol homeostasis in colorectal cancer. SCIENCE ADVANCES 2022; 8:eabm3108. [PMID: 35486727 PMCID: PMC9054024 DOI: 10.1126/sciadv.abm3108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Dysregulated Wnt/β-catenin signaling is implicated in the pathogenesis of many human cancers, including colorectal cancer (CRC), making it an attractive clinical target. With the aim of inhibiting oncogenic Wnt activity, we developed a high-throughput screening AlphaScreen assay to identify selective small-molecule inhibitors of the interaction between β-catenin and its coactivator BCL9. We identified a compound that consistently bound to β-catenin and specifically inhibited in vivo native β-catenin/BCL9 complex formation in CRC cell lines. This compound inhibited Wnt activity, down-regulated expression of the Wnt/β-catenin signature in gene expression studies, disrupted cholesterol homeostasis, and significantly reduced the proliferation of CRC cell lines and tumor growth in a xenograft mouse model of CRC. This study has therefore identified a specific small-molecule inhibitor of oncogenic Wnt signaling, which may have value as a probe for functional studies and has important implications for the development of novel therapies in patients with CRC.
Collapse
Affiliation(s)
- Helen Tanton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tomasz Sewastianik
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine,, Warsaw, Poland
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Roodolph St. Pierre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Daulet Aitymbayev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Peter Dennis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Keith Adler
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ezekiel Geffken
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zoe Yeoh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicholas Vangos
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Filip Garbicz
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine,, Warsaw, Poland
| | - David Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ruben D. Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Identification of Reference Genes for Expression Studies in the Whole-Blood from Three Cattle Breeds under Two States of Livestock Weather Safety. Animals (Basel) 2021; 11:ani11113073. [PMID: 34827805 PMCID: PMC8614315 DOI: 10.3390/ani11113073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Reductions in the fertility, body weight, and growth rate of cattle across the world are associated with the global warming phenomenon. Developing optimal management strategies is an important aspect of breeding programs for different breeds. Blood tissue undergoes dramatic physiological and metabolic changes during heat stress conditions, which involves the expression and regulation of a great number of genes across species. Real-time quantitative PCR (qPCR) is a method for the rapid and reliable quantification of mRNA transcription. Reference genes are used to normalize mRNA levels between different samples. Thus, the selection of high-quality reference genes is necessary for the interpretation of data generated by real-time PCR. Abstract Real-time PCR is widely used to study the relative abundance of mRNA due to its specificity, sensitivity, and repeatability quantification. However, relative quantification requires a reference gene, which should be stable in its expression, showing lower variation by experimental conditions or tissues. The aim of this study was to evaluate the stability of the expression of five commonly used reference genes (actb, ywhaz, b2m, sdha, and 18s rRNA) at different physiological stages (alert and emergency) in three different cattle breeds. In this study, five genes (actb, ywhaz, b2m, sdha, and 18s rRNA) were selected as candidate reference genes for expression studies in the whole blood from three cattle breeds (Romosinuano, Gyr, and Brahman) under heat stress conditions. The transcription stability of the candidate reference genes was evaluated using geNorm and NormFinder. The results showed that actb, 18SrRNA, and b2m expression were the most stable reference genes for whole blood of Gyr and Brahman breeds under two states of livestock weather safety (alert and emergency). Meanwhile, actb, b2m, and ywhaz were the most stable reference genes for the Romosinuano breed.
Collapse
|
3
|
Rafieenia F, Nikkhah E, Nourmohammadi F, Hosseini S, Abdollahi A, Sharifi N, Aliakbarian M, Forghani Fard MM, Gholamin M, Abbaszadegan MR. Allogeneic tumor cell line-based vaccines: A good alternative to autologous and cancer stem cell vaccines in colorectal cancer. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1231-1239. [PMID: 35083010 PMCID: PMC8751741 DOI: 10.22038/ijbms.2021.56732.12671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/27/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Besides the uncertainty about colorectal cancer stem cell (CCSC) markers, isolating, purifying, and enriching CCSCs to produce CCSC vaccines is highly challenging. However, allogeneic vaccines developed from CRC cell lines can provide universal, comprehensive, inexpensive, simple, and fast approach to cancer treatment. MATERIALS AND METHODS CCSCs were isolated from human CRC tissue using the in vitro sphere formation assay and then characterized through gene expression analysis, in vivo and in vitro tumor formation assay, karyotyping, and surface marker detection. Subsequently, CCSCs and two CRC cell lines (HT-29 and SW-480) were inactivated with cisplatin (CDDP) and administrated as vaccines to the three groups of athymic C57BL/6 nude mice. Afterward, tumorigenesis was challenged with HT-29 cells. The antitumor effect of vaccines was evaluated by tumor and spleen examination and immune response analysis. The cytotoxic activity of splenocytes and serum levels of TGF-β and IFN-γ were measured by Calcein-AM cytotoxicity assay and enzyme-linked immunosorbent assay (ELISA), respectively. RESULTS The results of gene expression analysis showed that CCSCs are CD44+CD133-LGR5-. All vaccinations resulted in decreased tumor growth, spleen enlargement, enhanced serum level of IFN-γ and TGF-β, and increased cytotoxic activity of natural killer (NK) cells. The antitumor efficacy of the CCSC vaccine was not more than CRC cell line-based vaccines. Interestingly, the allogeneic SW-480 vaccine could effectively inhibit tumorigenesis. CONCLUSION Despite the great challenge in developing CCSC vaccines, allogeneic vaccines based on CRC cell lines can efficiently induce antitumor immunity in CRC.
Collapse
Affiliation(s)
- Fatemeh Rafieenia
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Nikkhah
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Susan Hosseini
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Abdollahi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nurieh Sharifi
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Aliakbarian
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mehran Gholamin
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
4
|
Solis-Hernandez MP, Martín C, García B, Pérez-López N, García-Mesa Y, González-Fernández S, García-Suárez O, Merayo J, Fernández-Vega I, Quirós LM. The Genes Encoding Small Leucine-Rich Proteoglycans Undergo Differential Expression Alterations in Colorectal Cancer, Depending on Tumor Location. Cells 2021; 10:cells10082002. [PMID: 34440771 PMCID: PMC8391422 DOI: 10.3390/cells10082002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022] Open
Abstract
Small leucine-rich proteoglycans (SLRPs) regulate different processes and undergo significant alterations in various diseases. Colon carcinomas (CCs) are heterogeneous pathologies with important clinical and molecular differences depending on their location, which makes it interesting to analyze the alterations in SLRPs in right- and left-sided tumors (RS- and LSCCs). SLRP transcription levels were studied in 32 CCs using qPCR compared to healthy colon mucosae samples from the same patients, 20 of them from LSCCs and the remaining 12 from RSCCs. Protein expression of genes with significant differences in their transcriptions was analyzed by immunohistochemistry. The alterations observed were related to survival data. The arrangement of transcription of SLRPs was quite similar in ascending and descending colon, but RS- and LSCCs displayed different patterns of alteration, with a greater number of deregulations occurring in the latter. The analysis of protein expression also indicated changes in the location of these molecules, largely moving to the cell interior. While podocan underexpression showed a trend toward better outcomes, no differences were observed in terms of overall survival. In vitro studies using the HT29 tumor cell line suggest that deregulation of SLRPs could affect cell proliferation. SLRPs constitute new differential markers of RS- and LSCCs, showing differences dependent on the anatomical location of the tumor.
Collapse
Affiliation(s)
- Maria Pilar Solis-Hernandez
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Av. Roma, s/n, 33011 Oviedo, Spain;
| | - Carla Martín
- Department of Functional Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (C.M.); (B.G.); (N.P.-L.); (S.G.-F.)
- Instituto Universitario Fernández-Vega, University of Oviedo, Av. Drs Fernández Vega, 34, 33012 Oviedo, Spain;
| | - Beatriz García
- Department of Functional Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (C.M.); (B.G.); (N.P.-L.); (S.G.-F.)
- Instituto Universitario Fernández-Vega, University of Oviedo, Av. Drs Fernández Vega, 34, 33012 Oviedo, Spain;
| | - Natalia Pérez-López
- Department of Functional Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (C.M.); (B.G.); (N.P.-L.); (S.G.-F.)
| | - Yolanda García-Mesa
- Department of Morphology and Cell Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (Y.G.-M.); (O.G.-S.)
| | - Sara González-Fernández
- Department of Functional Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (C.M.); (B.G.); (N.P.-L.); (S.G.-F.)
| | - Olivia García-Suárez
- Department of Morphology and Cell Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (Y.G.-M.); (O.G.-S.)
| | - Jesús Merayo
- Instituto Universitario Fernández-Vega, University of Oviedo, Av. Drs Fernández Vega, 34, 33012 Oviedo, Spain;
- Department of Surgery, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain
| | - Iván Fernández-Vega
- Instituto Universitario Fernández-Vega, University of Oviedo, Av. Drs Fernández Vega, 34, 33012 Oviedo, Spain;
- Department of Surgery, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain
- Department of Pathology, Hospital Universitario Central de Asturias, Av. Roma, s/n, 33011 Oviedo, Spain
- Correspondence: (I.F.-V.); (L.M.Q.)
| | - Luis M. Quirós
- Department of Functional Biology, University of Oviedo, Av. Julián Clavería, 6, 33006 Oviedo, Spain; (C.M.); (B.G.); (N.P.-L.); (S.G.-F.)
- Instituto Universitario Fernández-Vega, University of Oviedo, Av. Drs Fernández Vega, 34, 33012 Oviedo, Spain;
- Correspondence: (I.F.-V.); (L.M.Q.)
| |
Collapse
|
5
|
Becker W, Alrafas HR, Busbee PB, Walla MD, Wilson K, Miranda K, Cai G, Putluri V, Putluri N, Nagarkatti M, Nagarkatti PS. Cannabinoid Receptor Activation on Haematopoietic Cells and Enterocytes Protects against Colitis. J Crohns Colitis 2020; 15:1032-1048. [PMID: 33331878 PMCID: PMC8218712 DOI: 10.1093/ecco-jcc/jjaa253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Cannabinoid receptor [CB] activation can attenuate inflammatory bowel disease [IBD] in experimental models and human cohorts. However, the roles of the microbiome, metabolome, and the respective contributions of haematopoietic and non-haematopoietic cells in the anti-colitic effects of cannabinoids have yet to be determined. METHODS Female C57BL/6 mice were treated with either cannabidiol [CBD], Δ 9-tetrahydrocannabinol [THC], a combination of CBD and THC, or vehicle, in several models of chemically induced colitis. Clinical parameters of colitis were assessed by colonoscopy, histology, flow cytometry, and detection of serum biomarkers; single-cell RNA sequencing and qRT-PCR were used to evaluate the effects of cannabinoids on enterocytes. Immune cell transfer from CB2 knockout mice was used to evaluate the contribution of haematopoietic and non-haematopoietic cells to colitis protection. RESULTS We found that THC prevented colitis and that CBD, at the dose tested, provided little benefit to the amelioration of colitis, nor when added synergistically with THC. THC increased colonic barrier integrity by stimulating mucus and tight junction and antimicrobial peptide production, and these effects were specific to the large intestine. THC increased colonic Gram-negative bacteria, but the anti-colitic effects of THC were independent of the microbiome. THC acted both on immune cells via CB2 and on enterocytes, to attenuate colitis. CONCLUSIONS Our findings demonstrate how cannabinoid receptor activation on both immune cells and colonocytes is critical to prevent colonic inflammation. These studies also suggest how cannabinoid receptor activation can be used as a preventive and therapeutic modality against colitis.
Collapse
Affiliation(s)
- William Becker
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Haider Rasheed Alrafas
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Philip B Busbee
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Michael D Walla
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Kiesha Wilson
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Kathryn Miranda
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Guoshuai Cai
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Vasanta Putluri
- Dan L. Duncan Cancer Center, Advanced Technology Core, Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Nagireddy Putluri
- Dan L. Duncan Cancer Center, Advanced Technology Core, Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA,Corresponding author: Prakash S. Nagarkatti, PhD, Department of Pathology, Microbiology and Immunology, University of South Carolina, Columbia, SC 29208, USA. Tel.: [803] 777–5458; fax: [803] 777–5457;
| |
Collapse
|
6
|
Vermani L, Kumar R, Senthil Kumar N. GAPDH and PUM1: Optimal Housekeeping Genes for Quantitative Polymerase Chain Reaction-Based Analysis of Cancer Stem Cells and Epithelial-Mesenchymal Transition Gene Expression in Rectal Tumors. Cureus 2020; 12:e12020. [PMID: 33457124 PMCID: PMC7797410 DOI: 10.7759/cureus.12020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The overwhelming majority of published articles have taken colon and rectal cancer as a single group, i.e., colorectal cancer, when normalizing gene expression data with housekeeping genes (HKG) in quantitative polymerase chain reaction (qPCR) experiments though there are published reports that suggest the differential expression pattern of genes between the colon and rectal cancer groups and hence the current experiment was attempted to find out the optimal set of housekeeping genes from the list of common HKG for rectal tumor gene expression analysis. Methods The expression of five potential housekeeping genes GAPDH, RPNI, PUM1, B2M, and PMM1 was analyzed through qPCR and Bestkeeper software (http://www.wzw.tum.de/gene-quantification/bestkeeper.html) in 20 stage II-IV rectal cancer samples to check for uniformity in their expression pattern. Cancer stem cell (CSC) marker ALDH1 and epithelial-mesenchymal transition marker (EMT) markers E cadherin, vimentin, Twist, and SNAI2 expression were evaluated in conjunction with the two optimal reference genes in 10 rectal cancers as part of validation. Results The standard deviation of the cycle threshold value of GAPDH was found the lowest at 0.65 followed by RPN1 at 0.88, PUM1 at 0.94, PMM1 at 0.94, and B2M at 1.21 when analyzed with BestKeeper software. Using GAPDH and PUM1 as the reference gene for the validation phase, rectal cancer patients with stage III/IV showed a 4.79-fold change (P=0.006) in ALDH1 expression, and an 11.76-fold change in Twist expression (P=0.003) with respect to stage II rectal tumor when normalized with GAPDH and PUM1. Conclusion GAPDH and PUM1 can be used as an optimal set of housekeeping genes for gene expression-related experiments in rectal tumors. ALDH1 and Twist were found significantly overexpressed in stage III/IV rectal tumors in comparison to stage II rectal cancer. Genes associated with cancer stem cells and EMT markers could be optimally analyzed by normalizing them with GAPDH and PUM1 as housekeeping genes.
Collapse
Affiliation(s)
| | - Rajeev Kumar
- Research, Cachar Cancer Hospital and Research Centre, Silchar, IND
| | | |
Collapse
|
7
|
Collagen and fibronectin promote an aggressive cancer phenotype in breast cancer cells but drive autonomous gene expression patterns. Gene 2020; 761:145024. [PMID: 32755659 DOI: 10.1016/j.gene.2020.145024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/08/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Understanding how various pathologies of breast cancer respond to their environment may be imperative in the creation of novel therapeutic targets. Central to the organisation and behaviour of cells within the tumour microenvironment is the extracellular matrix (ECM), a meshwork of fibrous proteins and glycoproteins that directly influences cell behaviour and the bioavailability of signalling molecules. Our appreciation on how the composition of the ECM can influence cancer behaviour has evolved significantly and although we are highly cognisant of the dramatic impact the ECM can have on cancer cell behaviour, we continue to neglect this during diagnosis and treatment. In the following study, we aimed to identify how three breast cancer cell lines respond functionally and genetically to common components of the ECM. Using real time and end point assays we have identified similar patterns of behaviour among the three breast cancer cell lines in response to commonly found ECM components of the breast. Using a selected gene panel, we have been able to identify cell line specific changes in gene differentiation when breast cancer cells are in contact with these elements. Although the response of our cells to these elements differ at the genetic level, their functional responses are consistent. This work adds to the growing arguments that highlight a need for histologically assessing ECM composition of breast tumours. In particular monitoring of fibrous protein deposition at the site of malignancy could provide critical information during clinical assessment influencing disease prognosis and treatment decisions for breast cancer patients.
Collapse
|
8
|
Expression of Annexin A2 Promotes Cancer Progression in Estrogen Receptor Negative Breast Cancers. Cells 2020; 9:cells9071582. [PMID: 32629869 PMCID: PMC7407301 DOI: 10.3390/cells9071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/22/2020] [Accepted: 06/27/2020] [Indexed: 12/26/2022] Open
Abstract
When breast cancer progresses to a metastatic stage, survival rates decline rapidly and it is considered incurable. Thus, deciphering the critical mechanisms of metastasis is of vital importance to develop new treatment options. We hypothesize that studying the proteins that are newly synthesized during the metastatic processes of migration and invasion will greatly enhance our understanding of breast cancer progression. We conducted a mass spectrometry screen following bioorthogonal noncanonical amino acid tagging to elucidate changes in the nascent proteome that occur during epidermal growth factor stimulation in migrating and invading cells. Annexin A2 was identified in this screen and subsequent examination of breast cancer cell lines revealed that Annexin A2 is specifically upregulated in estrogen receptor negative (ER-) cell lines. Furthermore, siRNA knockdown showed that Annexin A2 expression promotes the proliferation, wound healing and directional migration of breast cancer cells. In patients, Annexin A2 expression is increased in ER- breast cancer subtypes. Additionally, high Annexin A2 expression confers a higher probability of distant metastasis specifically for ER- patients. This work establishes a pivotal role of Annexin A2 in breast cancer progression and identifies Annexin A2 as a potential therapeutic target for the more aggressive and harder to treat ER- subtype.
Collapse
|
9
|
Sahoo PK, Parida S, Mohapatra A, Mohanty J. Selection of candidate reference genes for RT-qPCR analysis in Argulus siamensis and their validation through screening of drugs and drug targets. Sci Rep 2019; 9:18365. [PMID: 31798003 PMCID: PMC6892791 DOI: 10.1038/s41598-019-54881-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Argulus spp. are economically important fish ectoparasites. The development of antiparasitic drugs is thus important and real time PCR is an indispensable tool in drug development. The analytical potential of RT-PCR depends upon accurate normalisation by the use of stable reference genes. Here, we identified stable reference genes of Argulus siamensis for validation of efficacy of drugs and drug targets. Seven candidate genes were evaluated by evaluating their expression under different states of Argulus using the RefFinder tool. The four algorithms together generated a comprehensive ranking with elongation factor-1 alpha (EF-1α) being the most stable and 18S ribosomal protein (18S) the least stable gene. Taking EF-1α and 18S genes as references, the effectiveness of six anti-parasitic compounds against Argulus was evaluated by studying their effect on the expression pattern of few ion channel genes; this was to understand their mode of action, besides validating the reference genes. EF-1α was found to be the most stable gene in the validation. Collectively, this study is the first report to validate the optimal reference genes of A. siamensis for normalisation, and the potential of the ion channel genes for evaluating effective drug targets in parasite control.
Collapse
Affiliation(s)
- Pramoda Kumar Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India.
| | - Sonali Parida
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| | - Amruta Mohapatra
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| | - Jyotirmaya Mohanty
- Fish Genetics & Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| |
Collapse
|
10
|
Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS. Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues. BMC MEDICAL GENETICS 2019; 20:138. [PMID: 31409279 PMCID: PMC6693228 DOI: 10.1186/s12881-019-0867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Background Reference genes are often interchangeably called housekeeping genes due to 1) the essential cellular functions their proteins provide and 2) their constitutive expression across a range of normal and pathophysiological conditions. However, given the proliferative drive of malignant cells, many reference genes such as beta-actin (ACTB) and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) which play critical roles in cell membrane organization and glycolysis, may be dysregulated in tumors versus their corresponding normal controls Methods Because Next Generation Sequencing (NGS) technology has several advantages over hybridization-based technologies, such as independent detection and quantitation of transcription levels, greater sensitivity, and increased dynamic range, we evaluated colorectal cancers (CRC) and their histologically normal tissue counterparts by NGS to evaluate the expression of 21 “classical” reference genes used as normalization standards for PCR based methods. Seventy-nine paired tissue samples of CRC and their patient matched healthy colonic tissues were subjected to NGS analysis of their mRNAs. Results We affirmed that 17 out of 21 classical reference genes had upregulated expression in tumors compared to normal colonic epithelial tissue and dramatically so in some cases. Indeed, tumors were distinguished from normal controls in both unsupervised hierarchical clustering analyses (HCA) and principal component analyses (PCA). We then identified 42 novel potential reference genes with minimal coefficients of variation (CV) across 79 CRC tumor pairs. Though largely consistently expressed across tumors and normal control tissues, a subset of high stage tumors (HSTs) as well as some normal tissue samples (HSNs) located adjacent to these HSTs demonstrated dysregulated expression, thus identifying a subset of tumors with a potentially distinct and aggressive biological profile. Conclusion While classical CRC reference genes were found to be differentially expressed between tumors and normal controls, novel reference genes, identified via NGS, were more consistently expressed across malignant and normal colonic tissues. Nonetheless, a subset of HST had profound dysregulation of such genes as did many of the histologically normal tissues adjacent to such HSTs, indicating that the HSTs so distinguished may have unique biological properties and that their histologically normal tissues likely harbor a small population of microscopically undetected but metabolically active tumors. Electronic supplementary material The online version of this article (10.1186/s12881-019-0867-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lai Xu
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA. .,Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA. .,, Silver Spring, USA.
| | - Helen Luo
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Rong Wang
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Je-Nie Phue
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | | | - Leihong Wu
- OCS/NCTR/DBB, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | - Lorraine Pelosof
- Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA
| | | |
Collapse
|
11
|
Majerník M, Jendželovský R, Babinčák M, Košuth J, Ševc J, Tonelli Gombalová Z, Jendželovská Z, Buríková M, Fedoročko P. Novel Insights into the Effect of Hyperforin and Photodynamic Therapy with Hypericin on Chosen Angiogenic Factors in Colorectal Micro-Tumors Created on Chorioallantoic Membrane. Int J Mol Sci 2019; 20:E3004. [PMID: 31248208 PMCID: PMC6627608 DOI: 10.3390/ijms20123004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 01/06/2023] Open
Abstract
Photodynamic therapy with hypericin (HY-PDT) and hyperforin (HP) could be treatment modalities for colorectal cancer (CRC), but evidence of their effect on angiogenic factors in CRC is missing. Convenient experimental model utilization is essential for angiogenesis research. Therefore, not only 2D cell models, but also 3D cell models and micro-tumors were used and compared. The micro-tumor extent and interconnection with the chorioallantoic membrane (CAM) was determined by histological analyses. The presence of proliferating cells and HY penetration into the tumor mass were detected by fluorescence microscopy. The metabolic activity status was assessed by an colorimetric assay for assessing cell metabolic activity (MTT assay) and HY accumulation was determined by flow cytometry. Pro-angiogenic factor expression was determined by Western blot and quantitative real-time polymerase chain reaction (RT-qPCR). We confirmed the cytotoxic effect of HY-PDT and HP and showed that their effect is influenced by structural characteristics of the experimental model. We have pioneered a method for analyzing the effect of HP and cellular targeted HY-PDT on pro-angiogenic factor expression in CRC micro-tumors. Despite the inhibitory effect of HY-PDT and HP on CRC, the increased expression of some pro-angiogenic factors was observed. We also showed that CRC experimental micro-tumors created on quail CAM could be utilized for analyses of gene and protein expression.
Collapse
Affiliation(s)
- Martin Majerník
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Rastislav Jendželovský
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Marián Babinčák
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Ján Košuth
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Juraj Ševc
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Zuzana Tonelli Gombalová
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Zuzana Jendželovská
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| | - Monika Buríková
- Cancer Research Institute BMC, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - Peter Fedoročko
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54 Košice, Slovakia.
| |
Collapse
|
12
|
Shirafkan N, Shomali N, Kazemi T, Shanehbandi D, Ghasabi M, Baghbani E, Ganji M, Khaze V, Mansoori B, Baradaran B. microRNA-193a-5p inhibits migration of human HT-29 colon cancer cells via suppression of metastasis pathway. J Cell Biochem 2019; 120:8775-8783. [PMID: 30506718 DOI: 10.1002/jcb.28164] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/08/2018] [Indexed: 01/24/2023]
Abstract
PURPOSE Altered expression of microRNAs (miRNAs) is indicated strongly in colorectal cancer (CRC). This study aims to evaluate the inhibitory role of miR-193a-5p on epithelial-mesenchymal transition markers in CRC lines. The cellular effects and potential mechanisms of miR-193a-5p were also examined. METHODS Quantitative reverse-transcription polymerase chain reaction (RT-PCR) was performed to determine the expression of miR-193a-5p in three CRC cell lines (HCT-116, SW-480, and HT-29) and its impact on metastasis-related genes ( vimentin and CXCR4) before and after mimic transfection. Of those, the cell line with the highest changes was selected for the next upcoming experiments such as wound-healing assay, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and annexin-V staining tests. RESULTS Our results revealed that miR-193a-5p was significantly downregulated in three CRC cell lines and that HT-29 displayed the most decrease ( P < 0.0001). The restoration of miR-193a-5p in human HT-29 cell line inhibited cell migration. But, miR-193a-5p transfection did not affect cell viability and had no significant effect on apoptosis induction. Also, the quantitative RT-PCR analysis of miR-193a-5p mimic transfected cells revealed a significant increase in miR-193a-5p messenger RNA (mRNA) expression level ( P < 0.0001) with reduction of vimentin and CXCR4 mRNA expression levels in HT-29 cell line ( P < 0.01 and < 0.05, respectively). CONCLUSION Our results indicated that miR-193a-5p acts as a tumor suppressor miRNA and its downregulation plays an important role in metastasis via upregulation of metastasis-related genes in CRC. Therefore, it can be considered as a potential therapeutic target for applying in CRC management in the future.
Collapse
Affiliation(s)
- Naghmeh Shirafkan
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Shomali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tohid Kazemi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dariush Shanehbandi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehri Ghasabi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Baghbani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maziar Ganji
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Khaze
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
13
|
Freitag D, Koch A, Lawson McLean A, Kalff R, Walter J. Validation of Reference Genes for Expression Studies in Human Meningiomas under Different Experimental Settings. Mol Neurobiol 2017; 55:5787-5797. [PMID: 29079997 DOI: 10.1007/s12035-017-0800-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 02/06/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is a sensitive technique for the quantitative analysis of gene expression levels. To compare mRNA transcripts across tumour and non-pathological tissue, appropriate reference genes are required for internal standardisation. Validation of these reference genes in meningiomas has not yet been reported. After mRNA transcription of meningioma (WHO grade I-III) and meningeal tissue from three different experimental sample types (fresh tissue, primary cell cultures and FFPE tissue), 13 candidate reference genes (ACTB, B2M, HPRT, VIM, GAPDH, YWHAZ, EIF4A2, MUC1, ATP5B, GNB2L, TUBB, CYC1, RPL13A) were chosen for quantitative expression analysis. Two statistical algorithms (GeNorm and NormFinder) were used for validation of gene expression stability. All candidate housekeepers tested for stability were checked within and across the three tissue analysis groups. Pearson correlation, the ΔC t method and ranking analysis identified the most non-regulated genes suitable for internal standardisation. TUBB, HPRT and ACTB were the most stably expressed genes for all analysis groups across meningioma and non-pathological meningeal tissue combined. In contrast, analysis of the consistency of reference gene expression within specific meningioma and meningeal tissues resulted in specific reference gene rankings for each tissue type. Future gene expression analyses require reference genes to be chosen that are suitable for the tissue types and for the experimental paradigms being studied. Validation of candidate housekeeper genes in meningiomas for quantitative real-time polymerase chain reaction revealed for the first time TUBB, ACTB and HPRT as the most consistently expressed genes among meningioma and non-pathological meningeal tissue across a range of experimental settings.
Collapse
Affiliation(s)
- Diana Freitag
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany.
| | - Arend Koch
- Institute of Neuropathology, Charité-Universitätsmedizin Berlin, Charitéplatz 1 - Virchowweg 15, 10117, Berlin, Germany
| | - Aaron Lawson McLean
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Rolf Kalff
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Jan Walter
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| |
Collapse
|
14
|
Nuñez-Sánchez MA, González-Sarrías A, García-Villalba R, Monedero-Saiz T, García-Talavera NV, Gómez-Sánchez MB, Sánchez-Álvarez C, García-Albert AM, Rodríguez-Gil FJ, Ruiz-Marín M, Pastor-Quirante FA, Martínez-Díaz F, Tomás-Barberán FA, Espín JC, García-Conesa MT. Gene expression changes in colon tissues from colorectal cancer patients following the intake of an ellagitannin-containing pomegranate extract: a randomized clinical trial. J Nutr Biochem 2017; 42:126-133. [PMID: 28183047 DOI: 10.1016/j.jnutbio.2017.01.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/19/2016] [Accepted: 01/19/2017] [Indexed: 12/12/2022]
Abstract
The clinical evidence of dietary polyphenols as colorectal cancer (CRC) chemopreventive compounds is very weak. Verification in humans of tissue-specific molecular regulation by the intake of polyphenols requires complex clinical trials that allow for the procurement of sufficient pre- and postsupplementation tissue samples. Ellagitannins (ETs), ellagic acid (EA) and their gut microbiota-derived metabolites, the urolithins, modify gene expression in colon normal and cancer cultured cells. We conducted here the first clinical trial with 35 CRC patients daily supplemented with 900 mg of an ET-containing pomegranate extract (PE) and evaluated the expression of various CRC-related genes in normal and cancerous colon tissues before (biopsies) and after (surgical specimens) 5-35 days of supplementation. Tissues were also obtained from 10 control patients (no supplementation) that confirmed a large, gene- and tissue-specific interindividual variability and impact of the experimental protocol on gene expression, with some genes induced (MYC, CD44, CDKN1A, CTNNB1), some repressed (CASP3) and others not affected (KRAS). Despite these issues, the consumption of the PE was significantly associated with a counterbalance effect in the expression of CD44, CTNNB1, CDKN1A, EGFR and TYMs, suggesting that the intake of this PE modulated the impact of the protocol on gene expression in a gene- and tissue-specific manner. These effects were not associated with the individuals' capacity to produce specific urolithins (i.e., metabotypes) or the levels of urolithins and EA in the colon tissues and did not reproduce in vitro effects evidencing the difficulty of demonstrating in vivo the in vitro results.
Collapse
Affiliation(s)
- María A Nuñez-Sánchez
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | - Antonio González-Sarrías
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | - Rocío García-Villalba
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | - Tamara Monedero-Saiz
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain; Nutrition, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | | | - María B Gómez-Sánchez
- Nutrition, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | - Carmen Sánchez-Álvarez
- Nutrition, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | - Ana M García-Albert
- Digestive, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | | | - Miguel Ruiz-Marín
- Surgery, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | - Francisco A Pastor-Quirante
- Anatomical Pathology Services, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | - Francisco Martínez-Díaz
- Anatomical Pathology Services, Hospital Reina Sofía, Avda. Intendente Jorge Palacios s/n, 30003 Murcia, Spain
| | - Francisco A Tomás-Barberán
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain
| | - Juan Carlos Espín
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain.
| | - María-Teresa García-Conesa
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, P.O. Box 164, 30100 Campus de Espinardo, Murcia, Spain.
| |
Collapse
|
15
|
Hayes CJ, Dowling CM, Dwane S, McCumiskey ME, Tormey SM, Anne Merrigan B, Coffey JC, Kiely PA, Dalton TM. Extracellular matrix gene expression profiling using microfluidics for colorectal carcinoma stratification. BIOMICROFLUIDICS 2016; 10:054124. [PMID: 27822332 PMCID: PMC5097046 DOI: 10.1063/1.4966245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/14/2016] [Indexed: 05/15/2023]
Abstract
In cancer, biomarkers have many potential applications including generation of a differential diagnosis, prediction of response to treatment, and monitoring disease progression. Many molecular biomarkers have been put forward for different diseases but most of them do not possess the required specificity and sensitivity. A biomarker with a high sensitivity has a low specificity and vice versa. The inaccuracy of the biomarkers currently in use has led to a compelling need to identify more accurate markers with diagnostic and prognostic significance. The aim of the present study was to use a novel, droplet-based, microfluidic platform to evaluate the prognostic value of a panel of thirty-four genes that regulate the composition of extracellular matrices in colorectal carcinoma. Our method is a novel approach as it uses using continuous-flowing Polymerase Chain Reaction for the sensitive detection and accurate quantitation of gene expression. We identified a panel of relevant extracellular matrix genes whose expression levels were measured by real-time quantitative polymerase chain reaction using Taqman® reagents in twenty-four pairs of matched colorectal cancer tumour and associated normal tissue. Differential expression patterns occurred between the normal and malignant tissue and correlated with histopathological parameters and overall surgical staging. The findings demonstrate that a droplet-based microfluidic quantitative PCR system enables biomarker classification. It was further possible to sub-classify colorectal cancer based on extracellular matrix protein expressing groups which in turn correlated with prognosis.
Collapse
Affiliation(s)
| | | | - Susan Dwane
- Stokes Laboratories, Bernal Institute, University of Limerick , Limerick, Ireland
| | | | - Shona M Tormey
- Department of Surgery, University Hospital Limerick , Limerick, Ireland
| | - B Anne Merrigan
- Department of Surgery, University Hospital Limerick , Limerick, Ireland
| | | | | | - Tara M Dalton
- Stokes Laboratories, Bernal Institute, University of Limerick , Limerick, Ireland
| |
Collapse
|
16
|
Liu G, Qiu X, Cao L, Zhang Y, Zhan Z, Han R. Evaluation of Reference Genes for Reverse Transcription Quantitative PCR Studies of Physiological Responses in the Ghost Moth, Thitarodes armoricanus (Lepidoptera, Hepialidae). PLoS One 2016; 11:e0159060. [PMID: 27392023 PMCID: PMC4938418 DOI: 10.1371/journal.pone.0159060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/27/2016] [Indexed: 12/18/2022] Open
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the sensitive method to quantify the expression levels of target genes on the basis of endogenous control. An appropriate reference gene set for normalization is essential for reliable results. The ghost moth, Thitarodes armoricanus, a host species of a medicinal fungus, Ophiocordyceps sinensis, is an economically important member of the Lepidoptera. Recent studies have focused on the mechanism of adaptation of this species to its high-altitude environment and host immune response to O. sinensis infection and RT-qPCR is commonly used in these studies to decipher the genetic basis of physiological functions. However, a thorough assessment of candidate reference genes in the genus Thitarodes is lacking. Here, the expression levels of eight candidate reference genes (ACT, EF, EIF4A, GAPDH, G6PDH, RPL13A, TUB and 18S) in T. armoricanus at different developmental stages and in different body parts of the seventh instar larvae were analyzed, along with larvae kept under low temperatures, larvae exposed to two fungal infections and larvae fed different diets. Three established software programs–Bestkeeper, geNorm and NormFinder–were employed to calculate variation among the treatments. The results revealed that the best-suited reference genes differed across the treatments, with EF, EIF4A and GAPDH found to be the best suited for the different developmental stages and larvae body parts; EF, EIF4A and RPL13A found to be the best suited for low-temperature challenge; and EF, EIF4A and TUB found to be the best suited for the fungal infections and dietary treatments. This study thus further contributes to the establishment of an accurate method for normalizing RT-qPCR results for T. armoricanus and serves as a reference for gene expression studies of related insect species.
Collapse
Affiliation(s)
- Guiqing Liu
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Xuehong Qiu
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Li Cao
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Yi Zhang
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zubing Zhan
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Richou Han
- Guangdong Key Laboratory of IPM in Agriculture and Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
- * E-mail:
| |
Collapse
|
17
|
Dowling CM, Walsh D, Coffey JC, Kiely PA. The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue. F1000Res 2016. [PMID: 26962435 DOI: 10.12688/f1000research.7656.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.
Collapse
Affiliation(s)
- Catríona M Dowling
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Dara Walsh
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - John C Coffey
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Patrick A Kiely
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| |
Collapse
|
18
|
Dowling CM, Walsh D, Coffey JC, Kiely PA. The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue. F1000Res 2016; 5:99. [PMID: 26962435 PMCID: PMC4768652 DOI: 10.12688/f1000research.7656.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2016] [Indexed: 12/16/2022] Open
Abstract
Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results.
Collapse
Affiliation(s)
- Catríona M Dowling
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Dara Walsh
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - John C Coffey
- 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Patrick A Kiely
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland; Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| |
Collapse
|