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Slušná ĽK, Balog M. Review of Indicators in the Context of Biobanking. Biopreserv Biobank 2023; 21:318-326. [PMID: 36099204 DOI: 10.1089/bio.2022.0073] [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
Background: Biobanks that intend to serve as high-performing and stable elements of an innovative research ecosystem must have an established system for regular measurement and evaluation using appropriately set indicators. The main objective of this study was to provide a comprehensive overview of indicators in the context of biobanking, with new perspectives to highlight the existence of numerous options and introduce indicators that could help overcome problems associated with the difficult assessment of the impact of biobanks. Methods: A literature review was performed to identify publications relevant to the topic of indicators in biobanking. The Web of Science Core Collection and PubMed databases were searched using specific keywords. In addition, three articles that focused on indicators designed for the evaluation of research infrastructures were included in the review. Results: Based on the scientific literature for the biobanking field, many types of quantitative and qualitative indicators exist. They are mainly related to the quantity and quality of data and samples, their distribution, the monitoring of research projects, and subsequent publication outputs. The indicators identified in the biobanking literature primarily focus on the outcome, not the impact. Conclusions: Indicators identified in the biobanking literature may be further expanded with suggestions designed for other types of research infrastructures, while considering the context where biobanks operate and the needs of individual biobanking stakeholders. The establishment of a comprehensive monitoring system that captures all necessary elements is crucial for modern biobanks.
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Affiliation(s)
| | - Miroslav Balog
- Centre of Social and Psychological Sciences, SAS, Bratislava, Slovakia
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2
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Gao Z, Tan J, Wang S, Yu H, Zhou Z, Zhang Y, Zhou M, Xia X, Yao F, Huang J. The Xiangya Ocular Tumor Bank: A Disease-Specific Biobank for Advancing Translational Research Into Ocular Tumors. Front Med (Lausanne) 2022; 8:774624. [PMID: 35155464 PMCID: PMC8829723 DOI: 10.3389/fmed.2021.774624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenesis and etiology of various ocular tumors remain largely unclear, limiting the development of diagnostic and treatment approaches for such tumors. Tissue samples from patients are also valuable resource to elucidate mechanisms underlying tumorigenesis. Here we present the early phase setup of an ocular tumor biobank at Xiangya Hospital. Blood and tissue samples along with associated clinical data were obtained from patients who underwent surgery in the Department of Ophthalmology of Xiangya Hospital from December 1, 2018 to January 31, 2020. Standardized operating protocols were developed for the collection, transportation, processing and preservation of ocular tumor samples. A total of 92 clinical cases suffered from 21 types of eye tumors and several undiagnosed eye diseases were covered. A total of 846 samples were preserved in the ocular tumor biobank, including 356 blood samples (42.1%), 324 plasma samples (38.3%), and 166 tissue samples (19.6%). Using the clinical data, we analyzed the prevalence of malignant ocular tumors in association with variables of age, gender, tumors' location and size, and presenting complaints of lump and proptosis. The factors predictive of malignant ocular tumors, included gender (B = 1.599; P = 0.025) and the symptom of proptosis (B = −2.534; P = 0.001). Overall, the setup of clinically-based ophthalmologic biobank could support pathological and translational research into ocular tumors.
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Affiliation(s)
- Zhaolin Gao
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jia Tan
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Sha Wang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
| | - Haiyang Yu
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Ziyu Zhou
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Yun Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Mushi Zhou
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xiaobo Xia
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
| | - Fei Yao
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
| | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Jufang Huang
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Chen Y, Sang C, Bian Z, Zhang Y, Jiang E, Zhou X, Chen T, Tang H, Wang C. The Scale, Collections, and Biospecimen Distribution of Grade A Tertiary Hospital Biobanks in China: A National Survey. Front Med (Lausanne) 2021; 7:560600. [PMID: 33537321 PMCID: PMC7848138 DOI: 10.3389/fmed.2020.560600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Chinese clinical biobanks were built rapidly in grade A tertiary hospitals. However, the general information of biorepositories in China remained largely unknown. The aim of this study was to investigate the size, collections, biospecimens distribution and other characteristics of Chinese biobanks in grade A tertiary hospitals. In 2018, we launched a national survey among biobank leaders to provide a comprehensive understanding of Chinese grade A tertiary hospital biobanks. A total of 70 biobank managers or directors completed an online questionnaire to collect information about the biorepositories. Nearly 20% of biobanks stored over one million specimens, while almost one-third of biobanks stored 50-200,000 specimens. In general, plasma and serum were the specimens most commonly stored. For the use of collections, biospecimens were most commonly applied by internal clinical departments. Further analyses revealed that the large-scale biobanks were characterized by earlier establishment, more types of specimens in storage and distribution compared with small-scale biobanks. Moreover, specimens in large-scale biobanks were more commonly used for basic research (62.86% vs. 34.29%, P = 0.017) and clinical research (57.14% vs. 28.57%, P = 0.016). Large-scale biobanks also had more opportunities to cooperate with domestic research institutes (34.29% vs. 5.71%, P = 0.003). Our survey revealed diversity in collections, distribution and utilization of biospecimens among Chinese grade A tertiary hospital biobanks. Although the biobanks had relatively large collections, the underutilization of stored biospecimens and lack of sharing could hamper clinical and biological research.
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Affiliation(s)
- Yuanyuan Chen
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chao Sang
- Center for Translational Medicine, Shanghai Sixth People's Hospital, Shanghai, China
| | - Zhouliang Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinan Zhang
- The Metabolic Diseases Biobank, Shanghai Key Laboratory of Diabetes, Shanghai Sixth People's Hospital, Shanghai, China
| | - Erpeng Jiang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Tianlu Chen
- Center for Translational Medicine, Shanghai Sixth People's Hospital, Shanghai, China
| | - Hongming Tang
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Congrong Wang
- Department of Endocrinology, Shanghai Fourth People's Hospital Affiliated to Tongji University, Shanghai, China
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Gao H, Liu Y, Ding J, Yang J, Zhang B, Hu Y, Ge M, Ye Q. A Nucleic Acid Quality Control Strategy for Frozen Tissues from a Biobank of High-Risk Pregnancy. Biopreserv Biobank 2018; 17:18-26. [PMID: 30256683 DOI: 10.1089/bio.2018.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The preservation of placental and fetal tissues will contribute to studying the pathogenesis of high-risk pregnancy diseases. However, few studies have focused on the effects of different preservation methods and cold ischemia time (CIT) on the quality of nucleic acids. An available quality control (QC) strategy will be beneficial to evaluate these effects for high-risk pregnancy biobanks. METHODS We established an evaluation strategy of nucleic acid QC by analyzing total RNA and genomic DNA (gDNA). Through this strategy, the effects of CIT, cryoprotectants (CPAs), and freeze/thaw cycles on the yield and integrity of placental RNA were analyzed. In addition, the effects of CIT on the yield and integrity of fetal DNA were determined. RESULTS For placental samples, there was no significant difference in RNA integrity (CIT <2 hours). After several freeze/thaw cycles, the RNA quality number values of placental samples in the CPA-free group and in the RNasin (TRIzol) group were decreased. For fetal samples, the DNA integrity of different organs (CIT <24 hours) was completely satisfactory, but it declined with the extension of CIT. Furthermore, different organs had different tolerances to cold ischemia, and the rank was as follows: skin, heart, liver, and placenta. In addition, the content of medium-length (600 bp) and long (1310 bp) fragments of gDNA were mainly reduced with the extension of CIT. CONCLUSION The RNA integrity of placental tissue was affected by CIT significantly. It is recommended that placenta should be cryopreserved within 2 hours (4°C) from isolation. To ensure DNA quality of fetal tissues, the samples are suggested to be frozen within 24 hours (4°C) from isolation. On the contrary, if samples have a long CIT, skin is superior to other organs in the aspect of biobanking donor's genetic information.
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Affiliation(s)
- Hong Gao
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yanhong Liu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jie Ding
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jun Yang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Biao Zhang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Meiling Ge
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Qing Ye
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
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Zhang H, Yang X, Feng X, Xu H, Yang Q, Zou L, Yan M, Liu D, Su X, Jiao B. Chromosome-wide gene dosage rebalance may benefit tumor progression. Mol Genet Genomics 2018; 293:895-906. [DOI: 10.1007/s00438-018-1429-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/09/2018] [Indexed: 01/22/2023]
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Kong F, Zhang W, Qiao L, Li Q, Li H, Cao J, He W, Dong C, He Y, He L, Liu L, Fu W, Liu L, Li Z, Wang Y. Establishment and quality evaluation of a glioma biobank in Beijing Tiantan Hospital. PeerJ 2018; 6:e4450. [PMID: 29576945 PMCID: PMC5855883 DOI: 10.7717/peerj.4450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background We established a glioma biobank at Beijing Tiantan Hospital in November, 2010. Specialized residents have been trained to collect, store and manage the biobank in accordance with standard operating procedures. Methods One hundred samples were selected to evaluate the quality of glioma samples stored in the liquid nitrogen tank during different periods (from 2011 to 2015) by morphological examination, RNA integrity determination, DNA integrity determination and housekeeping gene expression determination. Results The majority of samples (95%) had high RNA quality for further analysis with RIN ≥6. Quality of DNA of all samples were stable without significant degradation. Conclusion Storage conditions of our biobank are suitable for long-term (at least five years) sample preservation with high molecular quality.
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Affiliation(s)
- Fanhong Kong
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenli Zhang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Qiao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haowen Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jingli Cao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenyan He
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chengya Dong
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanjiao He
- Neuropathological department, Beijing Neurosugical Institute, Capital Medical University, Beijing, China
| | - Lu He
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Li Liu
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weilun Fu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zirui Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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Gao S, Ge A, Xu S, You Z, Ning S, Zhao Y, Pang D. PSAT1 is regulated by ATF4 and enhances cell proliferation via the GSK3β/β-catenin/cyclin D1 signaling pathway in ER-negative breast cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:179. [PMID: 29216929 PMCID: PMC5721480 DOI: 10.1186/s13046-017-0648-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/22/2017] [Indexed: 01/04/2023]
Abstract
Background A growing amount of evidence has indicated that PSAT1 is an oncogene that plays an important role in cancer progression and metastasis. In this study, we explored the expression and function of PSAT1 in estrogen receptor (ER)-negative breast cancer. Method The expression level of PSAT1 in breast cancer tissues and cells was analyzed using real-time-PCR (RT-PCR), TCGA datasets or immunohistochemistry (IHC). The overall survival of patients with ER-negative breast cancer stratified by the PSAT1 expression levels was evaluated using Kaplan-Meier analysis. The function of PSAT1 was analyzed using a series of in vitro assays. Moreover, a nude mouse model was used to evaluate the function of PSAT1 in vivo. qRT-PCR and western blot assays were used to evaluate gene and protein expression, respectively, in the indicated cells. In addition, we demonstrated that PSAT1 was activated by ATF4 by chromatin immunoprecipitation (ChIP) assays. Results mRNA expression of PSAT1 was up-regulated in ER-negative breast cancer. A tissue microarray that included 297 specimens of ER-negative breast cancer was subjected to an immunohistochemistry assay, which demonstrated that PSAT1 was overexpressed and predicted a poor clinical outcome of patients with this disease. Our data showed that PSAT1 promoted cell proliferation and tumorigenesis in vitro and in vivo. We further found that PSAT1 induced up-regulation of cyclin D1 via the GSK3β/β-catenin pathway, which eventually led to the acceleration of cell cycle progression. Furthermore, ATF4 was also overexpressed in ER-negative breast cancers, and a positive correlation between the ATF4 and PSAT1 mRNA levels was observed in ER-negative breast cancers. We further demonstrated that knockdown of ATF4 by siRNA reduced PSAT1 expression. Finally, chromatin immunoprecipitation (ChIP) assays showed that PSAT1 was a target of ATF4. Conclusions PSAT1, which is overexpressed in ER-negative breast cancers, is activated by ATF4 and promotes cell cycle progression via regulation of the GSK3β/β-catenin/cyclin D1 pathway. Electronic supplementary material The online version of this article (doi: 10.1186/s13046-017-0648-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Song Gao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, China
| | - Anqi Ge
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, China
| | - Zilong You
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, China. .,Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang, 150081, China.
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