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1
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Dolu S, Cengiz MB, Döngelli H, Gürbüz M, Arayici ME. Importance of hematological and inflammatory markers in the localization of gastric cancer. World J Gastrointest Oncol 2025; 17:104455. [DOI: 10.4251/wjgo.v17.i4.104455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 01/20/2025] [Accepted: 02/07/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND Gastric cancer is a major global health concern, often diagnosed at advanced stages, leading to poor prognosis. Proximal and distal gastric cancers exhibit distinct clinicopathological features.
AIM To investigate the diagnostic value of hematological and inflammatory markers in differentiating proximal and distal gastric cancers and to evaluate their association with clinical outcomes.
METHODS A retrospective cohort study was conducted on 150 patients diagnosed with gastric adenocarcinoma through histopathological analysis. Patients were categorized into proximal gastric cancer and distal gastric cancer groups. Laboratory parameters were analyzed.
RESULTS Of the 150 patients, 84 had proximal gastric cancer and 66 had distal gastric cancer. Dysphagia was significantly more common in the proximal gastric cancer group, while anemia and higher platelet-to-lymphocyte ratio values were observed in the distal gastric cancer group (P = 0.031). Tumor stage and neutrophil-to-lymphocyte ratio emerged as independent predictors of all-cause mortality. No significant differences were found in other laboratory or biochemical parameters between the groups.
CONCLUSION Proximal and distal gastric cancers demonstrate distinct clinical and laboratory profiles. The platelet-to-lymphocyte ratio may serve as a valuable marker in differentiating cancer localization, while the neutrophil-to-lymphocyte ratio is a prognostic indicator for mortality. These findings highlight the potential of hematological markers in optimizing diagnosis and treatment strategies for gastric cancer.
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Affiliation(s)
- Süleyman Dolu
- Department of Gastroenterology, Faculty of Medicine, Dokuz Eylul University, İzmir 35340, Türkiye
| | - Mehmet B Cengiz
- Department of Internal Medicine, Ağrı Training and Research Hospital, Ağrı 04000, Türkiye
| | - Hüseyin Döngelli
- Department of Internal Medicine, Dokuz Eylul Universitesy, İzmir 35330, Türkiye
| | - Mustafa Gürbüz
- Department of Medical Oncology, Ağrı Training and Research Hospital, Ağrı 04000, Türkiye
| | - Mehmet E Arayici
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, İzmir 35330, Türkiye
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2
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Chen YY, Han QY, Chen QY, Zhou WJ, Zhang JG, Zhang X, Lin A. Impact of Sample Processing and Storage Conditions on RNA Quality of Fresh-Frozen Cancer Tissues. Biopreserv Biobank 2023; 21:510-517. [PMID: 37040277 DOI: 10.1089/bio.2022.0069] [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: 04/12/2023] Open
Abstract
Background: A biobank is a central resource that supports basic and clinical research. RNA quality of fresh-frozen tissue specimens in the biobank is highly associated with the success of downstream applications. Therefore, it is very important to evaluate the impact of tissue processing and storage conditions on RNA quality. Methods: A total of 238 surgically removed tissue specimens, including esophagus, lung, liver, stomach, colon, and rectal cancer, were used to evaluate RNA quality. Two tissue homogenization methods, manual and TissueLyser, were compared and the impacts of temperature fluctuation, tissue types, storage period, and clinicopathological parameters on RNA quality were analyzed. Results: RNA integrity was not influenced by tissue homogenization methods and tissue types. However, RNA integrity number (RIN) values were significantly correlated with temperature fluctuation. When the power of a -80°C freezer was cut off, RNA integrity of frozen tissues was not significantly affected until the temperature increased to 0°C. When the temperature rose to room temperature and remained for 4 hours, RNA integrity was almost completely destroyed. In addition, various cancer tissues with short-term storage at -80°C (<5 years) or high tumor differentiation had higher RINs. Conclusions: Tissue processing and storage conditions affected RNA quality of fresh-frozen cancer tissues. It is necessary to keep storage temperature stable and keep specimens at ultralow temperatures during homogenization. Also, for a biobank containing multiple types of cancer tissue samples, it is better to store them in liquid nitrogen if the storage duration is more than 5 years.
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Affiliation(s)
- Yuan-Yuan Chen
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qiu-Yue Han
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qiong-Yuan Chen
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Wen-Jun Zhou
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Jian-Gang Zhang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Xia Zhang
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Aifen Lin
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province, Linhai, China
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
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3
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Cho YD, Cho ES, Song JS, Kim YY, Hwang I, Kim SY. Standard operating procedures for the collection, processing, and storage of oral biospecimens at the Korea Oral Biobank Network. J Periodontal Implant Sci 2023; 53:336-346. [PMID: 36919006 PMCID: PMC10627733 DOI: 10.5051/jpis.2203680184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/02/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
PURPOSE The Korea Oral Biobank Network (KOBN) was established in 2021 as a branch of the Korea Biobank Network under the Korea Centers for Disease Control and Prevention to provide infrastructure for the collection, management, storage, and utilization of human bioresources from the oral cavity and associated clinical data for basic research and clinical studies. METHODS To address the need for the unification of the biobanking process, the KOBN organized the concept review for all the processes. RESULTS The KOBN established standard operating procedures for the collection, processing, and storage of oral samples. CONCLUSIONS The importance of collecting high-quality bioresources to generate accurate and reproducible research results has always been emphasized. A standardized procedure is a basic prerequisite for implementing comprehensive quality management of biological resources and accurate data production.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Eunae Sandra Cho
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, Korea
| | - Je Seon Song
- Department of Pediatric Dentistry, Yonsei University College of Dentistry, Seoul, Korea
| | - Young-Youn Kim
- Department of Oral and Maxillofacial Surgery, Apple Tree Institute of Biomedical Science, Apple Tree Dental Hospital, Seoul, Korea
| | | | - Sun-Young Kim
- Department of Conservative Dentistry, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea.
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4
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Yang HJ, Seo SI, Lee J, Huh CW, Kim JS, Park JC, Kim H, Shin H, Shin CM, Park CH, Lee SK. Sample Collection Methods in Upper Gastrointestinal Research. J Korean Med Sci 2023; 38:e255. [PMID: 37582502 PMCID: PMC10427214 DOI: 10.3346/jkms.2023.38.e255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023] Open
Abstract
In recent years, significant translational research advances have been made in the upper gastrointestinal (GI) research field. Endoscopic evaluation is a reasonable option for acquiring upper GI tissue for research purposes because it has minimal risk and can be applied to unresectable gastric cancer. The optimal number of biopsy samples and sample storage is crucial and might influence results. Furthermore, the methods for sample acquisition can be applied differently according to the research purpose; however, there have been few reports on methods for sample collection from endoscopic biopsies. In this review, we suggested a protocol for collecting study samples for upper GI research, including microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid culture, through a comprehensive literature review. For microbiome analysis, one or two pieces of biopsied material obtained using standard endoscopic forceps may be sufficient. Additionally, 5 mL of gastric fluid and 3-4 mL of saliva is recommended for microbiome analyses. At least one gastric biopsy tissue is necessary for most DNA or RNA analyses, while proteomics analysis may require at least 2-3 biopsy tissues. Single cell-RNA sequencing requires at least 3-5 tissues and additional 1-2 tissues, if possible. For successful organoid culture, multiple sampling is necessary to improve the quality of specimens.
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Affiliation(s)
- Hyo-Joon Yang
- Division of Gastroenterology, Department of Internal Medicine and Gastrointestinal Cancer Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung In Seo
- Division of Gastroenterology, Department of Internal Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Jin Lee
- Department of Internal Medicine, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Korea
| | - Cheal Wung Huh
- Division of Gastroenterology, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Korea
| | - Joon Sung Kim
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Incheon, Korea
| | - Jun Chul Park
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, Sejong University, Seoul, Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chan Hyuk Park
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea.
| | - Sang Kil Lee
- Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea.
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5
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [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] [Indexed: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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6
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Acharayothin O, Thiengtrong B, Juengwiwattanakitti P, Anekwiang P, Riansuwan W, Chinswangwatanakul V, Tanjak P. Impact of Washing Processes on RNA Quantity and Quality in Patient-Derived Colorectal Cancer Tissues. Biopreserv Biobank 2023; 21:31-37. [PMID: 35230139 DOI: 10.1089/bio.2021.0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a common and lethal cancer worldwide. Extraction of high-quality RNA from CRC samples plays a key role in scientific research and translational medicine. Specimen collection and washing methods that do not compromise RNA quality or quantity are needed to ensure high quality specimens for gene expression analysis and other RNA-based downstream applications. We investigated the effect of tissue specimen collection and different preparation processes on the quality and quantity of RNA extracted from surgical CRC tissues. Materials and Methods: After surgical resection, tissues were harvested and prepared with various washing processes in a room adjacent to the operating room. One hundred fourteen tissues from 36 CRC patients were separately washed in either cold phosphate-buffered saline reagent (n = 34) or Dulbecco's modified Eagle's medium (DMEM; n = 34) for 2-3 minutes until the stool was removed, and unwashed specimens served as controls (n = 34). Six tissue specimens were washed and immersed in DMEM for up to 1 hour at 4°C. Before RNA extraction, all specimens were kept in the stabilizing reagent for 3 months at -80°C. RNA was extracted, and the concentration per milligram of tissue was measured. RNA quality was assessed using the RNA integrity number (RIN) value. Results: Different washing processes did not result in significant differences in RNA quantity or RIN values. In the six tissues that were washed and immersed in DMEM for 1 hour, RIN values significantly decreased. The quality of the extracted RNA from most specimens was excellent with the average RIN greater than 7. Conclusions: RNA is stable in specimens washed in different processes for short periods, but RIN values may decrease with prolonged wash times.
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Affiliation(s)
- Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Benjarat Thiengtrong
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panudeth Juengwiwattanakitti
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panatna Anekwiang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Woramin Riansuwan
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vitoon Chinswangwatanakul
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pariyada Tanjak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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7
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Zheng XH, Zhou T, Li XZ, Zhang PF, Jia WH. Banking of Tumor Tissues: Effect of Preanalytical Variables in the Phase of Pre- and Postacquisition on RNA Integrity. Biopreserv Biobank 2023; 21:56-64. [PMID: 35377214 DOI: 10.1089/bio.2021.0124] [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: 11/02/2022] Open
Abstract
Background: RNA integrity of tumor tissues from 12 common organs was measured, and tumor tissues from liver were found to have the best RNA integrity in our previous study. The effects of preanalytical variables in the phase of pre- and postacquisition on RNA integrity were further assessed in hepatocellular carcinoma (HCC) tissues in this study. Methods: RNA integrity number (RIN) was measured in tissues from 146 HCC patients. First, 42 fresh HCC tumor tissues were newly collected to assess the effect of various preanalytical variables in the phase of preacquisition on RNA integrity. Second, eight paired HCC tumor and normal tissues were newly collected and used in the gradient course study of ex vivo ischemia time and freeze-thaw cycles on RNA integrity. Finally, 96 stock-frozen tumor tissues with various years of frozen storage were used to assess the effect of cryopreservation time. Results: RNA integrity was found to be independent of patient age, sex, clinical stage, tumor location, HBV infection status, tumor diameter, and surgical approach, but affected by tumor grade. Tumor tissues with a greater tumor grade had lower RIN. With the prolongation of ex vivo ischemia time, freeze-thaw cycles, and cryopreservation time, the RIN of HCC tissues showed decreasing trends. Significant decreases in RIN of the tumor and normal tissues were observed at 6 and 2 hours of ex vivo ischemia time, respectively, and significantly decreased RIN of tumor tissues was observed after six freeze-thaw cycles and 6 years of cryopreservation. Conclusions: Preanalytical variables in the phase of preacquisition such as tumor grade, and in the postacquisition phase such as ex vivo ischemia time, freeze-thaw times, and freeze-storage time both have effects on RNA integrity of HCC tissues. Tissue-based translational research should pay attention to preanalytical variables when collecting and utilizing tumor tissues.
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Affiliation(s)
- Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Department of Biobank, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P.R. China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Department of Biobank, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P.R. China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Department of Biobank, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P.R. China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Department of Biobank, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P.R. China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Department of Biobank, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P.R. China
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8
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He Y, Dong L, Yi H, Zhang L, Shi X, Su L, Gan B, Guo R, Wang Y, Luo Q, Li X. Improper preanalytical processes on peripheral blood compromise RNA quality and skew the transcriptional readouts of mRNA and LncRNA. Front Genet 2023; 13:1091685. [PMID: 36685907 PMCID: PMC9845260 DOI: 10.3389/fgene.2022.1091685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Genetic and epigenetic reprogramming caused by disease states in other tissues is always systemically reflected in peripheral blood leukocytes (PBLs). Accurate transcriptional readouts of Messenger RNA (mRNA) and Long non-coding RNA (lncRNA) in peripheral blood leukocytes are fundamental for disease-related study, diagnosis and treatment. However, little is known about the impact of preanalytical variables on RNA quality and downstream messenger RNA and Long non-coding RNA readouts. In this study, we explored the impact of RNA extraction kits and timing of blood placement on peripheral blood leukocyte-derived RNA quality. A novel enhanced evaluation system including RNA yields, purity, RNA integrity number (RIN) values and β-actin copies was employed to more sensitively identify RNA quality differences. The expression levels of informative mRNAs and Long non-coding RNAs in patients with chronic obstructive pulmonary disease (COPD) or triple-negative breast cancer (TNBC) were measured by Quantitative reverse transcription polymerase chain reaction (qRT-PCR) to investigate the impact of RNA quality on transcriptional readouts. Our results showed that the quality of RNA extracted by different kits varies greatly, and commercial kits should be evaluated and managed before batch RNA extraction. In addition, the quality of extracted RNA was highly correlated with the timing of blood placement, and the copy number of β-actin was significantly decreased after leaving blood at RT over 12 h. More importantly, compromised RNA leads to skewed transcriptional readouts of informative mRNAs and Long non-coding RNAs in patients with chronic obstructive pulmonary disease or triple-negative breast cancer. These findings have significant implications for peripheral blood leukocyte-derived RNA quality management and suggest that quality control is necessary prior to the analysis of patient messenger RNA and Long non-coding RNA expression.
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Affiliation(s)
- Yinli He
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Lele Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Hongyang Yi
- National Clinical Research Centre for Infectious Diseases, The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xue Shi
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Lin Su
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Ruirui Guo
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China,*Correspondence: Xiaojiao Li, ; Qinying Luo, ; Yawen Wang,
| | - Qinying Luo
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China,*Correspondence: Xiaojiao Li, ; Qinying Luo, ; Yawen Wang,
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China,*Correspondence: Xiaojiao Li, ; Qinying Luo, ; Yawen Wang,
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9
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Role of Biobanks for Cancer Research and Precision Medicine in Hepatocellular Carcinoma. J Gastrointest Cancer 2021; 52:1232-1247. [PMID: 34807351 DOI: 10.1007/s12029-021-00759-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is a highly complex and deadly cancer. There is an urgent need for new and effective treatment modalities. Since the primary goal in the management of cancer is to cure and improve survival, personalized therapy can increase survival, reduce mortality rates, and improve quality of life. Biobanks hold potential in leading to breakthroughs in biomedical research and precision medicine (PM). They serve as a biorepository, collecting, processing, storing, and supplying specimens and relevant data for basic, translational, and clinical research. OBJECTIVE We aimed to highlight the fundamental role of biobanks, harboring high quality, sustainable collections of patient samples in adequate size and variability, for developing diagnostic, prognostic, and predictive biomarkers to develop and PM approaches in the management of HCC. METHOD We obtained information from previously published articles and BBMRI directory. RESULTS AND CONCLUSION Biobanking of high-quality biospecimens along with patient clinical information provides a fundamental scientific infrastructure for basic, translational, and clinical research. Biobanks that control and eliminate pre-analytical variability of biospecimens, provide a platform to identify reliable biomarkers for the application of PM. We believe, establishing HCC biobanks will empower to underpin molecular mechanisms of HCC and generate strategies for PM. Thus, first, we will review current therapy approaches in HCC care. Then, we will summarize challenges in HCC management. Lastly, we will focus on the best practices for establishing HCC biobanking to support research, translational medicine in the light of new experimental research conducted with the aim of delivering PM for HCC patients.
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10
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Speirs V. Quality Considerations When Using Tissue Samples for Biomarker Studies in Cancer Research. Biomark Insights 2021; 16:11772719211009513. [PMID: 33958852 PMCID: PMC8060748 DOI: 10.1177/11772719211009513] [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: 11/27/2020] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
Tissue obtained from biobanks is frequently employed in biomarker studies. Biomarkers define objective, measurable characteristics of biological and biomedical procedures and have been used as indicators of clinical outcome. This article outlines some of the steps scientists should consider when embarking on biomarker research in cancer research using samples from biobanks and the importance and challenges of linking clinical data to biological samples.
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Affiliation(s)
- Valerie Speirs
- Institute of Medical Sciences, School of Medicine,
Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland,
UK
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11
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Liu N, Luo Y, Zhu Y, Peng H, Zou C, Zhou Z, Chen W, Wang H, Liu H, Hu Y, Zhang S, Qian K. Effects of Warm Ischemia Time, Cryopreservation, and Grinding Methods on RNA Quality of Mouse Kidney Tissues. Biopreserv Biobank 2021; 19:306-311. [PMID: 33577406 DOI: 10.1089/bio.2020.0129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: High-quality RNA extraction from tissue samples is of key importance for scientific research and translational medicine. Tissue collection and preparation may affect RNA quality. In this study, we investigated effects of warm ischemia time, cryopreservation, and grinding methods on RNA quality. Methods: Total RNA was extracted from mouse kidney tissues with warm ischemia times of 0, 30, 60, 90, and 120 minutes. Half of the tissues were used to extract RNA immediately, while the others were cryopreserved in the vapor phase of liquid nitrogen for 6 months before RNA extraction. A mortar, homogenizer, and tissue lyser were used to grind tissues. RNA was extracted by TRIzol, and RNA integrity was assessed by the RNA integrity number (RIN) value. Results: For fresh tissues and frozen tissues with warm ischemia time within 60 minutes, RIN values were above 7.0 and remained above 6.0 with warm ischemia time within 120 minutes. For the same warm ischemia time, RIN values of frozen tissues were slightly lower than those of fresh tissues. No significant RIN value alterations were observed among grinding methods, but for RNA extraction efficiency, a mortar was much less efficient than the homogenizer or tissue lyser. For frozen tissues, RNA tended to degrade within 8 minutes at room temperature. Conclusions: Mouse kidney tissues with a warm ischemia time within 120 minutes are suitable for general RNA-related research. For tissues with a warm ischemia time within 60 minutes, cryopreservation may not affect RNA quality. The duration of frozen tissues held at room temperature before grinding affects the integrity of RNA, while grinding methods do not affect RNA integrity.
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Affiliation(s)
- Nan Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| | - Hongwei Peng
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Cong Zou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zongning Zhou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huiqin Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Hu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shanshan Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
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12
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Compared DNA and RNA quality of breast cancer biobanking samples after long-term storage protocols in - 80 °C and liquid nitrogen. Sci Rep 2020; 10:14404. [PMID: 32873858 PMCID: PMC7462979 DOI: 10.1038/s41598-020-71441-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/11/2020] [Indexed: 11/08/2022] Open
Abstract
Molecular investigations are crucial for further developments in precision medicine. RNA sequencing, alone or in combination with further omic-analyses, resulted in new therapeutic strategies. In this context, biobanks represent infrastructures to store tissue samples and body fluids in combination with clinical data to promote research for new predictive and prognostic biomarkers as well as therapeutic candidate molecules. Until today, the optimal storage conditions are a matter of debate especially with view to the storage temperature. In this unique approach we compared parallel samples from the same tumour, one half stored at - 80 °C and one half in the vapor phase of liquid nitrogen, with almost identical pre-analytical conditions. We demonstrated that RNA isolated from breast cancer samples revealed significantly higher RINe-values after 10 years of storage in the vapor phase of liquid nitrogen compared to storage at - 80 °C. In contrast, no significant difference was found regarding the DIN-values after DNA isolation. Morphological changes of the nucleus and cytoplasm, especially in the samples stored at - 80 °C, gave insights to degenerative effects, most possibly due to the storage protocol and its respective peculiarities. In addition, our results indicate that exact point-to point documentation beginning at the sample preparation is mandatory.
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13
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Esteva-Socias M, Gómez-Romano F, Carrillo-Ávila JA, Sánchez-Navarro AL, Villena C. Impact of different stabilization methods on RT-qPCR results using human lung tissue samples. Sci Rep 2020; 10:3579. [PMID: 32108147 PMCID: PMC7046779 DOI: 10.1038/s41598-020-60618-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Aiming to increase the reproducibility of biomedical research results, biobanks obtain human tissues of the highest quality and carry out different storage methods adapted to the needs of analytical technique to be performed by the biomedical researchers. However, there is much controversy and little data concerning the real impact of different stabilization methods on tissue quality, integrity and functionality of derived biomolecules. The influence of four stabilization methods [RNAlater (RNL), snap freezing (SF), snap freezing using Optimal Cutting Tissue compound (SF-OCT) and formalin-fixed paraffin-embedded (FFPE)] on RNA quality and integrity was evaluated in paired samples of lung tissue. RNA integrity was evaluated through PCR-endpoint assays amplifying six fragments of different length of the HPRT1 gene and RNA Integrity Number (RIN). To evaluate the difference of tissue functionality among the stabilization methods tested, RT-qPCRs were performed focusing on the differential expression of the HPRT1, SNRPD3 and Jun genes. RNA from the samples preserved with the RNL or SF-OCT method showed better integrity compared to SF and FFPE, measured by PCR-endpoint and RT-qPCR assays. However, only statistically significant differences were observed between the RNA from FFPE and other stabilization methods when gene expression of HPRT1, SNRPD3 and Jun housekeeping genes were determined by RT-qPCR. For the three mentioned genes, Cq and RIN values were highly correlated. The present work describes the fragility of SF samples, being critical the moment just before RNA extraction, although further experiments of tissue RNA are needed. Standardization pre-analytic workflow can lead to improved reproducibility between biomedical research studies. The present study demonstrated clear evidences about the impact of the stabilization method on RNA derived from lung human tissue samples.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Gómez-Romano
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - José Antonio Carrillo-Ávila
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
- Andalusian Public Health System Biobank, Granada. Instituto de Investigación Biosanitaria ibs. Granada. Complejo Universitario de Granada/Universidad de Granada, Granada, Spain
| | - Alicia Loreto Sánchez-Navarro
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain.
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14
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Zheng H, Tao YP, Chen FQ, Li HF, Zhang ZD, Zhou XX, Yang Y, Zhou WP. Temporary Ischemia Time Before Snap Freezing Is Important for Maintaining High-Integrity RNA in Hepatocellular Carcinoma Tissues. Biopreserv Biobank 2019; 17:425-432. [PMID: 31025876 DOI: 10.1089/bio.2019.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Hao Zheng
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Yuan-Ping Tao
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Feng-Qiu Chen
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
- Biobank of Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Fen Li
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Zhi-De Zhang
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Xue-Xun Zhou
- Shanghai Avantech Bioscience Co., Ltd., Shanghai, China
| | - Yuan Yang
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Wei-Ping Zhou
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
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15
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Pelisek J, Hegenloh R, Bauer S, Metschl S, Pauli J, Glukha N, Busch A, Reutersberg B, Kallmayer M, Trenner M, Wendorff H, Tsantilas P, Schmid S, Knappich C, Schaeffer C, Stadlbauer T, Biro G, Wertern U, Meisner F, Stoklasa K, Menges AL, Radu O, Dallmann-Sieber S, Karlas A, Knipfer E, Reeps C, Zimmermann A, Maegdefessel L, Eckstein HH. Biobanking: Objectives, Requirements, and Future Challenges-Experiences from the Munich Vascular Biobank. J Clin Med 2019; 8:jcm8020251. [PMID: 30781475 PMCID: PMC6406278 DOI: 10.3390/jcm8020251] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/01/2019] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
Collecting biological tissue samples in a biobank grants a unique opportunity to validate diagnostic and therapeutic strategies for translational and clinical research. In the present work, we provide our long-standing experience in establishing and maintaining a biobank of vascular tissue samples, including the evaluation of tissue quality, especially in formalin-fixed paraffin-embedded specimens (FFPE). Our Munich Vascular Biobank includes, thus far, vascular biomaterial from patients with high-grade carotid artery stenosis (n = 1567), peripheral arterial disease (n = 703), and abdominal aortic aneurysm (n = 481) from our Department of Vascular and Endovascular Surgery (January 2004–December 2018). Vascular tissue samples are continuously processed and characterized to assess tissue morphology, histological quality, cellular composition, inflammation, calcification, neovascularization, and the content of elastin and collagen fibers. Atherosclerotic plaques are further classified in accordance with the American Heart Association (AHA), and plaque stability is determined. In order to assess the quality of RNA from FFPE tissue samples over time (2009–2018), RNA integrity number (RIN) and the extent of RNA fragmentation were evaluated. Expression analysis was performed with two housekeeping genes—glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (ACTB)—using TaqMan-based quantitative reverse-transcription polymerase chain reaction (qRT)-PCR. FFPE biospecimens demonstrated unaltered RNA stability over time for up to 10 years. Furthermore, we provide a protocol for processing tissue samples in our Munich Vascular Biobank. In this work, we demonstrate that biobanking is an important tool not only for scientific research but also for clinical usage and personalized medicine.
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Affiliation(s)
- Jaroslav Pelisek
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
| | - Renate Hegenloh
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sabine Bauer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Susanne Metschl
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Jessica Pauli
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Nadiya Glukha
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Albert Busch
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Benedikt Reutersberg
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Michael Kallmayer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Matthias Trenner
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Heiko Wendorff
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Pavlos Tsantilas
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sofie Schmid
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christoph Knappich
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christoph Schaeffer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Thomas Stadlbauer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Gabor Biro
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Uta Wertern
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Franz Meisner
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Kerstin Stoklasa
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Anna-Leonie Menges
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Oksana Radu
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Sabine Dallmann-Sieber
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Angelos Karlas
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Eva Knipfer
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Christian Reeps
- University Centre for Vascular Medicine and Department of Vascular Surgery, University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany.
| | - Alexander Zimmermann
- Department of Vascular and Endovascular Surgery, Technische Universität München, 81675 Munich, Germany.
| | - Lars Maegdefessel
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
| | - Hans-Henning Eckstein
- DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, 80636 Munich, Germany.
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