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Rao A, Stosic MS, Mohanty C, Suresh D, Wang AR, Lee DL, Nickel KP, Chandrashekar DS, Kimple RJ, Lambert PF, Kendziorski C, Rounge TB, Iyer G. Targeted inhibition of BET proteins in HPV16-positive head and neck squamous cell carcinoma reveals heterogeneous transcriptional responses. Front Oncol 2024; 14:1440836. [PMID: 39301555 PMCID: PMC11410754 DOI: 10.3389/fonc.2024.1440836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024] Open
Abstract
Human papillomaviruses (HPV), most commonly HPV16, are associated with a subset of head and neck squamous cell carcinoma (HNSCC) tumors, primarily oropharyngeal carcinomas, with integration of viral genomes into host chromosomes associated with worse survival outcomes. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. The role of BET protein-mediated transcription of viral-cellular genes in the viral-HNSCC genomes needs to be better understood. Using a combination of TAME-Seq, qRT-PCR, and immunoblot analyses, we show that BET inhibition downregulates E6 and E7 significantly, with heterogeneity in the downregulation of viral transcription across different HPV+ HNSCC cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4, mirroring the downregulation of viral E6 and E7 expression. We found that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A (p21) expression, leading to a G1-cell cycle arrest with apoptotic activity. Overall, our studies demonstrate that BET inhibition regulates both E6 and E7 viral and key cellular cell cycle regulator E2F gene expression and cellular gene expression in HPV-associated HNSCC and highlight the potential of BET inhibitors as a therapeutic strategy for this disease while also underscoring the importance of considering the heterogeneity in cellular responses to BET inhibition.
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Affiliation(s)
- Aakarsha Rao
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Milan S. Stosic
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhruthi Suresh
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Albert R. Wang
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Denis L. Lee
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
| | - Kwangok P. Nickel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
| | - Darshan S. Chandrashekar
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Randall J. Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Trine B. Rounge
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
- Norwegian Institute of Public Health, Cancer Registry of Norway, Oslo, Norway
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
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Le TQ, Meesiripan N, Sanggrajang S, Suwanpidokkul N, Prayakprom P, Bodhibukkana C, Khaowroongrueng V, Suriyachan K, Thanasitthichai S, Srisubat A, Surawongsin P, Rungsipipat A, Sakarin S, Rattanapinyopituk K. Anti-proliferative and apoptotic effect of cannabinoids on human pancreatic ductal adenocarcinoma xenograft in BALB/c nude mice model. Sci Rep 2024; 14:6515. [PMID: 38499634 PMCID: PMC10948389 DOI: 10.1038/s41598-024-55307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) is a highly malignant and lethal tumor of the exocrine pancreas. Cannabinoids extracted from the hemp plant Cannabis sativa have been suggested as a potential therapeutic agent in several human tumors. However, the anti-tumor effect of cannabinoids on human PDAC is not entirely clarified. In this study, the anti-proliferative and apoptotic effect of cannabinoid solution (THC:CBD at 1:6) at a dose of 1, 5, and 10 mg/kg body weight compared to the negative control (sesame oil) and positive control (5-fluorouracil) was investigated in human PDAC xenograft nude mice model. The findings showed that cannabinoids significantly decreased the mitotic cells and mitotic/apoptotic ratio, meanwhile dramatically increased the apoptotic cells. Parallelly, cannabinoids significantly downregulated Ki-67 and PCNA expression levels. Interestingly, cannabinoids upregulated BAX, BAX/BCL-2 ratio, and Caspase-3, meanwhile, downregulated BCL-2 expression level and could not change Caspase-8 expression level. These findings suggest that cannabinoid solution (THC:CBD at 1:6) could inhibit proliferation and induce apoptosis in human PDAC xenograft models. Cannabinoids, including THC:CBD, should be further studied for use as the potent PDCA therapeutic agent in humans.
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Affiliation(s)
- Trung Quang Le
- Department of Veterinary Pathology, Center of Excellent for Companion Animal Cancer-(CECAC), Chulalongkorn University, Bangkok, 10330, Thailand
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, 94000, Vietnam
| | - Nuntana Meesiripan
- Division of Research and Academic Support, National Cancer Institute, Bangkok, 10400, Thailand
| | - Suleeporn Sanggrajang
- Division of Research and Academic Support, National Cancer Institute, Bangkok, 10400, Thailand
| | | | | | | | | | - Kankanit Suriyachan
- Institute of Medical Research and Technology Assessment, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Somchai Thanasitthichai
- Institute of Medical Research and Technology Assessment, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Attasit Srisubat
- Division of Medical Technical and Academic Affairs, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Pattamaporn Surawongsin
- Research and Technology Assessment Department, Ophthalmology Department, Lerdsin Hospital, Bangkok, 10500, Thailand
| | - Anudep Rungsipipat
- Department of Veterinary Pathology, Center of Excellent for Companion Animal Cancer-(CECAC), Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siriwan Sakarin
- Division of Research and Academic Support, National Cancer Institute, Bangkok, 10400, Thailand.
| | - Kasem Rattanapinyopituk
- Department of Veterinary Pathology, Center of Excellent for Companion Animal Cancer-(CECAC), Chulalongkorn University, Bangkok, 10330, Thailand.
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Rao A, Ni Z, Suresh D, Mohanty C, Wang AR, Lee DL, Nickel KP, Varambally SRJ, Lambert PF, Kendziorski C, Iyer G. Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560587. [PMID: 37873389 PMCID: PMC10592929 DOI: 10.1101/2023.10.02.560587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.
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Affiliation(s)
- Aakarsha Rao
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dhruthi Suresh
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Albert R. Wang
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Denis L Lee
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Kwangok P. Nickel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Sooryanarayana Randall J. Varambally
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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Kim S, Park JY, Lee HW, Bae SU, Kim KE, Byun SJ, Seo I. YWHAZ and TBP are potential reference gene candidates for qPCR analysis of response to radiation therapy in colorectal cancer. Sci Rep 2023; 13:12902. [PMID: 37558778 PMCID: PMC10412564 DOI: 10.1038/s41598-023-39488-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
The expression profiles of conventional reference genes (RGs), including ACTB and GAPDH, used in quantitative real-time PCR (qPCR), vary depending on tissue types and environmental conditions. We searched for suitable RGs for qPCR to determine the response to radiotherapy in colorectal cancer (CRC) cell lines, organoids, and patient-derived tissues. Ten CRC cell lines (Caco-2, COLO 205, DLD-1, HCT116, HCT-15, HT-29, RKO, SW1116, SW480, and SW620) and organoids were selected and irradiated with 2, 10 or 21 grays (Gy) based on the previous related studies conducted over the last decade. The expression stability of 14 housekeeping genes (HKGs; ACTB, B2M, G6PD, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, PPIA, TBP, TFRC, UBC, and YWHAZ) after irradiation was evaluated using RefFinder using raw quantification cycle (Cq) values obtained from samples before and after irradiation. The expression stability of HKGs were also evaluated for paired fresh frozen tissues or formalin-fixed, paraffin-embedded samples obtained from CRC patients before and after chemoradiotherapy. The expression of YWHAZ and TBP encoding 14-3-3-zeta protein and TATA-binding protein were more stable than the other 12 HKGs in CRC cell lines, organoids, and patient-derived tissues after irradiation. The findings suggest that YWHAZ and TBP are potential RG candidates for normalizing qPCR results in CRC radiotherapy experiments.
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Affiliation(s)
- Shin Kim
- Department of Immunology, Keimyung University School of Medicine, Daegu, Republic of Korea
- Institute for Cancer Research, Keimyung University, Daegu, Republic of Korea
- Institute of Medical Science, Keimyung University, Daegu, Republic of Korea
| | - Jee Young Park
- Department of Immunology, Keimyung University School of Medicine, Daegu, Republic of Korea
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Hye Won Lee
- Institute for Cancer Research, Keimyung University, Daegu, Republic of Korea
- Department of Pathology, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Sung Uk Bae
- Institute for Cancer Research, Keimyung University, Daegu, Republic of Korea
- Institute of Medical Science, Keimyung University, Daegu, Republic of Korea
- Department of Surgery, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Kyeong Eui Kim
- Department of Surgery, Keimyung University Dongsan Medical Center, Daegu, Republic of Korea
| | - Sang Jun Byun
- Department of Radiation Oncology, Keimyung University School of Medicine, Daegu, Republic of Korea.
| | - Incheol Seo
- Department of Immunology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.
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Xu J, Yang M, Shao AZ, Pan HW, Fan YX, Chen KP. Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9125242. [PMID: 36467891 PMCID: PMC9711964 DOI: 10.1155/2022/9125242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 09/04/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.
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Affiliation(s)
- Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ming Yang
- Department of General Surgery, Fifth People's Hospital of Huaian City, Huaian, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ai-zhong Shao
- Department of Cardiothorac Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Hui-wen Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi-xuan Fan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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HPRT1 Most Suitable Reference Gene for Accurate Normalization of mRNA Expression in Canine Dermal Tissues with Radiation Therapy. Genes (Basel) 2022; 13:genes13111928. [DOI: 10.3390/genes13111928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/04/2022] Open
Abstract
Reference genes are crucial in molecular biological studies as an internal control for gene re-search as they exhibit consistent expression patterns across many tissue types. In canines, radiation therapy is the most important therapeutic tool to cure various diseases like cancer. However, when using radiation for therapeutic strategy, radiation exposure to healthy tissues leads to some possible side effects such as acute radiation-induced skin injury and alters gene expression. Therefore, the analysis of a change in reference gene expression during the skin recovery process after radiation therapy is essential in healthy canine tissue. In the present study, we analyzed eight reference genes (ACTB, GAPDH, YWHAZ, GUSB, HPRT1, RPL4, RPS5, and TBP) in canine dermal tissues at 0, 1, 2, 3, 4, 5, 7, and 9 weeks of radiation exposure that affected the skin condition of canines. The stability of reference genes is determined by evaluating radiation therapy’s effect on healthy canine dermal tissue. Epidermal marker, Keratin 10 expression varies each week after irradiation, and HPRT1 is found to be the most suitable for normalization of mRNA expression in radiation-exposed canine dermal tissues. Changes in the gene expression level were evaluated by using a reliable tool such as quantitative real-time polymerase chain reaction (qRT-PCR). In order to achieve a valid qRT-PCR result, the most stable reference genes used for normalization after the radiation exposure process are important. Therefore, the current study was designed to evaluate the most stable reference gene for the post-irradiation canine tissues. After radiation exposure, the alternation of reference gene expression was estimated by three algorithms (geNorm, Normfinder, and Bestkeeper). The RG validation programs (GeNorm and NormFinder) suggested that HPRT1, RPL4, and TBP were suitable for normalization in qRT-PCR. Furthermore, three algorithms suggested that HPRT1 was the most stable reference gene for normalization with qRT-PCR results, regardless of before and after radiation exposure. Whereas GAPDH was found to be the most unstable reference gene. In addition, the use of stable or unstable reference genes for the normalization of Keratin 10 expression showed statistical differences. Therefore, we observed that, to obtain accurate and suitable PCR results of the canine tissues with and without radiation exposure, the HPRT1 reference gene is recommended for normalization with its high stability. Additionally, the use of RGs such as HPRT1, RPL4, and TBP for normalization in qRT-PCR experiments is recommended for post-radiation canine tissues to generate more accurate and reliable data. These results will provide fundamental information regarding internal controls for gene expression studies and can be used for the analysis of gene patterns in regenerative medicine.
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Parsons TM, Buelow KL, Hanna A, Brake MA, Poma C, Hosch SE, Westrick RJ, Villa-Diaz LG, Wilson GD, Madlambayan GJ. Intratumoural haematopoietic stem and progenitor cell differentiation into M2 macrophages facilitates the regrowth of solid tumours after radiation therapy. Br J Cancer 2022; 126:927-936. [PMID: 34931040 PMCID: PMC8927108 DOI: 10.1038/s41416-021-01652-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/03/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Bone-marrow-derived haematopoietic stem and progenitor cells (HSPCs) are a prominent part of the highly complex tumour microenvironment (TME) where they localise within tumours and maintain haematopoietic potency. Understanding the role HSPCs play in tumour growth and response to radiation therapy (RT) may lead to improved patient treatments and outcomes. METHODS We used a mouse model of non-small cell lung carcinoma where tumours were exposed to RT regimens alone or in combination with GW2580, a pharmacological inhibitor of colony stimulating factor (CSF)-1 receptor. RT-PCR, western blotting and immunohistochemistry were used to quantify expression levels of factors that affect HSPC differentiation. DsRed+ HSPC intratumoural activity was tracked using flow cytometry and confocal microscopy. RESULTS We demonstrated that CSF-1 is enhanced in the TME following exposure to RT. CSF-1 signaling induced intratumoural HSPC differentiation into M2 polarised tumour-associated macrophages (TAMs), aiding in post-RT tumour survival and regrowth. In contrast, hyperfractionated/pulsed radiation therapy (PRT) and GW2580 ablated this process resulting in improved tumour killing and mouse survival. CONCLUSIONS Tumours coopt intratumoural HSPC fate determination via CSF-1 signaling to overcome the effects of RT. Thus, limiting intratumoural HSPC activity represents an attractive strategy for improving the clinical treatment of solid tumours.
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Affiliation(s)
- Tyler M Parsons
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Department of Radiation Oncology, Beaumont Research Institute, Royal Oak, MI, USA
| | - Katie L Buelow
- Department of Radiation Oncology, Beaumont Research Institute, Royal Oak, MI, USA
| | - Alaa Hanna
- Department of Radiation Oncology, Beaumont Research Institute, Royal Oak, MI, USA
| | - Marisa A Brake
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - Crystal Poma
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - Sarah E Hosch
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Department of Bioengineering, Oakland University, Rochester, MI, USA
- Oakland University Center for Data Science and Big Data Analytics, Rochester, MI, USA
| | - Luis G Villa-Diaz
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
- Department of Bioengineering, Oakland University, Rochester, MI, USA
| | - George D Wilson
- Department of Radiation Oncology, Beaumont Research Institute, Royal Oak, MI, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Department of Bioengineering, Oakland University, Rochester, MI, USA.
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9
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Identification of appropriate housekeeping genes for gene expression studies in human renal cell carcinoma under hypoxic conditions. Mol Biol Rep 2022; 49:3885-3891. [PMID: 35277789 DOI: 10.1007/s11033-022-07236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Hypoxia pathways are deregulated in clear renal cell carcinoma (ccRCC) because of the loss of the von Hippel-Lindau tumor suppressor function. Quantitative PCR is a powerful tool for quantifying differential expression between normal and cancer cells. Reliable gene expression analysis requires the use of genes encoding housekeeping genes. Therefore, in this study, eight reference candidate genes were evaluated to determine their stability in 786-0 cells under normoxic and hypoxic conditions. METHODS AND RESULTS Four different tools were used to rank the most stable genes-geNorm, NormFinder, BestKeeper, and Comparative Ct (ΔCt), and a general ranking was performed using RankAggreg. According to the four algorithms, the TFRC reference gene was identified as the most stable. There was no agreement among the results from the algorithms for the 2nd and 3rd positions. A general classification was then established using the RankAggreg tool. Finally, the three most suitable reference genes for use in 786-0 cells under normoxic and hypoxic conditions were TFRC, RPLP0, and SDHA. CONCLUSIONS To the best of our knowledge, this is the first study to identify reliable genes that can be used for gene expression analysis in ccRCC in a hypoxic environment.
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10
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Moretti R, Lampazzi E, Damiani C, Fabbri G, Lombardi G, Pioli C, Desiderio A, Serrao A, Calvitti M. Increased biting rate and decreased Wolbachia density in irradiated Aedes mosquitoes. Parasit Vectors 2022; 15:67. [PMID: 35209944 PMCID: PMC8867665 DOI: 10.1186/s13071-022-05188-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Background Releasing considerable numbers of radiation-sterilized males is a promising strategy to suppress mosquito vectors. However, releases may also include small percentages of biting females, which translate to non-negligible numbers when releases are large. Currently, the effects of irradiation on host-seeking and host-biting behaviors have not been exhaustively investigated. Information is also lacking regarding the effects of sterilizing treatment on the endosymbiotic bacterium Wolbachia, which is known to affect the vector competence of infected mosquitos. Methods To ascertain the effects of irradiation on females, the pupae of two Aedes albopictus strains, differing in their natural or artificial Wolbachia infection type, and Aedes aegypti—which is not infected by Wolbachia—were treated with various doses of X-rays and monitored for key fitness parameters and biting behavior over a period of 2 weeks. The effect of radiation on Wolbachia was investigated by quantitative polymerase chain reaction (qPCR) and fluorescence in situ hybridization (FISH) analysis. Results Partial Aedes albopictus female sterility was achieved at 28 Gy, but the number of weekly bites more than doubled compared to that of the controls. Radiation doses of 35 and 45 Gy completely inhibited progeny production but did not significantly affect the survival or flight ability of Ae. albopictus females and caused a tripling of the number of bites per female per week (compared to untreated controls). These results were also confirmed in Ae. aegypti after treatment at 50 Gy. Wolbachia density decreased significantly in 45-Gy-irradiated females, with the greatest decreases in the early irradiation group (26 ± 2-h-old pupae). Wolbachia density also decreased as adults aged. This trend was confirmed in ovaries but not in extra-ovarian tissues. FISH analysis showed a strongly reduced Wolbachia-specific fluorescence in the ovaries of 13 ± 1-day-old females. Conclusions These results suggest that, under sterile insect technique (SIT) programs, the vector capacity of a target population could increase with the frequency of the irradiated females co-released with the sterile males due to an increased biting rate. In the context of successful suppression, the related safety issues are expected to be generally negligible, but they should be conservatively evaluated when large-scale programs relying on imperfect sexing and high overflooding release ratios are run for long periods in areas endemic for arboviral diseases. Also, the effects of irradiation on the vector competence deserve further investigation. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05188-9.
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Affiliation(s)
- Riccardo Moretti
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.
| | - Elena Lampazzi
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Claudia Damiani
- School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy.,Biovecblok S.r.L, Camerino, MC, Italy
| | - Giulia Fabbri
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.,School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy
| | - Giulia Lombardi
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy.,School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy
| | - Claudio Pioli
- Laboratory of Biomedical Technologies, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Angiola Desiderio
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
| | - Aurelio Serrao
- School of Biosciences and Medical Veterinary, University of Camerino, Camerino, MC, Italy.,Biovecblok S.r.L, Camerino, MC, Italy
| | - Maurizio Calvitti
- Biotechnology and Agroindustry Division, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Casaccia Research Center, Rome, Italy
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11
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Functional Transient Receptor Potential Ankyrin 1 and Vanilloid 1 Ion Channels Are Overexpressed in Human Oral Squamous Cell Carcinoma. Int J Mol Sci 2022; 23:ijms23031921. [PMID: 35163843 PMCID: PMC8836603 DOI: 10.3390/ijms23031921] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 12/29/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a common cancer with poor prognosis. Transient Receptor Potential Ankyrin 1 (TRPA1) and Vanilloid 1 (TRPV1) receptors are non-selective cation channels expressed on primary sensory neurons and epithelial and immune cells. TRPV1 mRNA and immunopositivity, as well as TRPA1-like immunoreactivity upregulation, were demonstrated in OSCC, but selectivity problems with the antibodies still raise questions and their functional relevance is unclear. Therefore, here, we investigated TRPA1 and TRPV1 expressions in OSCC and analyzed their functions. TRPA1 and TRPV1 mRNA were determined by RNAscope in situ hybridization and qPCR. Radioactive 45Ca2+ uptake and ATP-based luminescence indicating cell viability were measured in PE/CA-PJ41 cells in response to the TRPA1 agonist allyl-isothiocyanate (AITC) and TRPV1 agonist capsaicin to determine receptor function. Both TRPA1 and TRPV1 mRNA are expressed in the squamous epithelium of the human oral mucosa and in PE/CA-PJ41 cells, and their expressions are significantly upregulated in OSCC compared to healthy mucosa. TRPA1 and TRPV1 activation (100 µM AITC, 100 nM capsaicin) induced 45Ca2+-influx into PE/CA-PJ41 cells. Both AITC (10 nM-5 µM) and capsaicin (100 nM-45 µM) reduced cell viability, reaching significant decrease at 100 nM AITC and 45 µM capsaicin. We provide the first evidence for the presence of non-neuronal TRPA1 receptor in the OSCC and confirm the expression of TRPV1 channel. These channels are functionally active and might regulate cancer cell viability.
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12
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García-Pérez O, Melgar-Vilaplana L, Córdoba-Lanús E, Fernández-de-Misa R. Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes. Curr Issues Mol Biol 2021; 43:2167-2176. [PMID: 34940125 PMCID: PMC8928935 DOI: 10.3390/cimb43030151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.
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Affiliation(s)
- Omar García-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
| | - Leticia Melgar-Vilaplana
- Pathology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
| | - Elizabeth Córdoba-Lanús
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
| | - Ricardo Fernández-de-Misa
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Dermatology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
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13
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Rashid M, Shah SG, Natu A, Verma T, Rauniyar S, Gera PB, Gupta S. RPS13, a potential universal reference gene for normalisation of gene expression in multiple human normal and cancer tissue samples. Mol Biol Rep 2021; 48:7967-7974. [PMID: 34657252 DOI: 10.1007/s11033-021-06828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reference genes are considered stable genes and are used for normalizing the gene expression profile across different cell types; as well as, in normal and diseased samples. However, these gene associates with different biological processes, and hence expression vary in different pathological conditions. Therefore, in the present study, eight different reference genes were used and compared to identify common reference gene usable for an array of different cell types and human cancers. METHODS AND RESULTS The expression stability of the eight reference genes across eleven normal and cancerous tissues was confirmed through real time-qPCR. Ribosomal protein S13 (RPS13) was found to be a common and stable reference gene across intra- and inter-comparison between various normal and tumor tissue types. Further, TCGA data analysis across and between normal and tumor tissue types also showed minimum deviation in expression of RPS13 gene out of eight routinely used reference genes. CONCLUSION RPS13 is the common stable reference gene in normalization for gene expression based analysis in cancer research.
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Affiliation(s)
- Mudasir Rashid
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanket Girish Shah
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Tripti Verma
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sukanya Rauniyar
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Poonam B Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India.
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14
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O’Rourke D, Wang D, Sanchez-Garcia JF, Cusano MP, Miller W, Cai T, Scheuenpflug J, Feng Z. Fit-for-purpose quantitative liquid biopsy based droplet digital PCR assay development for detection of programmed cell death ligand-1 (PD-L1) RNA expression in PAXgene blood samples. PLoS One 2021; 16:e0250849. [PMID: 33970922 PMCID: PMC8109819 DOI: 10.1371/journal.pone.0250849] [Citation(s) in RCA: 2] [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: 01/15/2021] [Accepted: 04/14/2021] [Indexed: 11/19/2022] Open
Abstract
Development of a clinically applicable liquid biopsy-based test for PD-L1 mRNA expression would be beneficial in providing complementary evidence to current immunohistochemistry assays. Hence, we report the development of a fit-for-purpose assay for detection of blood PD-L1 mRNA expression using droplet digital polymerase chain reaction (ddPCR). TaqMan® assays were selected based on coverage of the PD-L1 gene and were tested for linearity and efficiency using real-time quantitative PCR. Four reference genes were analyzed in positive control cell line (A549 treated with interferon gamma, [IFN γ]) genomic DNA. The PD-L1 primer/probe sets were also evaluated in ddPCR for limit of blank, limit of detection, and precision. Finally, thirty-five healthy volunteer samples were evaluated to establish a baseline level of PD-L1 expression. In ddPCR, the limit of blank was determined to be 0 copies and the limit of detection was determined to be less than or equal to 19 copies of PD-L1. The average intra-run coefficient of variation in the ddPCR assay was 7.44% and average inter-run CV was 7.70%. Treatment of A549 cells with IFN γ resulted in a 6.7-fold increase in PD-L1 expression (21,580 copies in untreated cDNA versus 145,000 copies in treated cDNA). Analysis of healthy human samples yielded a median value of 1659 PD-L1 copies/μL with a range of 768-7510 copies/μL. The assay was transferred to an external service provider and results from our in-house experiments and those conducted externally shows a correlation of 0.994. In conclusion, a fit-for-purpose liquid biopsy-based, purely quantitative ddPCR assay for the detection of PD-L1 mRNA expression was developed and validated using PAXgene RNA blood samples. Linearity, reproducibility, limit of blank and limit of detection were measured and deemed suitable for clinical application. This ultra-sensitive liquid biopsy ddPCR assay has promising clinical potential in screening, longitudinal monitoring and disease progression detection.
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Affiliation(s)
- Dennis O’Rourke
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
| | - Danyi Wang
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
| | - Jorge F. Sanchez-Garcia
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
| | - Maria Perella Cusano
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
| | - Waldemar Miller
- Biosample Informatics and Biobanking, Clinical Trial Management, Global Clinical Operations, Global Development, Merck KGaA, Darmstadt, Germany
| | - Ti Cai
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
| | - Juergen Scheuenpflug
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, Merck KGaA, Darmstadt, Germany
| | - Zheng Feng
- Global Clinical Biomarkers & Companion Diagnostics, Translational Medicine, Global Development, EMD Serono Research and Development Institute, Inc. a division of Merck KGaA, Billerica, MA, United States of America
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15
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Tyrosine kinase inhibitors protect the salivary gland from radiation damage by increasing DNA double-strand break repair. J Biol Chem 2021; 296:100401. [PMID: 33571522 PMCID: PMC7973138 DOI: 10.1016/j.jbc.2021.100401] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/23/2022] Open
Abstract
We have previously shown that the tyrosine kinase inhibitors (TKIs) dasatinib and imatinib can protect salivary glands from irradiation (IR) damage without impacting tumor therapy. However, how they induce this protection is unknown. Here we show that TKIs mediate radioprotection by increasing the repair of DNA double-stranded breaks. DNA repair in IR-treated parotid cells, but not oral cancer cells, occurs more rapidly following pretreatment with imatinib or dasatinib and is accompanied by faster formation of DNA damage-induced foci. Similar results were observed in the parotid glands of mice pretreated with imatinib prior to IR, suggesting that TKIs "prime" cells for DNA repair. Mechanistically, we observed that TKIs increased IR-induced activation of DNA-PK, but not ATM. Pretreatment of parotid cells with the DNA-PK inhibitor NU7441 reversed the increase in DNA repair induced by TKIs. Reporter assays specific for homologous recombination (HR) or nonhomologous end joining (NHEJ) verified regulatation of both DNA repair pathways by imatinib. Moreover, TKIs also increased basal and IR-induced expression of genes associated with NHEJ (DNA ligase 4, Artemis, XLF) and HR (Rad50, Rad51 and BRCA1); depletion of DNA ligase 4 or BRCA1 reversed the increase in DNA repair mediated by TKIs. In addition, TKIs increased activation of the ERK survival pathway in parotid cells, and ERK was required for the increased survival of TKI-treated cells. Our studies demonstrate a dual mechanism by which TKIs provide radioprotection of the salivary gland tissues and support exploration of TKIs clinically in head and neck cancer patients undergoing IR therapy.
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16
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Mikhalkevich N, O’Carroll IP, Tkavc R, Lund K, Sukumar G, Dalgard CL, Johnson KR, Li W, Wang T, Nath A, Iordanskiy S. Response of human macrophages to gamma radiation is mediated via expression of endogenous retroviruses. PLoS Pathog 2021; 17:e1009305. [PMID: 33556144 PMCID: PMC7895352 DOI: 10.1371/journal.ppat.1009305] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2021] [Accepted: 01/11/2021] [Indexed: 01/11/2023] Open
Abstract
Ionizing radiation-induced tissue damage recruits monocytes into the exposed area where they are differentiated to macrophages. These implement phagocytic removal of dying cells and elicit an acute inflammatory response, but can also facilitate tumorigenesis due to production of anti-inflammatory cytokines. Using primary human monocyte-derived macrophages (MDMs) and the THP1 monocytic cell line, we demonstrate that gamma radiation triggers monocyte differentiation toward the macrophage phenotype with increased expression of type I interferons (IFN-I) and both pro- and anti-inflammatory macrophage activation markers. We found that these changes correlate with significantly upregulated expression of 622 retroelements from various groups, particularly of several clades of human endogenous retroviruses (HERVs). Elevated transcription was detected in both sense and antisense directions in the HERV subgroups tested, including the most genetically homogeneous clade HML-2. The level of antisense transcription was three- to five-fold higher than of the sense strand levels. Using a proximity ligation assay and immunoprecipitation followed by RNA quantification, we identified an increased amount of the dsRNA receptors MDA-5 and TLR3 bound to an equivalent number of copies of sense and antisense chains of HERVK HML-2 RNA. This binding triggered MAVS-associated signaling pathways resulting in increased expression of IFN-I and inflammation related genes that enhanced the cumulative inflammatory effect of radiation-induced senescence. HML-2 knockdown was accompanied with reduced expression and secretion of IFNα, pro-inflammatory (IL-1β, IL-6, CCL2, CCL3, CCL8, and CCL20) and anti-inflammatory (IL10) modulators in irradiated monocytes and MDMs. Taken together, our data indicate that radiation stress-induced HERV expression enhances the IFN-I and cytokine response and results in increased levels of pro-inflammatory modulators along with expression of anti-inflammatory factors associated with the macrophage tumorigenic phenotype. Ionizing radiation is a powerful stressogenic factor that induces massive cell damage. The signals released from radiation-damaged tissues recruit the monocytes, which are differentiated into macrophages that remove dying cells via phagocytosis and facilitate inflammation but can also contribute to tumorigenesis through anti-inflammatory and regenerative activities. The mechanism of this dual response of macrophages to irradiation is not fully understood. Using primary human macrophages and a monocytic cell line, we demonstrated that gamma radiation doses activate expression of various human endogenous retroviruses (HERVs). At the molecular level, we have shown that increased numbers of sense and antisense transcripts of tested HERV subgroups bind to double-stranded RNA receptors inducing the expression of type I interferons, multiple pro-inflammatory and some anti-inflammatory factors. At the phenotypic level, polarized macrophages exhibit a potent inflammatory response along with potentially tumorigenic characteristics. Our data suggest that endogenous retroviruses represent an important contributor of the macrophage-mediated inflammation in response to radiation-induced stress but may also indirectly influence tumorigenesis via biased macrophage polarization.
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Affiliation(s)
- Natallia Mikhalkevich
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Ina P. O’Carroll
- Department of Chemistry, United States Naval Academy, Annapolis, Maryland, United States of America
| | - Rok Tkavc
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kateryna Lund
- Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Gauthaman Sukumar
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Clifton L. Dalgard
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Kory R. Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongguang Wang
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (AN); (SI)
| | - Sergey Iordanskiy
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail: (AN); (SI)
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17
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de Mattos RC, Guimarães IDS, Thiago LDS, de Melo AC. Evaluation of HIF-1α and VEGF-A expression in radiation-induced cystitis: A case-control study. Int Braz J Urol 2020; 47:295-305. [PMID: 33146980 PMCID: PMC7857752 DOI: 10.1590/s1677-5538.ibju.2020.0054] [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: 01/22/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
The standard treatment for locally advanced cervical cancer (CC) is chemoradiotherapy. Once the bladder receives part of the radiation, a typical inflammatory condition that configures radiation-induced cystitis may develop. Chronic radiation-induced cystitis is commonly characterized by the bladder new submucosal vascularization, which is typically fragile and favors hematuria. The current study aims to investigate if Hypoxia-Induced Factor (HIF-1α) and its transcriptional target Vascular Endothelial Growth Factor A (VEGF-A) could be a primary pathway leading to increased submucosal vascularization. HIF-1α and VEGF-A mRNA levels in bladder core biopsies from CC patients treated with radiotherapy versus untreated (non-irradiated) patients were analyzed using a droplet digital polymerase chain reaction technology. Gene expression results showed that HIF-1α and VEGF-A had no significant differences between bladder samples from patients previously irradiated and untreated patient samples. However, a direct relationship between the degree of late morbidity and the expression of HIF-1α and VEGF-A has been demonstrated. Despite the lack of statistical significance precludes a definitive conclusion, the data presented herein suggests that further studies investigating the role of HIF-1α in bladder neovascularization in radiation-induced cystitis are highly recommended.
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Affiliation(s)
| | | | - Leandro de Souza Thiago
- Divisão de Pesquisa Clínica, Instituto Nacional do Câncer - INCA, Rio de Janeiro, RJ, Brasil
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Verma YK, Singh AK, Gurudutta GU. Survival genes expression analysis following ionizing radiation to LiCl treated KG1a cells. Int J Radiat Biol 2020; 96:671-688. [PMID: 31985347 DOI: 10.1080/09553002.2020.1721592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose: Lithium chloride (LiCl) is clinically used for manic disorders. Its role has been shown in improving cell survival by decreasing Bax and p53 expression and increasing Bcl-2 concentration in the cell. This potential of LiCl is responsible for reducing irradiated cell death. In this study, we have explored the role of LiCl as a radioprotectant affecting survival genes.Materials and methods: To find out the cellular response upon LiCl pretreatment to radiation-exposed KG1a cells; viability, clonogenic assay and microarray studies were performed. This was followed by the detection of transcription factor binding motif in coregulated genes. These results were confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and chromatin immunoprecipitation (CHIP).Results: LiCl improved irradiated KG1a cell survival and its clonogenicity at 2 mM concentration (clinically used). Microarray data analysis showed differential expression of cell-protecting genes playing an important role in apoptosis, cell cycle, adhesion and inflammation, etc. The coregulation analysis revealed genes involved in bile acid biosynthesis were also affected by LiCl treatment, these genes are likely to be responsible for radiation-induced gastrointestinal (GI) syndrome through bile production.Conclusions: This is the first study with respect to global genetic expression upon LiCl treatment to radiation-exposed cells. Our results suggest considering repurposing of LiCl as a protective agent for radiation injury.
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Affiliation(s)
- Yogesh Kumar Verma
- Division of Stem Cell & Gene Therapy Research, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Ajay Kumar Singh
- Division of Stem Cell & Gene Therapy Research, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Gangenahalli Ugraiah Gurudutta
- Division of Stem Cell & Gene Therapy Research, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
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Patel RB, Ye M, Carlson PM, Jaquish A, Zangl L, Ma B, Wang Y, Arthur I, Xie R, Brown RJ, Wang X, Sriramaneni R, Kim K, Gong S, Morris ZS. Development of an In Situ Cancer Vaccine via Combinational Radiation and Bacterial-Membrane-Coated Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902626. [PMID: 31523868 PMCID: PMC6810793 DOI: 10.1002/adma.201902626] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/03/2019] [Indexed: 05/08/2023]
Abstract
Neoantigens induced by random mutations and specific to an individual's cancer are the most important tumor antigens recognized by T cells. Among immunologically "cold" tumors, limited recognition of tumor neoantigens results in the absence of a de novo antitumor immune response. These "cold" tumors present a clinical challenge as they are poorly responsive to most immunotherapies, including immune checkpoint inhibitors (ICIs). Radiation therapy (RT) can enhance immune recognition of "cold" tumors, resulting in a more diversified antitumor T-cell response, yet RT alone rarely results in a systemic antitumor immune response. Therefore, a multifunctional bacterial membrane-coated nanoparticle (BNP) composed of an immune activating PC7A/CpG polyplex core coated with bacterial membrane and imide groups to enhance antigen retrieval is developed. This BNP can capture cancer neoantigens following RT, enhance their uptake in dendritic cells (DCs), and facilitate their cross presentation to stimulate an antitumor T-cell response. In mice bearing syngeneic melanoma or neuroblastoma, treatment with BNP+RT results in activation of DCs and effector T cells, marked tumor regression, and tumor-specific antitumor immune memory. This BNP facilitates in situ immune recognition of a radiated tumor, enabling a novel personalized approach to cancer immunotherapy using off-the-shelf therapeutics.
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Affiliation(s)
- Ravi B Patel
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Mingzhou Ye
- Department of Biomedical Engineering, University of Wisconsin, 330 N Orchard St. B1162, Madison, WI, 53715, USA
| | - Peter M Carlson
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Abigail Jaquish
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Luke Zangl
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Ben Ma
- Department of Biomedical Engineering, University of Wisconsin, 330 N Orchard St. B1162, Madison, WI, 53715, USA
| | - Yuyuan Wang
- Department of Biomedical Engineering, University of Wisconsin, 330 N Orchard St. B1162, Madison, WI, 53715, USA
| | - Ian Arthur
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Ruosen Xie
- Department of Biomedical Engineering, University of Wisconsin, 330 N Orchard St. B1162, Madison, WI, 53715, USA
| | - Ryan J Brown
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - Xing Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin, WARF Office Bldg, 610 Walnut St, 2nd Fl., Madison, WI, 53726, USA
| | - Raghava Sriramaneni
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
| | - KyungMann Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, WARF Office Bldg, 610 Walnut St, 2nd Fl., Madison, WI, 53726, USA
| | - Shaoqin Gong
- Department of Biomedical Engineering, University of Wisconsin, 330 N Orchard St. B1162, Madison, WI, 53715, USA
| | - Zachary S Morris
- Department of Human Oncology, University of Wisconsin, WIMR-I, Room 3131, 1111 Highland Ave, Madison, WI, 53705, USA
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Dessels C, Pepper MS. Reference Gene Expression in Adipose-Derived Stromal Cells Undergoing Adipogenic Differentiation. Tissue Eng Part C Methods 2019; 25:353-366. [PMID: 31062665 PMCID: PMC6589494 DOI: 10.1089/ten.tec.2019.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
IMPACT STATEMENT As the use of adipose-derived stromal cells (ASCs) in clinical trials increases, so does the amount of experimental data from research groups, many of which use human ASCs to study adipogenesis in obesity. Different conditions are constantly being applied to ASCs in vitro, to obtain a therapeutic product for potential downstream applications. Few articles have looked at the effect of different conditions on ASC reference gene (RG) expression and stability, which was the aim of this research, as such this article will assist other researchers to make an informed decision about RG selection for gene expression studies using ASCs including those for adipogenesis.
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Affiliation(s)
- Carla Dessels
- Institute for Cellular and Molecular Medicine, Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael Sean Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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21
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Enhanced cytotoxic and genotoxic effects of gadolinium-doped ZnO nanoparticles on irradiated lung cancer cells at megavoltage radiation energies. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 103:109739. [PMID: 31349426 DOI: 10.1016/j.msec.2019.109739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/10/2023]
Abstract
The purpose of this study was to investigate the radiation dose enhancement effects of gadolinium-doped zinc oxide nanoparticles (Gd-doped ZnO NPs) under the megavoltage (MV) X-ray irradiation. ZnO NPs have preferred photocatalytic properties under UV light for cancer killing. UV light has limited applications in cancer treatment and it is necessary to use X-ray photons with MV energies. In order to increase the absorption of radiation and also to enhance the imaging visualization capabilities of ZnO NPs, gadolinium (Gd) as a high atomic number element was selected for doping into the structure of ZnO NPs. Gd-doped ZnO NPs were synthesized by a chemical precipitation method and characterized by transmission electron microscopy, powder X-ray diffraction, ultraviolet-visible spectroscopy, and energy-dispersive X-ray techniques. Cellular uptake was assessed by TEM and inductively coupled plasma mass spectrometry. NPs cytotoxicity was analyzed by MTT assay and radiation dose enhancement was measured by clonogenic survival assay. Apoptosis induction, cell cycle progression, micronucleus formation and expression of DNA double-strand break repair genes of XRCC2 and XRCC4 were determined by flow cytometry, micronucleus assay, and quantitative real-time polymerase chain reaction. CT and MR imaging were used to analyze the image visualization capabilities of NPs. NPs characterization showed that highly pure crystalline Gd-doped ZnO NPs with a narrow size distribution and grain size of 9 nm were synthesized. Gd-doped ZnO NPs were distributed in the cells and showed dose-dependent toxicity. Combination of Gd-doped ZnO NPs with 6 MV X-rays induced dose-dependent radiosensitivity with sensitizer enhancement ratios (SER) of 1.47 and 1.61 for 10 and 20 μg/mL NPs concentrations. Cancer cells blocked in G1, apoptosis rates, and micronuclei formation was enhanced and inversely, the DNA repair efficiency was impaired by down regulation of the mRNA levels of XRCC2 and XRCC4 genes. Gd-doped ZnO NPs enhanced the contrasts of CT and MR images of cancer cells. Overall, the results of this study provide detailed biological insights on the dose enhancement of Gd-doped ZnO NPs at MV radiations, which would contribute to the further development of this potent theranostic platform for clinical applications.
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Pin-On P, Aporntewan C, Siriluksana J, Bhummaphan N, Chanvorachote P, Mutirangura A. Targeting high transcriptional control activity of long mononucleotide A-T repeats in cancer by Argonaute 1. Gene 2019; 699:54-61. [PMID: 30858133 DOI: 10.1016/j.gene.2019.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 02/01/2023]
Abstract
Epigenetic regulatory changes alter the gene regulation function of DNA repeat elements in cancer and consequently promote malignant phenotypes. Some short tandem repeat sequences, distributed throughout the human genome, can play a role as cis-regulatory elements of the genes. Distributions of tandem long (≥10) and short (<10) A-T repeats in the genome are different depending on gene functions. Long repeats are more commonly found in housekeeping genes and may regulate genes in harmonious fashion. Mononucleotide A-repeats around transcription start sites interact with Argonaute proteins (AGOs) to regulate gene expression. miRNA-bound AGO alterations in cancer have been reported; consequently, these changes would affect genes containing mononucleotide A- and T-repeats. Here, we showed an unprecedented hallmark of gene regulation in cancer. We evaluated the gene expression profiles reported in the Gene Expression Omnibus and found a high density of 13-27 A-T repeats in the up-regulated genes in malignancies derived from the bladder, cervix, head and neck, ovary, vulva, breast, colon, liver, lung, prostate, kidney, thyroid, adrenal gland, bone, blood cells, muscle and brain. Transfection of cell-penetrating protein tag AGO1 containing poly uracils (CPP-AGO1-polyUs) to the lung cancer cell lines altered gene regulation depending on the presence of long A-T repeats. CPP-AGO1-polyUs limited cell proliferation and the ability of a cancer cell to grow into a colony in lung cancer cell lines. In conclusion, long A-T repeats up-regulated many genes in cancer that can be targeted by AGO1 to change the expression of many genes and limited cancer growth.
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Affiliation(s)
- Piyapat Pin-On
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand; Center of Excellence in Molecular Genetic of Cancer and Human Disease, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Chatchawit Aporntewan
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jirattha Siriluksana
- Center of Excellence in Molecular Genetic of Cancer and Human Disease, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Narumol Bhummaphan
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pithi Chanvorachote
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetic of Cancer and Human Disease, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand.
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Su H, Tao T, Yang Z, Kang X, Zhang X, Kang D, Wu S, Li C. Circular RNA cTFRC acts as the sponge of MicroRNA-107 to promote bladder carcinoma progression. Mol Cancer 2019; 18:27. [PMID: 30782157 PMCID: PMC6379985 DOI: 10.1186/s12943-019-0951-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/04/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Circular RNA (circRNA) represents a broad and diverse endogenous RNAs that can regulate gene expression in cancer. However, the regulation and function of bladder cancer (BC) circRNAs remain largely unknown. METHODS Here we generated circRNA microarray data from three BC tissues and paired non-cancerous matched tissues, and detected circular RNA-cTFRC up-regulated and correlated with tumor grade and poor survival rate of BC patients. We subsequently performed functional analyses in cell lines and an animal model to support clinical findings. Mechanistically, we demonstrated that cTFRC could directly bind to miR-107 and relieve suppression for target TFRC expression. RESULTS We detected circular RNA-cTFRC up-regulated and correlated with tumor grade and poor survival rate of BC patients. Knock down of cTFRC inhibited invasion and proliferation of BC cell lines in vitro and tumor growth in vivo. Furthermore, the expression of cTFRC correlated with TFRC and negatively correlated with miR-107 both in BC cell lines and BC clinical samples. In addition, up-regulation of cTFRC promoted TFRC expression and contributed to an epithelial to mesenchymal transition phenotype in BC cells. Finally, we found that cTFRC acts as a competing endogenous RNA (ceRNA) for miR-107 to regulate TFRC expression. CONCLUSIONS cTFRC may exert regulatory functions in BC and may be a potential marker of BC diagnosis or progression.
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Affiliation(s)
- Hongwei Su
- Department of urology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646699, China
| | - Tao Tao
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Department of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
| | - Zhao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Beijing Jianlan Institute of Medicine, Beijing, 100190, China
| | - Xing Kang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xu Zhang
- Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Danyue Kang
- Michigan State University, 426 Auditorium Rd, East Lansing, MI, 48824, USA
| | - Song Wu
- Department of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China. .,Department of Urology, Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China. .,Department of Clinical Medicine, School of Medicine, Anhui University of Science and Technology, Huainan, 232001, China. .,Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China.
| | - Chong Li
- Department of urology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646699, China. .,Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Department of Urology, The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China. .,Beijing Jianlan Institute of Medicine, Beijing, 100190, China. .,Beijing Zhongke Jianlan Biotechnology Co., Ltd., Beijing, 101400, China.
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24
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Baker S, Ali I, Silins I, Pyysalo S, Guo Y, Högberg J, Stenius U, Korhonen A. Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer. Bioinformatics 2018; 33:3973-3981. [PMID: 29036271 PMCID: PMC5860084 DOI: 10.1093/bioinformatics/btx454] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/12/2017] [Indexed: 11/23/2022] Open
Abstract
Motivation To understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases. One way to organize existing knowledge on cancer is to utilize the widely accepted framework of the Hallmarks of Cancer. These hallmarks refer to the alterations in cell behaviour that characterize the cancer cell. Results We created an extensive Hallmarks of Cancer taxonomy and developed automatic text mining methodology and a tool (CHAT) capable of retrieving and organizing millions of cancer-related references from PubMed into the taxonomy. The efficiency and accuracy of the tool was evaluated intrinsically as well as extrinsically by case studies. The correlations identified by the tool show that it offers a great potential to organize and correctly classify cancer-related literature. Furthermore, the tool can be useful, for example, in identifying hallmarks associated with extrinsic factors, biomarkers and therapeutics targets. Availability and implementation CHAT can be accessed at: http://chat.lionproject.net. The corpus of hallmark-annotated PubMed abstracts and the software are available at: http://chat.lionproject.net/about Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Simon Baker
- Computer Laboratory.,Language Technology Lab, Department of Theoretical and Applied Linguistics, University of Cambridge, Cambridge CB3 9DA, UK
| | - Imran Ali
- Institute of Environmental Medicine, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Ilona Silins
- Institute of Environmental Medicine, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Sampo Pyysalo
- Language Technology Lab, Department of Theoretical and Applied Linguistics, University of Cambridge, Cambridge CB3 9DA, UK
| | - Yufan Guo
- Language Technology Lab, Department of Theoretical and Applied Linguistics, University of Cambridge, Cambridge CB3 9DA, UK
| | - Johan Högberg
- Institute of Environmental Medicine, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Ulla Stenius
- Institute of Environmental Medicine, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Anna Korhonen
- Language Technology Lab, Department of Theoretical and Applied Linguistics, University of Cambridge, Cambridge CB3 9DA, UK
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Karyopherins in cancer. Curr Opin Cell Biol 2018; 52:30-42. [PMID: 29414591 DOI: 10.1016/j.ceb.2018.01.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/08/2018] [Accepted: 01/14/2018] [Indexed: 12/16/2022]
Abstract
Malfunction of nuclear-cytoplasmic transport contributes to many diseases including cancer. Defective nuclear transport leads to changes in both the physiological levels and temporal-spatial location of tumor suppressors, proto-oncogenes and other macromolecules that in turn affect the tumorigenesis process and drug sensitivity of cancer cells. In addition to their nuclear transport functions in interphase, Karyopherin nuclear transport receptors also have important roles in mitosis and chromosomal integrity. Therefore, alterations in the expressions or regular functions of Karyopherins may have substantial effects on the course and outcome of diseases.
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