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Sharma V, Varshney R, Sethy NK. Identification of Suitable Reference Genes for Lowlanders Exposed to High Altitude and Ladakhi Highlanders. High Alt Med Biol 2022; 23:319-329. [PMID: 36219748 DOI: 10.1089/ham.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sharma, Vandana, Rajeev Varshney, and Niroj Kumar Sethy. Identification of suitable reference genes for lowlanders exposed to high altitude and Ladakhi highlanders. High Alt Med Biol. 23:319-329, 2022. Background: Identifying a stable and reliable reference gene (RG) is a prerequisite for the unbiased and unambiguous analysis of gene expression data. It has become evident that conventionally used housekeeping genes such as beta-actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and peptidylprolyl Isomerase A (PPIA) exhibit varied expression patterns under hypoxia. Hence, the identification of stable RGs for humans exposed to hypobaric hypoxia can enhance the accuracy of gene expression studies by limiting the negligent use of random housekeeping genes. Methods: Using TaqMan™ array-based quantitative real-time quantitative polymerase chain reaction, we evaluated the expression of 32 commonly used human RGs among lowlanders at Delhi (altitude 216 m, SL), lowlanders at Leh (altitude 3,524 m) after 1 day (HA-D1) and 7 days (HA-D7), as well as indigenous Ladakhi highlanders at the same altitude. The expression stability of the RGs was evaluated using geNorm, NormFinder, BestKeeper, Delta CT method, and RefFinder algorithms. Results: Our studies identify TATA-box binding protein (TBP), proteasome 26S subunit, ATPase 4 (PSMC4), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the most stable human RGs for normalizing human gene expression under hypobaric hypoxia. In addition, we report the combination of TBP and cyclin-dependent kinase inhibitor 1B (CDKN1B) as the most stable RG for studying lowlander gene expression during high-altitude exposure. In contrast, RPL30 and 18S exhibited maximum variation across study groups and were identified as the least stable RGs.
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Affiliation(s)
- Vandana Sharma
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Rajeev Varshney
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Niroj Kumar Sethy
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organisation (DRDO), Delhi, India
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Whole Blood Transcriptional Fingerprints of High-Grade Glioma and Longitudinal Tumor Evolution under Carbon Ion Radiotherapy. Cancers (Basel) 2022; 14:cancers14030684. [PMID: 35158950 PMCID: PMC8833402 DOI: 10.3390/cancers14030684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Particle therapy with carbon ions is a promising novel option for the treatment of recurrent high-grade glioma (rHGG). Lack of initial and sequential biopsies limits the investigation of rHGG evolution under therapy. We hypothesized that peripheral blood transcriptome derived from liquid biopsies (lbx) as a minimal invasive method may provide a useful decision support for identification of glioma grade and provide novel means for longitudinal molecular monitoring of tumor evolution under carbon ion irradiation (CIR). We demonstrate feasibility and report patient, tumor and treatment fingerprints in whole blood transcriptomes of rHGG patients with pre-CIR and three post-CIR time points. Abstract Purpose: To assess the value of whole blood transcriptome data from liquid biopsy (lbx) in recurrent high-grade glioma (rHGG) patients for longitudinal molecular monitoring of tumor evolution under carbon ion irradiation (CIR). Methods: Whole blood transcriptome (WBT) analysis (Illumina HumanHT-12 Expression BeadChips) was performed in 14 patients with rHGG pre re-irradiation (reRT) with CIR and 3, 6 and 9 weeks post-CIR (reRT grade III:5, 36%, IV:9, 64%). Patients were irradiated with 30, 33, 36 GyRBE (n = 5, 6, 3) in 3GyRBE per fraction. Results: WTB analysis showed stable correlation with treatment characteristics and patients tumor grade, indicating a preserved tumor origin specific as well as dynamic transcriptional fingerprints of peripheral blood cells. Initial histopathologic tumor grade was indirectly associated with TMEM173 (STING), DNA-repair (ATM, POLD4) and hypoxia related genes. DNA-repair, chromatin remodeling (LIG1, SMARCD1) and immune response (FLT3LG) pathways were affected post-CIR. Longitudinal WTB fingerprints identified two distinct trajectories of rHGG evolution, characterized by differential and prognostic CRISPLD2 expression pre-CIR. Conclusions: Lbx based WTB analysis holds the potential for molecular stratification of rHGG patients and therapy monitoring. We demonstrate the feasibility of the peripheral blood transcriptome as a sentinel organ for identification of patient, tumor characteristics and CIR specific fingerprints in rHGG.
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Calaf GM, Crispin LA, Roy D, Aguayo F, Muñoz JP, Bleak TC. Gene Signatures Induced by Ionizing Radiation as Prognostic Tools in an In Vitro Experimental Breast Cancer Model. Cancers (Basel) 2021; 13:4571. [PMID: 34572798 PMCID: PMC8465284 DOI: 10.3390/cancers13184571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to analyze the expression of genes involved in radiation, using an Affymetrix system with an in vitro experimental breast cancer model developed by the combined treatment of low doses of high linear energy transfer (LET) radiation α particle radiation and estrogen yielding different stages in a malignantly transformed breast cancer cell model called Alpha model. Altered expression of different molecules was detected in the non-tumorigenic Alpha3, a malignant cell line transformed only by radiation and originally derived from the parental MCF-10F human cell line; that was compared with the Alpha 5 cell line, another cell line exposed to radiation and subsequently grown in the presence 17β-estradiol. This Alpha5, a tumorigenic cell line, originated the Tumor2 cell line. It can be summarized that the Alpha 3 cell line was characterized by greater gene expression of ATM and IL7R than control, Alpha5, and Tumor2 cell lines, it presented higher selenoprotein gene expression than control and Tumor2; epsin 3 gene expression was higher than control; stefin A gene expression was higher than Alpha5; and metallothionein was higher than control and Tumor2 cell line. Therefore, radiation, independently of estrogen, induced increased ATM, IL7R, selenoprotein, GABA receptor, epsin, stefin, and metallothioneins gene expression in comparison with the control. Results showed important findings of genes involved in cancers of the breast, lung, nervous system, and others. Most genes analyzed in these studies can be used for new prognostic tools and future therapies since they affect cancer progression and metastasis. Most of all, it was revealed that in the Alpha model, a breast cancer model developed by the authors, the cell line transformed only by radiation, independently of estrogen, was characterized by greater gene expression than other cell lines. Understanding the effect of radiotherapy in different cells will help us improve the clinical outcome of radiotherapies. Thus, gene signature has been demonstrated to be specific to tumor types, hence cell-dependency must be considered in future treatment planning. Molecular and clinical features affect the results of radiotherapy. Thus, using gene technology and molecular information is possible to improve therapies and reduction of side effects while providing new insights into breast cancer-related fields.
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Affiliation(s)
- Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (L.A.C.); (J.P.M.); (T.C.B.)
- Center for Radiological Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Leodan A. Crispin
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (L.A.C.); (J.P.M.); (T.C.B.)
| | - Debasish Roy
- Department of Natural Sciences, Hostos College of the City University of New York, Bronx, NY 10451, USA;
| | - Francisco Aguayo
- Laboratorio Oncovirología, Programa de Virología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago 8380000, Chile;
| | - Juan P. Muñoz
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (L.A.C.); (J.P.M.); (T.C.B.)
| | - Tammy C. Bleak
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (L.A.C.); (J.P.M.); (T.C.B.)
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Subbiahanadar Chelladurai K, Selvan Christyraj JD, Azhagesan A, Paulraj VD, Jothimani M, Yesudhason BV, Chellathurai Vasantha N, Ganesan M, Rajagopalan K, Venkatachalam S, Benedict J, John Samuel JK, Selvan Christyraj JRS. Exploring the effect of UV-C radiation on earthworm and understanding its genomic integrity in the context of H2AX expression. Sci Rep 2020; 10:21005. [PMID: 33273505 PMCID: PMC7713072 DOI: 10.1038/s41598-020-77719-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 11/17/2020] [Indexed: 01/28/2023] Open
Abstract
Maintaining genomic stability is inevitable for organism survival and it is challenged by mutagenic agents, which include ultraviolet (UV) radiation. Whenever DNA damage occurs, it is sensed by DNA-repairing proteins and thereby performing the DNA-repair mechanism. Specifically, in response to DNA damage, H2AX is a key protein involved in initiating the DNA-repair processes. In this present study, we investigate the effect of UV-C on earthworm, Perionyx excavatus and analyzed the DNA-damage response. Briefly, we expose the worms to different doses of UV-C and find that worms are highly sensitive to UV-C. As a primary response, earthworms produce coelomic fluid followed by autotomy. However, tissue inflammation followed by death is observed when we expose worm to increased doses of UV-C. In particular, UV-C promotes damages in skin layers and on the contrary, it mediates the chloragogen and epithelial outgrowth in intestinal tissues. Furthermore, UV-C promotes DNA damages followed by upregulation of H2AX on dose-dependent manner. Our finding confirms DNA damage caused by UV-C is directly proportional to the expression of H2AX. In short, we conclude that H2AX is present in the invertebrate earthworm, which plays an evolutionarily conserved role in DNA damage event as like that in higher animals.
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Affiliation(s)
- Karthikeyan Subbiahanadar Chelladurai
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Jackson Durairaj Selvan Christyraj
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Ananthaselvam Azhagesan
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India ,grid.412813.d0000 0001 0687 4946Present Address: Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, 632014 Tamilnadu India
| | - Vennila Devi Paulraj
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Muralidharan Jothimani
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India ,grid.411312.40000 0001 0363 9238Present Address: Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, 630004 Tamilnadu India
| | - Beryl Vedha Yesudhason
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Niranjan Chellathurai Vasantha
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Mijithra Ganesan
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Kamarajan Rajagopalan
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Saravanakumar Venkatachalam
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Johnson Benedict
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
| | - Jemima Kamalapriya John Samuel
- grid.252262.30000 0001 0613 6919Department of Biotechnology, Anna University of Technology, Tiruchirappalli, 620024 Tamilnadu India
| | - Johnson Retnaraj Samuel Selvan Christyraj
- grid.412427.60000 0004 1761 0622Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119 Tamilnadu India
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Asiabi P, Ambroise J, Giachini C, Coccia ME, Bearzatto B, Chiti MC, Dolmans MM, Amorim CA. Assessing and validating housekeeping genes in normal, cancerous, and polycystic human ovaries. J Assist Reprod Genet 2020; 37:2545-2553. [PMID: 32729067 DOI: 10.1007/s10815-020-01901-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Housekeeping genes (HKGs), reference or endogenous control genes, are vital to normalize mRNA levels between different samples. Since using inappropriate HKGs can lead to unreliable results, selecting the proper ones is critical for gene expression studies. To this end, normal human ovaries, as well as those from patients diagnosed with ovarian endometrioid adenocarcinoma (OEA), ovarian mucinous adenocarcinoma (OMA), ovarian serous papillary carcinoma (OSPC), and polycystic ovary syndrome (PCOS), were used to identify the most suitable housekeeping genes. METHODS RNA was isolated from 5 normal human ovaries (52-79 years of age), 9 cancerous ovaries (3 OEA, 3 OMA, 3 OSPC; 49-75 years of age), and 4 PCOS ovaries (18-35 years of age) in women undergoing hysterectomy. cDNA was synthesized using a whole transcriptome kit, and quantitative real-time PCR was performed using TaqMan array 96-well plates containing 32 human endogenous controls in triplicate. RESULTS Among 32 HKGs studied, RPS17, RPL37A, PPIA, 18srRNA, B2M, RPLP0, RPLP30, HPRT1, POP4, CDKN1B, and ELF1 were selected as the best reference genes. CONCLUSIONS This study confirms recent investigations demonstrating that conventional HKGs, such as GAPDH and beta-actin, are not suitable reference genes for specific pathological conditions, emphasizing the importance of determining the best HKGs on a case-by-case basis and according to tissue type. Our results have identified reliable HKGs for studies of normal human ovaries and those affected by OEA, OMA, OSPC, or PCOS, as well as combined studies of control subjects vs. each cancer or PCOS group.
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Affiliation(s)
- P Asiabi
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
| | - J Ambroise
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - C Giachini
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - M E Coccia
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - B Bearzatto
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - M C Chiti
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
| | - M M Dolmans
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium
- Gynecology Department, Cliniques Universitaires Saint-Luc, 1200, Brussels, Belgium
| | - C A Amorim
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Avenue Mounier 52, bte B1.52.02, 1200, Brussels, Belgium.
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Jo J, Choi S, Oh J, Lee SG, Choi SY, Kim KK, Park C. Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research. BMC Bioinformatics 2019; 20:245. [PMID: 31138119 PMCID: PMC6538551 DOI: 10.1186/s12859-019-2809-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identification and validation of reference genes for human cancer research are still being regarded as a critical point, because cancerous tissues often represent genetic instability and heterogeneity. Recent pan-cancer studies have demonstrated the importance of the appropriate selection of reference genes for use as internal controls for the normalization of gene expression; however, no stably expressed, consensus reference genes valid for a range of different human cancers have yet been identified. RESULTS In the present study, we used large-scale cancer gene expression datasets from The Cancer Genome Atlas (TCGA) database, which contains 10,028 (9,364 cancerous and 664 normal) samples from 32 different cancer types, to confirm that the expression of the most commonly used reference genes is not consistent across a range of cancer types. Furthermore, we identified 38 novel candidate reference genes for the normalization of gene expression, independent of cancer type. These genes were found to be highly expressed and highly connected to relevant gene networks, and to be enriched in transcription-translation regulation processes. The expression stability of the newly identified reference genes across 29 cancerous and matched normal tissues were validated via quantitative reverse transcription PCR (RT-qPCR). CONCLUSIONS We reveal that most commonly used reference genes in current cancer studies cannot be appropriate to serve as representative control genes for quantifying cancer-related gene expression levels, and propose in this study three potential reference genes (HNRNPL, PCBP1, and RER1) to be the most stably expressed across various cancerous and normal human tissues.
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Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Sunkyung Choi
- Department of Biochemistry, Chungnam National University, 99 Daehak-Ro, Yuseong-Ku, Daejeon, 34134, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea
| | - Song Yi Choi
- Department of Pathology, Chungnam National University, 282 Munhwa-Ro, Jung-Ku, Daejeon, 35015, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, Chungnam National University, 99 Daehak-Ro, Yuseong-Ku, Daejeon, 34134, Republic of Korea.
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-Ro, Buk-Ku, GwangJu, 61186, Republic of Korea.
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Nielsen S, Bassler N, Grzanka L, Swakon J, Olko P, Andreassen CN, Alsner J, Sørensen BS. Optimal reference genes for normalization of qPCR gene expression data from proton and photon irradiated dermal fibroblasts. Sci Rep 2018; 8:12688. [PMID: 30139945 PMCID: PMC6107545 DOI: 10.1038/s41598-018-30946-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/08/2018] [Indexed: 12/29/2022] Open
Abstract
The transcriptional response of cells exposed to proton radiation is not equivalent to the response induced by traditional photon beams. Changes in cellular signalling is most commonly studied using the method Quantitative polymerase chain reaction (qPCR). Stable reference genes must be used to accurately quantify target transcript expression. The study aim was to identify suitable reference genes for normalisation of gene expression levels in normal dermal fibroblasts irradiated with either proton or photon beams. The online tool RefFinder was used to analyse and identify the most stably expressed genes from a panel of 22 gene candidates. To assess the reliability of the identified reference genes, a selection of the most and least stable reference genes was used to normalise target transcripts of interest. Fold change levels varied considerably depending on the used reference gene. The top ranked genes IPO8, PUM1, MRPL19 and PSMC4 produced highly similar target gene expression, while expression using the worst ranked genes, TFRC and HPRT1, was clearly modified due to reference gene instability.
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Affiliation(s)
- Steffen Nielsen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
| | - Niels Bassler
- Medical Radiation Physics, Department of Physics, Stockholm University, Stockholm, Sweden
| | - Leszek Grzanka
- Proton Radiotherapy Group, Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | - Jan Swakon
- Proton Radiotherapy Group, Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | - Pawel Olko
- Proton Radiotherapy Group, Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Brita Singers Sørensen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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Matsumoto Y, Furusawa Y, Uzawa A, Hirayama R, Koike S, Ando K, Tsuboi K, Sakurai H. Antimetastatic Effects of Carbon-Ion Beams on Malignant Melanomas. Radiat Res 2018; 190:412-423. [DOI: 10.1667/rr15075.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoshitaka Matsumoto
- Radiation Oncology, Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Yoshiya Furusawa
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Akiko Uzawa
- Department of Charged Particle Therapy Research, Clinical Research Cluster, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Ryoichi Hirayama
- Department of Charged Particle Therapy Research, Clinical Research Cluster, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Sachiko Koike
- Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan
| | - Koichi Ando
- Medicine & Biology Division, Heavy Ion Medical Center, Gunma University, Gunma, 371-8511, Japan
| | - Koji Tsuboi
- Radiation Oncology, Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Hideyuki Sakurai
- Radiation Oncology, Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
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Dai Y, Wei Q, Schwager C, Hanne J, Zhou C, Herfarth K, Rieken S, Lipson KE, Debus J, Abdollahi A. Oncogene addiction and radiation oncology: effect of radiotherapy with photons and carbon ions in ALK-EML4 translocated NSCLC. Radiat Oncol 2018; 13:1. [PMID: 29304828 PMCID: PMC5756447 DOI: 10.1186/s13014-017-0947-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
Background Patients with Echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) positive lung cancer are sensitive to ALK-kinase inhibitors. TAE684 is a potent second generation ALK inhibitor that overcomes Crizotinib resistance. Radiotherapy is an integral therapeutic component of locally advanced lung cancer. Therefore, we sought to investigate the effects of combined radiotherapy and ALK-inhibition via TAE684 in ALK-positive vs. wild type lung cancer cells. Methods Human non-small cell lung cancer (NSCLC) cell lines harboring wild-type ALK (A549), EML4-ALK translocation (H3122) and murine Lewis Lung Cancer (LLC) cells were investigated. Cells were irradiated with 1–4 Gy X-Rays (320 keV) and carbon ions (Spread-out Bragg Peak, SOBP (245.4–257.0 MeV/u)) at Heidelberg Ion Therapy center. TAE684 was administered at the dose range 0–100 nM. Clonogenic survival, proliferation and apoptosis via caspase 3/7 expression level were assessed in all three cell lines using time-lapse live microscopy. Results TAE684 inhibited the proliferation of H3122 cells in a dose-dependent manner with a half maximal inhibitory concentration (IC50) of ~ 8.2 nM. However, A549 and LLC cells were relatively resistant to TAE684 and IC50 was not reached at concentrations tested (up to 100 nM) in proliferation assay. The antiproliferative effect of TAE684 was augmented by radiotherapy in H3122 cells. TAE684 significantly sensitized H3122 cells to particle therapy with carbon ions (sensitizer enhancement ratio ~1.61, p < 0.05). Caspase 3/7 activity was evidently enhanced after combination therapy in H3122 cells. Conclusions This is the first report demonstrating synergistic effects of combined TAE684 and radiotherapy in EML4-ALK positive lung cancer cells. In addition to conventional photon radiotherapy, ALK-inhibition also enhanced the effects of particle irradiation using carbon ions. Our data indicate beneficial effects of combined ALK-inhibition and radiotherapy in treatment of this distinct subpopulation of NSCLC that warrant further evaluation.
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Affiliation(s)
- Ying Dai
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany.,Department of Oncology, the 1st Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Quanxiang Wei
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Christian Schwager
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Janina Hanne
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Cheng Zhou
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Klaus Herfarth
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Stefan Rieken
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | | | - Jürgen Debus
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Heidelberg, Germany. .,Divisions of Molecular & Translational Radiation Oncology and Thoracic Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), University of Heidelberg Medical School and National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 450, 69120, Heidelberg, Germany.
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10
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Sharan RN, Vaiphei ST, Nongrum S, Keppen J, Ksoo M. Consensus reference gene(s) for gene expression studies in human cancers: end of the tunnel visible? Cell Oncol (Dordr) 2015; 38:419-31. [PMID: 26384826 DOI: 10.1007/s13402-015-0244-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene expression studies are increasingly used to provide valuable information on the diagnosis and prognosis of human cancers. Also, for in vitro and in vivo experimental cancer models gene expression studies are widely used. The complex algorithms of differential gene expression analyses require normalization of data against a reference or normalizer gene, or a set of such genes. For this purpose, mostly invariant housekeeping genes are used. Unfortunately, however, there are no consensus (housekeeping) genes that serve as reference or normalizer for different human cancers. In fact, scientists have employed a wide range of reference genes across different types of cancer for normalization of gene expression data. As a consequence, comparisons of these data and/or data harmonizations are difficult to perform and challenging. In addition, an inadequate choice for a reference gene may obscure genuine changes and/or result in erroneous gene expression data comparisons. METHODS In our effort to highlight the importance of selecting the most appropriate reference gene(s), we have screened the literature for gene expression studies published since the turn of the century on thirteen of the most prevalent human cancers worldwide. CONCLUSIONS Based on the analysis of the data at hand, we firstly recommend that in each study the suitability of candidate reference gene(s) should carefully be evaluated in order to yield reliable differential gene expression data. Secondly, we recommend that a combination of PPIA and either GAPDH, ACTB, HPRT and TBP, or appropriate combinations of two or three of these genes, should be employed in future studies, to ensure that results from different studies on different human cancers can be harmonized. This approach will ultimately increase the depth of our understanding of gene expression signatures across human cancers.
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Affiliation(s)
- R N Sharan
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India.
| | - S Thangminlal Vaiphei
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Saibadaiahun Nongrum
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Joshua Keppen
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Mandahakani Ksoo
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
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11
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Chiblak S, Tang Z, Campos B, Gal Z, Unterberg A, Debus J, Herold-Mende C, Abdollahi A. Radiosensitivity of Patient-Derived Glioma Stem Cell 3-Dimensional Cultures to Photon, Proton, and Carbon Irradiation. Int J Radiat Oncol Biol Phys 2015; 95:112-119. [PMID: 26254681 DOI: 10.1016/j.ijrobp.2015.06.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/05/2015] [Accepted: 06/08/2015] [Indexed: 11/30/2022]
Abstract
PURPOSE To investigate the radiosensitivity of primary glioma stem cell (GSC) cultures with different CD133 status in a 3-dimensional (3D) model after photon versus proton versus carbon irradiation. METHODS AND MATERIALS Human primary GSC spheroid cultures were established from tumor specimens of six consented glioblastoma patients. Human U87MG was used as a classical glioblastoma radioresistant cell line. Cell suspensions were generated by mechanical dissociation of GSC spheroids and embedded in a semi-solid 3D matrix before irradiation. Spheroid-like colonies were manually counted by microscopy. Cells were also recovered and quantified by fluorescence. CD133 expression and DNA damage were evaluated by flow cytometry. RESULTS The fraction of CD133(+) cells varied between 0.014% and 96% in the six GSC cultures and showed a nonsignificant correlation with plating efficiency and survival fractions. The 4 most photon-radioresistant GSC cultures were NCH644, NCH421k, NCH441, and NCH636. Clonogenic survival for proton irradiation revealed relative biologic effectiveness (RBE) in the range of 0.7-1.20. However, carbon irradiation rendered the photon-resistant GSC cultures sensitive, with average RBE of 1.87-3.44. This effect was partly attributed to impaired capability of GSC to repair carbon ion-induced DNA double-strand breaks as determined by residual DNA repair foci. Interestingly, radiosensitivity of U87 cells was comparable to GSC cultures using clonogenic survival as the standard readout. CONCLUSIONS Carbon irradiation is effective in GSC eradication with similar RBE ranges approximately 2-3 as compared with non-stem GSC cultures (U87). Our data strongly suggest further exploration of GSC using classic radiobiology endpoints such as the here-used 3D clonogenic survival assay and integration of additional GSC-specific markers.
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Affiliation(s)
- Sara Chiblak
- German Cancer Consortium, Heidelberg, Germany; Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center, Heidelberg Institute of Radiation Oncology, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Zili Tang
- German Cancer Consortium, Heidelberg, Germany; Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center, Heidelberg Institute of Radiation Oncology, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Benito Campos
- Division of Neurological Research, Department of Neurosurgery, University of Heidelberg Medical School, Heidelberg, Germany
| | - Zoltan Gal
- Division of Neurological Research, Department of Neurosurgery, University of Heidelberg Medical School, Heidelberg, Germany
| | - Andreas Unterberg
- Division of Neurological Research, Department of Neurosurgery, University of Heidelberg Medical School, Heidelberg, Germany
| | - Jürgen Debus
- German Cancer Consortium, Heidelberg, Germany; Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center, Heidelberg Institute of Radiation Oncology, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Neurological Research, Department of Neurosurgery, University of Heidelberg Medical School, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium, Heidelberg, Germany; Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center, Heidelberg Institute of Radiation Oncology, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany.
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12
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Milewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A. Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation. PLoS One 2015; 10:e0129859. [PMID: 26065894 PMCID: PMC4466796 DOI: 10.1371/journal.pone.0129859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/13/2015] [Indexed: 01/15/2023] Open
Abstract
BRAF functions in the RAS-extracellular signal-regulated kinase (ERK) signaling cascade. Activation of this pathway is necessary to mediate the transforming potential of oncogenic BRAF, however, it may also cause a negative feedback that inhibits the epidermal growth factor receptor (EGFR). Mitogen-inducible gene-6 (MIG-6) is a potent inhibitor of the EGFR and has been demonstrated to function as a tumor suppressor. As MIG-6 can be induced via RAS-ERK signaling, we investigated its potential involvement in this negative regulatory loop. Focus formation assays were performed and demonstrated that MIG-6 significantly reduces malignant transformation induced by oncogenic BRAF. Although this genetic interaction was mirrored by a physical interaction between MIG-6 and BRAF, we did not observe a direct regulation of BRAF kinase activity by MIG-6. Interestingly, a selective chemical EGFR inhibitor suppressed transformation to a similar degree as MIG-6, whereas combining these approaches had no synergistic effect. By analyzing a range of BRAF mutated and wildtype cell line models, we could show that BRAF V600E causes a strong upregulation of MIG-6, which was mediated at the transcriptional level via the RAS-ERK pathway and resulted in downregulation of EGFR activation. This feedback loop is operational in tumors, as shown by the analysis of almost 400 patients with papillary thyroid cancer (PTC). Presence of BRAF V600E correlated with increased MIG-6 expression on the one hand, and with inactivation of the EGFR and of PI3K/AKT signaling on the other hand. Importantly, we also observed a more aggressive disease phenotype when BRAF V600E coexisted with low MIG-6 expression. Finally, analysis of methylation data was performed and revealed that higher methylation of MIG-6 correlated to its decreased expression. Taken together, we demonstrate that MIG-6 efficiently reduces cellular transformation driven by oncogenic BRAF by orchestrating a negative feedback circuit directed towards the EGFR.
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Affiliation(s)
| | - David Romano
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Ana Herrero
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | - Marc Birtwistle
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Franz Quehenberger
- Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Stefan Hatzl
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Boris N. Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Oreste Segatto
- Laboratory of Immunology, Regina Elena Cancer Institute, Rome, Italy
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Armin Zebisch
- Division of Hematology, Medical University of Graz, Graz, Austria
- * E-mail:
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13
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Lawlor H, Meunier A, McDermott N, Lynch TH, Marignol L. Identification of suitable endogenous controls for gene and miRNA expression studies in irradiated prostate cancer cells. Tumour Biol 2015; 36:6019-28. [PMID: 25750034 DOI: 10.1007/s13277-015-3278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/18/2015] [Indexed: 01/31/2023] Open
Abstract
This study aimed to to evaluate the stability of commonly used endogenous control genes for messenger RNA (mRNA) (N = 16) and miRNAs (N = 3) expression studies in prostate cell lines following irradiation. The stability of endogenous control genes expression in irradiated (6 Gy) versus unirradiated controls was quantified using NormFinder and coefficient of variation analyses. HPRT1 and 18S were identified as most and least stable endogenous controls, respectively, for mRNA expression studies in irradiated prostate cells. SNORD48 and miR16 miRNA endogenous controls tested were associated with low coefficient of variations following irradiation (6 Gy). This study highlights that commonly used endogenous controls can be responsive to radiation and validation is required prior to gene/miRNAs expression studies.
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Affiliation(s)
- H Lawlor
- Radiobiology and Molecular Oncology, Applied Radiation Therapy Trinity, Trinity College Dublin, Dublin, Ireland
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14
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Dai Y, Wei Q, Schwager C, Moustafa M, Zhou C, Lipson KE, Weichert W, Debus J, Abdollahi A. Synergistic effects of crizotinib and radiotherapy in experimental EML4–ALK fusion positive lung cancer. Radiother Oncol 2015; 114:173-81. [DOI: 10.1016/j.radonc.2014.12.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 02/07/2023]
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15
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Vaiphei ST, Keppen J, Nongrum S, Chaubey RC, Kma L, Sharan RN. Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo. JOURNAL OF RADIATION RESEARCH 2015; 56:177-185. [PMID: 25271263 PMCID: PMC4572586 DOI: 10.1093/jrr/rru074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/01/2014] [Accepted: 08/04/2014] [Indexed: 06/03/2023]
Abstract
In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving (60)Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of (60)Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min(-1) at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples.
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Affiliation(s)
- S Thangminlal Vaiphei
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Joshua Keppen
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - Saibadaiahun Nongrum
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - R C Chaubey
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, 400085, India
| | - L Kma
- Radiation Countermeasures Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
| | - R N Sharan
- Radiation and Molecular Biology Unit, Department of Biochemistry, North-Eastern Hill University (NEHU), Shillong, 793022, India
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16
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Deb R, Singh U, Kumar S, Kumar A, Singh R, Sengar G, Mann S, Sharma A. Genotypic to expression profiling of bovine calcium channel, voltage-dependent, alpha-2/delta subunit 1 gene, and their association with bovine mastitis among Frieswal (HFX Sahiwal) crossbred cattle of Indian origin. Anim Biotechnol 2014; 25:128-38. [PMID: 24555798 DOI: 10.1080/10495398.2013.836106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Calcium channel, voltage-dependent, alpha-2/delta subunit 1 (CACNA2D1) gene is considered to be an important noncytokine candidate gene influencing mastitis. Scanty of reports are available until today regarding the role play of CACNA2D1 gene on the susceptibility of bovine mastitis. We interrogated the CACNA2D1 G519663A [A>G] SNP by PCR-RFLP among two hundreds Frieswal (HF X Sahiwal) crossbred cattle of Indian origin. Genotypic frequency of AA (51.5, n=101) was comparatively higher than AG (35, n=70) and GG (14.5, n=29). Association of Somatic cell score (SCS) with genotypes revealed that, GG genotypes showing lesser count (less susceptible to mastitis) compare to AA and AG. Relative expression of CACNA2D1 transcript (in milk samples) was significantly higher among GG than AG and AA. Further we have also isolated blood sample from the all groups and PBMCs were cultured from each blood sample as per the standard protocol. They were treated with Calcium channel blocker and the expression level of the CACNA2D1 gene was evaluated by Real Time PCR. Results show that expression level decline in each genotypic group after treatment and expression level of GG are again significantly higher than AA and AG. Thus, it may be concluded that GG genotypic animals are favorable for selecting disease resistant breeds.
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Affiliation(s)
- Rajib Deb
- a Molecular Genetics Laboratory, Project Directorate on Cattle, Indian Council of Agricultural Research, Meerut Cantt , Uttar Pradesh , India
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17
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Suetens A, Moreels M, Quintens R, Chiriotti S, Tabury K, Michaux A, Grégoire V, Baatout S. Carbon ion irradiation of the human prostate cancer cell line PC3: a whole genome microarray study. Int J Oncol 2014; 44:1056-72. [PMID: 24504141 PMCID: PMC3977812 DOI: 10.3892/ijo.2014.2287] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/29/2013] [Indexed: 01/13/2023] Open
Abstract
Hadrontherapy is a form of external radiation therapy, which uses beams of charged particles such as carbon ions. Compared to conventional radiotherapy with photons, the main advantage of carbon ion therapy is the precise dose localization along with an increased biological effectiveness. The first results obtained from prostate cancer patients treated with carbon ion therapy showed good local tumor control and survival rates. In view of this advanced treatment modality we investigated the effects of irradiation with different beam qualities on gene expression changes in the PC3 prostate adenocarcinoma cell line. For this purpose, PC3 cells were irradiated with various doses (0.0, 0.5 and 2.0 Gy) of carbon ions (LET=33.7 keV/μm) at the beam of the Grand Accélérateur National d’Ions Lourds (Caen, France). Comparative experiments with X-rays were performed at the Belgian Nuclear Research Centre. Genome-wide gene expression was analyzed using microarrays. Our results show a downregulation in many genes involved in cell cycle and cell organization processes after 2.0 Gy irradiation. This effect was more pronounced after carbon ion irradiation compared with X-rays. Furthermore, we found a significant downregulation of many genes related to cell motility. Several of these changes were confirmed using qPCR. In addition, recurrence-free survival analysis of prostate cancer patients based on one of these motility genes (FN1) revealed that patients with low expression levels had a prolonged recurrence-free survival time, indicating that this gene may be a potential prognostic biomarker for prostate cancer. Understanding how different radiation qualities affect the cellular behavior of prostate cancer cells is important to improve the clinical outcome of cancer radiation therapy.
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Affiliation(s)
- Annelies Suetens
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Marjan Moreels
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Roel Quintens
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Sabina Chiriotti
- Radiation Protection, Dosimetry and Calibration Expert Group, SCK•CEN, Mol, Belgium
| | - Kevin Tabury
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Arlette Michaux
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Vincent Grégoire
- Department of Radiation Oncology and Center for Molecular Imaging, Radiotherapy and Oncology, Institute of Experimental and Clinical Research (IREC), Université Catholique de Louvain (UCL), Brussels, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
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18
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Magi S, Takemoto Y, Kobayashi H, Kasamatsu M, Akita T, Tanaka A, Takano K, Tashiro E, Igarashi Y, Imoto M. 5-Lipoxygenase and cysteinyl leukotriene receptor 1 regulate epidermal growth factor-induced cell migration through Tiam1 upregulation and Rac1 activation. Cancer Sci 2014; 105:290-6. [PMID: 24350867 PMCID: PMC4317946 DOI: 10.1111/cas.12340] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/12/2013] [Accepted: 12/14/2013] [Indexed: 12/18/2022] Open
Abstract
Cell migration is an essential step for tumor metastasis. The small GTPase Rac1 plays an important role in cell migration. Previously, we reported that epidermal growth factor (EGF) induced two waves of Rac1 activation; namely, at 5 min and 12 h after stimulation. A second wave of EGF-induced Rac1 activation was required for EGF-induced cell migration, however, the spatiotemporal regulation of the second wave of EGF-induced Rac1 activation remains largely unclear. In this study, we found that 5-lipoxygenase (5-LOX) is activated in the process of EGF-induced cell migration, and that leukotriene C4 (LTC4) produced by 5-LOX mediated the second wave of Rac1 activation, as well as cell migration. Furthermore, these effects caused by LTC4 were found to be blocked in the presence of the antagonist of cysteinyl leukotriene receptor 1 (CysLT1). This blockage indicates that LTC4-mediated CysLT1 signaling regulates the second EGF-induced wave of Rac1 activation. We also found that 5-LOX inhibitors, CysLT1 antagonists and the knockdown of CysLT1 inhibited EGF-induced T cell lymphoma invasion and metastasis-inducing protein 1 (Tiam1) expression. Tiam1 expression is required for the second wave of EGF-induced Rac1 activation in A431 cells. Therefore, our results indicate that the 5-LOX/LTC4/CysLT1 signaling pathway regulates EGF-induced cell migration by increasing Tiam1 expression, leading to a second wave of Rac1 activation. Thus, CysLT1 may serve as a new molecular target for antimetastatic therapy. In addition, the CysLT1 antagonist, montelukast, which is used clinically for allergy treatment, might have great potential as a novel type of antimetastatic agent.
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Affiliation(s)
- Shigeyuki Magi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
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19
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Deb R, Sajjanar B, Singh U, Kumar S, Brahmane MP, Singh R, Sengar G, Sharma A. Promoter variants at AP2 box region of Hsp70.1 affect thermal stress response and milk production traits in Frieswal cross bred cattle. Gene 2013; 532:230-5. [PMID: 24055724 DOI: 10.1016/j.gene.2013.09.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/14/2013] [Accepted: 09/07/2013] [Indexed: 12/23/2022]
Abstract
Heat shock proteins (Hsp) are known to play major role in protection of cells from thermal stress. Nucleotide polymorphisms within the promoter of Hsp affect degree of expression and inducibility of Hsp mRNA. The present study aimed to investigate the effect of polymorphism within promoter region on the cellular expression of Hsp70.1 mRNA and association of identified polymorphisms with the physiological parameters during summer stress and milk production traits in dairy cattle. Two hundred Frieswal cows were genotyped using double PCR-RFLP to identify deletion of cytosine within the Hsp70.1 promoter AP2 box at base position 895. Homozygous wild type genotypes (CC) were found in lower frequency (39.29, n=78) than heterozygous cytosine deletion mutant genotypes (C-) (60.71, n=122). In the observed physiological parameters (rectal temperature, respiration rate and heat tolerance coefficient), cows that were homozygous wild types had better significant (P<0.05) summer tolerance than the heterozygous deletion genotypes. Cytosine deletion mutation in the promoter region negatively affected (P<0.01) the expression of Hsp70.1 mRNA in peripheral bovine mononuclear cells (PBMC) subjected to in vitro heat stress. Further association of observed polymorphism with the milk production traits was significant as the heterozygous cytosine deletion cows had lower total milk yield, peak yield, yield at 300 days, protein% (P<0.01) and fat% (P<0.05) than the native wild type promoter cows. The results from the present study suggest that the promoter region of bovine hsp70.1 gene is polymorphic and may be useful in selection of dairy cows for relatively better thermotolerance and higher milk production.
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Affiliation(s)
- Rajib Deb
- Molecular Genetics Laboratory, Animal Genetics and Breeding Section Project Directorate on Cattle, Indian Council of Agricultural Research, Grass Farm Road, P. O. Box 17, Meerut Cantt., Meerut 250 001, Uttar Pradesh, India.
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