1
|
Yang T, Jin Y, Neogi A. Acoustic Attenuation and Dispersion in Fatty Tissues and Tissue Phantoms Influencing Ultrasound Biomedical Imaging. ACS OMEGA 2023; 8:1319-1330. [PMID: 36643513 PMCID: PMC9835773 DOI: 10.1021/acsomega.2c06750] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The development of ultrasonic imaging techniques is optimized using artificial tissue phantoms before the practical applications. However, due to the strong attenuation and dispersion, accumulated fatty tissues can significantly impact the resolution and even feasibility of certain ultrasonic imaging modalities. An appropriate characterization of the acoustic properties on fatty phantoms can help the community to overcome the limitations. Some of the existing methods heavily overestimate attenuation coefficients by including the reflection loss and dispersion effects. Hence, in this study, we use numerical simulation-based comparison between two major attenuation measurement configurations. We further pointed out the pulse dispersion in viscoelastic tissue phantoms by simulations, which barely attracted attention in the existing studies. Using the selected attenuation and dispersion testing methods that were selected from the numerical simulation, we experimentally characterized the acoustic properties of common fatty tissue phantoms and compared the acoustic properties with the natural porcine fatty tissue samples. Furthermore, we selected one of the tissue phantoms to construct ultrasound imaging samples with some biomasses. With the known attenuation and dispersion of the tissue phantom, we showed the clarity enhancement of ultrasound imaging by signal post-processing to weaken the attenuation and dispersion effects.
Collapse
Affiliation(s)
- Teng Yang
- Department
of Physics, University of North Texas, Denton, Texas76203, United States
- Department
of Materials Science and Engineering,University
of North Texas, Denton, Texas76207, United States
| | - Yuqi Jin
- Department
of Physics, University of North Texas, Denton, Texas76203, United States
| | - Arup Neogi
- Department
of Physics, University of North Texas, Denton, Texas76203, United States
- Institute
of Fundamental and Frontier Sciences, University
of Electronic Science and Technology of China, Chengdu611731, P. R. China
| |
Collapse
|
2
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
|
3
|
Zhang X, Han QY, Zhao ZS, Zhang JG, Zhou WJ, Lin A. Biobanking of Fresh-Frozen Gastric Cancer Tissues: Impact of Long-Term Storage and Clinicopathological Variables on RNA Quality. Biopreserv Biobank 2019; 17:58-63. [PMID: 30457887 DOI: 10.1089/bio.2018.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xia Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Qiu-Yue Han
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Zhang-Sheng Zhao
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Jian-Gang Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Wen-Jun Zhou
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| |
Collapse
|
4
|
Zheng XH, Zhang SD, Zhang PF, Li XZ, Hu YZ, Tian T, Zhu L, Wang RZ, Jia WH. Tumor Cell Content and RNA Integrity of Surgical Tissues from Different Types of Tumors and Its Correlation with Ex Vivo and In Vivo Ischemia. Ann Surg Oncol 2018; 25:3764-3770. [PMID: 30225832 DOI: 10.1245/s10434-018-6697-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Tissues from tumor patients are important resources for promoting cancer research, and therefore many biobanks have been established to collect tumor tissues; however, the quality of tumor tissues after surgical resection has not been well documented. METHODS A total of 896 cases of tissues from 12 types of tumors were chosen for this study. First, histopathological examination was conducted to evaluate the tumor cell content; second, microchip electrophoresis was used to determine the RNA integrity number (RIN) in 466 cases of tissues with a tumor cell content ≥ 75%; and, finally, a correlation test was used to analyze the effect of ischemia on RNA integrity in 384 cases of tissues with a recorded ischemia time. RESULTS Tumor tissues from 12 different organs had different tumor cell contents and RNA integrity. The liver had the highest percentage (69.7%) of tissue samples with a tumor cell content ≥ 75%, and the highest percentage (96%) of samples with an RIN ≥ 7. RNA integrity was not correlated with limited ex vivo ischemia time (5-60 min) in any of the 12 types of tumors. In contrast, a significant correlation with in vivo ischemia time was observed in several types of tumors. CONCLUSIONS Not every sample of excised tumor tissue has a sufficient amount of tumor cells and enough RNA integrity. In vivo ischemia has a more significant influence on RNA integrity, and tumor tissues have different tolerances to pre-analytical variables. Those conducting translational research should pay attention to pre-analytical variables when collecting and utilizing tumor tissues.
Collapse
Affiliation(s)
- Xiao-Hui Zheng
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China.,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Shao-Dan Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Pei-Fen Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Xi-Zhao Li
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Ye-Zhu Hu
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Tian Tian
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Lin Zhu
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Ruo-Zheng Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| | - Wei-Hua Jia
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China. .,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| |
Collapse
|
5
|
RFID as a New ICT Tool to Monitor Specimen Life Cycle and Quality Control in a Biobank. Int J Biol Markers 2018; 26:129-35. [DOI: 10.5301/jbm.2011.8323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2011] [Indexed: 02/04/2023]
Abstract
Background Biospecimen quality is crucial for clinical and translational research and its loss is one of the main obstacles to experimental activities. Beside the quality of samples, preanalytical variations render the results derived from specimens of different biobanks or even within the same biobank incomparable. Specimens collected along the years should be managed with a heterogeneous life cycle. Hence, we propose to collect detailed data concerning the whole life cycle of stored samples employing radio-frequency identification (RFID) technology. Methods We describe the processing chain of blood biosamples that is operative at the biobank of IRCSS San Raffaele, Rome, Italy (BioBIM). We focus on the problem of tracing the stages following automated preanalytical processing: we collected the time stamps of all events that could affect the biological quality of the specimens by means of RFID tags and readers. Results We developed a pilot study on a fragment of the life cycle, namely the storage between the end of the preanalytics and the beginning of the analytics, which is usually not traced by automated tools because it typically includes manual handling. By adopting RFID devices we identified the possible critical time delays. At 1, 3 and 6 months RFID-tagged specimens cryopreserved at -80°C were successfully read. Conclusions We were able to record detailed information about the storage phases and a fully documented specimen life cycle. This will allow us to promote and tune up the best practices in biobanking because i) it will be possible to classify sample features with a sharper resolution, which allows future utilization of stored material; ii) cost-effective policies can be adopted in processing, storing and selecting specimens; iii) after using each aliquot, we can study the life cycle of the specimen with a possible feedback on the procedures.
Collapse
|
6
|
Lianos GD, Glantzounis GK, Bali CD, Katsios C, Roukos DH. Identification of novel genes by whole-exome sequencing can improve gastric cancer precision oncology. Future Oncol 2017; 13:883-892. [DOI: 10.2217/fon-2016-0430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: By identifying cancer driver genes involved in tumorigenesis, whole-exome sequencing (WES) analyses enable the development of robust biomarkers and novel therapeutic targets to reach precision oncology. Patients & methods: WES analyses were performed in matched gastric cancer-normal gastric tissues from two patients. We compared genes highlighted with those of a database and recent WES/whole-genome sequencing studies. Results: We identified 32 highlighted gastric cancer genes, two of these (DEFB118 and RNF43) may provide future potential clinical implications. Conclusion: Definitive evidence on extensive genetic heterogeneity suggests the need for large-scale next-generation sequencing studies to validate gastric cancer driver genes catalog. This list represents the foundation for developing genome-based biomarkers to guide precision gastric cancer treatment.
Collapse
Affiliation(s)
- Georgios D Lianos
- Centre for Biosystems & Genomic Network Medicine, University of Ioannina, Ioannina, Greece
- Department of Surgery, School of Medicine, University of Ioannina, Ioannina, Greece
| | | | - Christina D Bali
- Department of Surgery, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Christos Katsios
- Centre for Biosystems & Genomic Network Medicine, University of Ioannina, Ioannina, Greece
- Department of Surgery, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems & Genomic Network Medicine, University of Ioannina, Ioannina, Greece
- Department of Surgery, School of Medicine, University of Ioannina, Ioannina, Greece
- Commision of Innovation & Research, University of Ioannina, Ioannina, Greece
- Biomedical Research Foundation of the Academy of Athens (BRFAA), Systems Biology, Athens, Greece
| |
Collapse
|
7
|
Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, Marchal Bressenot A, Boulagnon-Rombi C. Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality? PLoS One 2016; 11:e0154326. [PMID: 27124490 PMCID: PMC4849710 DOI: 10.1371/journal.pone.0154326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.
Collapse
Affiliation(s)
- Thibaut Galissier
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
| | - Christophe Schneider
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Saviz Nasri
- Tumorothèque de Champagne Ardenne, Reims, France
| | - Lukshe Kanagaratnam
- Unité d’Aide Méthodologique, Centre Hospitalier Universitaire, Reims, France
| | - Caroline Fichel
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | | | - Marie-Danièle Diebold
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Tumorothèque de Champagne Ardenne, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Reza Kianmanesh
- Service de Chirurgie Digestive, Centre Hospitalier Universitaire, Reims, France
| | - Georges Bellon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire de Biochimie, Centre Hospitalier Universitaire, Reims, France
| | - Stéphane Dedieu
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Aude Marchal Bressenot
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
- * E-mail:
| |
Collapse
|
8
|
Olsen J, Kirkeby LT, Eiholm S, Jess P, Troelsen JT, Gögenür I, Olsen J. Impact of in Vivo Ischemic Time on RNA Quality—Experiences from a Colon Cancer Biobank. Biopreserv Biobank 2015; 13:255-62. [DOI: 10.1089/bio.2015.0009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Jesper Olsen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Lene T. Kirkeby
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Susanne Eiholm
- Department of Pathology, Roskilde University, Roskilde, Denmark
| | - Per Jess
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Jesper T. Troelsen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Ismail Gögenür
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jorgen Olsen
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| |
Collapse
|
9
|
Condelli V, Lettini G, Patitucci G, D'Auria F, D'Amico M, Vita G, Musto P, Cuomo C, Landriscina M. Validation of Vacuum-Based Refrigerated System for Biobanking Tissue Preservation: Analysis of Cellular Morphology, Protein Stability, and RNA Quality. Biopreserv Biobank 2014; 12:35-45. [DOI: 10.1089/bio.2013.0065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Valentina Condelli
- Laboratory of Pre-Clinical and Translational Research, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Giacomo Lettini
- Laboratory of Pre-Clinical and Translational Research, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Giuseppe Patitucci
- Pathology Unit, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Fiorella D'Auria
- Laboratory of Clinical Research and Advanced Diagnostics, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Michele D'Amico
- Laboratory of Pre-Clinical and Translational Research, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Giulia Vita
- Pathology Unit, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Pellegrino Musto
- Scientific Direction, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Carmela Cuomo
- Onco-Hematology Department, IRCCS, Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Matteo Landriscina
- Clinical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| |
Collapse
|
10
|
Wei BR, Simpson RM. Digital pathology and image analysis augment biospecimen annotation and biobank quality assurance harmonization. Clin Biochem 2013; 47:274-9. [PMID: 24362266 DOI: 10.1016/j.clinbiochem.2013.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/03/2013] [Accepted: 12/08/2013] [Indexed: 01/08/2023]
Abstract
Standardization of biorepository best practices will enhance the quality of translational biomedical research utilizing patient-derived biobank specimens. Harmonization of pathology quality assurance procedures for biobank accessions has lagged behind other avenues of biospecimen research and biobank development. Comprehension of the cellular content of biorepository specimens is important for discovery of tissue-specific clinically relevant biomarkers for diagnosis and treatment. While rapidly emerging technologies in molecular analyses and data mining create focus on appropriate measures for minimizing pre-analytic artifact-inducing variables, less attention gets paid to annotating the constituent makeup of biospecimens for more effective specimen selection by biobank clients. Both pre-analytic tissue processing and specimen composition influence acquisition of relevant macromolecules for downstream assays. Pathologist review of biorepository submissions, particularly tissues as part of quality assurance procedures, helps to ensure that the intended target cells are present and in sufficient quantity in accessioned specimens. This manual procedure can be tedious and subjective. Incorporating digital pathology into biobank quality assurance procedures, using automated pattern recognition morphometric image analysis to quantify tissue feature areas in digital whole slide images of tissue sections, can minimize variability and subjectivity associated with routine pathologic evaluations in biorepositories. Whole-slide images and pathologist-reviewed morphometric analyses can be provided to researchers to guide specimen selection. Harmonization of pathology quality assurance methods that minimize subjectivity and improve reproducibility among collections would facilitate research-relevant specimen selection by investigators and could facilitate information sharing in an integrated network approach to biobanking.
Collapse
Affiliation(s)
- Bih-Rong Wei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH Building 37, 37 Convent Drive, Bethesda, MD 20892, USA
| | - R Mark Simpson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH Building 37, 37 Convent Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
11
|
Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, Yan WH, Lin A. Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol 2012; 20:1737-44. [PMID: 22711177 DOI: 10.1245/s10434-012-2440-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Biobanking plays an important role in translational cancer research. The impact of tissue ex-vivo ischemia time and storage period on RNA integrity is not well documented. METHODS Fresh-frozen colon tissues were collected in Taizhou Hospital of Zhejiang Province in China since 2004. Fifty-one colon cancer tissues with tumor cell content higher than 70 % and matched normal tissues during four storage periods (less than 15 months, 16-20 months, 21-25 months, and 26-40 months) were chosen to detect RNA quality. Fresh colon cancer tissues from 5 patients were cut into pieces and kept at room temperature or on ice for 0.5, 1, 2, and 4 h before snap freezing. RNA integrity was determined by microcapillary electrophoresis by the RNA integrity number (RIN) algorithm. RESULTS Sixty-seven percent of normal colon tissues and 94 % of colon cancer specimens yielded RNA with a RIN of ≥7. Matched colon cancer and normal tissues showed significant difference in RNA quality. RNA remained stable in colon cancer tissues kept at room temperature and on ice for up to 4 h, and long-term storage of banked colon specimens did not negatively influence RNA quality (RNA with RIN of ≥7 banked less than 15 months, 83 %; 16-20 months, 78 %; 21-25 months, 77 %; 26-40 months, 90 %). CONCLUSIONS Frozen colon tissues yield high-quality RNA in approximately 80 % of specimens. Ex-vivo ischemia times and storage periods did not adversely affect RNA quality. This study showed that standard operation protocols and the maintenance of high-quality tissue repositories were the keys to translational medicine research.
Collapse
Affiliation(s)
- Wei-Guang Bao
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical College, Zhejiang, China
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Ma Y, Dai H, Kong X. Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 2012; 423:229-35. [DOI: 10.1016/j.ab.2012.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/15/2012] [Accepted: 02/03/2012] [Indexed: 02/01/2023]
|
13
|
Hong SH, Baek HA, Jang KY, Chung MJ, Moon WS, Kang MJ, Lee DG, Park HS. Effects of delay in the snap freezing of colorectal cancer tissues on the quality of DNA and RNA. JOURNAL OF THE KOREAN SOCIETY OF COLOPROCTOLOGY 2010; 26:316-23. [PMID: 21152133 PMCID: PMC2998017 DOI: 10.3393/jksc.2010.26.5.316] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/06/2010] [Indexed: 02/04/2023]
Abstract
PURPOSE The success of basic molecular research using biospecimens strongly depends on the quality of the specimen. In this study, we evaluated the effects of delayed freezing time on the stability of DNA and RNA in fresh frozen tissue from patients with colorectal cancer. METHODS Tissues were frozen at 10, 30, 60, and 90 minutes after extirpation of colorectal cancer in 20 cases. Absorbance ratio of 260 to 280 nm (A(260)/A(280)) and agarose gel electrophoresis were evaluated. In addition, the RNA integrity number (RIN) was assayed for the analysis of the RNA integrity. RESULTS Regardless of delayed freezing time, all DNA and RNA samples revealed A(260)/A(280) ratios of more than 1.9, and all DNA samples showed a discrete, high-molecular-weight band on agarose gel electrophoresis. The RINs were 7.53 ± 2.04, 6.70 ± 1.88, 6.47 ± 2.58, and 4.22 ± 2.34 at 10, 30, 60, and 90 minutes, respectively. Though the concentration of RNA was not affected by delayed freezing, the RNA integrity was decreased with increasing delayed freezing time. CONCLUSION According to the RIN results, we recommend that the collection of colorectal cancer tissue should be done within 10 minutes for studies requiring RNA of high quality and within 30 minutes for usual RNA studies.
Collapse
Affiliation(s)
- Sang Hyun Hong
- Chonbuk National University Hospital National Biobank of Korea, Jeonju, Korea
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Yu YY, Zhu ZG. Significance of biological resource collection and tumor tissue bank creation. World J Gastrointest Oncol 2010; 2:5-8. [PMID: 21160810 PMCID: PMC2999151 DOI: 10.4251/wjgo.v2.i1.5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 07/04/2009] [Accepted: 07/11/2009] [Indexed: 02/05/2023] Open
Abstract
Progress in the molecular oncology of gastrointestinal carcinomas depends on high quality cancer tissues for research. Recent acceleration on new technological platforms as well as the “omics” revolution increases the demands on tissues and peripheral blood for research at the DNA, mRNA and protein levels. Tissue bank creation emerges as a priority. Tumor tissue banks are facilities that are organized to collect, store and distribute samples of tumor and normal tissue for further use in basic and translational cancer research. The samples are generally obtained immediately after excision, prior to fixation, to ensure optimal preservation of proteins and nucleic acids. It is possible for surgeons or pathologists to collect fresh tissue prospectively during their routine dissection procedures. Most tissue banks are “project-driven” tumor banks, which are specialized collections of tumor samples on which their research is based. Systematic collection of all available tumor tissue is much rarer. High quality tissue banks need the collaboration of clinicians and basic scientists, but also the informed consent of patients and ethical approval. Through the standard operation procedure, snap frozen fresh tissue collection, storage and quality control for cryopreserved tissues are the pivotal factors on tissue bank construction and maintaining. The purpose of the tissue bank creation is enhancing the quality and speed on both the basic and translational research on gastrointestinal cancer. The quality assurance and quality control are handled based on reviewing HE staining slides or touch imprint cytology by pathologists.
Collapse
Affiliation(s)
- Ying-Yan Yu
- Ying-Yan Yu, Zheng-Gang Zhu, Department of Surgery, Shanghai Institute of Digestive Surgery, School of Medicine, Shanghai Jiao Tong University, 200025 Shanghai, China
| | | |
Collapse
|
15
|
Voidonikolas G, Gingras MC, Hodges S, McGuire AL, Chen C, Gibbs RA, Brunicardi FC, Fisher WE. Developing a tissue resource to characterize the genome of pancreatic cancer. World J Surg 2009; 33:723-31. [PMID: 19137368 DOI: 10.1007/s00268-008-9877-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With recent advances in DNA sequencing technology, medicine is entering an era in which a personalized genomic approach to diagnosis and treatment of disease is feasible. However, discovering the role of altered DNA sequences in various disease states will be a challenging task. The genomic approach offers great promise for diseases, such as pancreatic cancer, in which the effect of current diagnostic and treatment modalities is disappointing. To facilitate the characterization of the genome of pancreatic cancer, high-quality and well-annotated tissue repositories are needed. This article summarizes the basic principles that guide the creation of such a repository, including sample processing and preservation techniques, sample size and composition, and collection of clinical data elements.
Collapse
Affiliation(s)
- Georgios Voidonikolas
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden, Suite 1500, Houston, TX 77030, USA
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Sandusky G, Dumaual C, Cheng L. Review Paper: Human Tissues for Discovery Biomarker Pharmaceutical Research: The Experience of the Indiana University Simon Cancer Center—Lilly Research Labs Tissue/Fluid BioBank. Vet Pathol 2009; 46:2-9. [DOI: 10.1354/vp.46-1-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- G. Sandusky
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
| | - C. Dumaual
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
| | - L. Cheng
- Simon Cancer Center and Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN
| |
Collapse
|
17
|
Kino-Oka M, Takezawa Y, Taya M. Quality control of cultured tissues requires tools for quantitative analyses of heterogeneous features developed in manufacturing process. Cell Tissue Bank 2008; 10:63-74. [DOI: 10.1007/s10561-008-9103-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
|
18
|
Tejpar S. The multidisciplinary management of gastrointestinal cancer. The use of molecular markers in the diagnosis and treatment of colorectal cancer. Best Pract Res Clin Gastroenterol 2007; 21:1071-87. [PMID: 18070704 DOI: 10.1016/j.bpg.2007.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Rapidly growing insights into the molecular biology of colorectal cancer led to high hopes for the identification of molecular markers to be used in optimised and tailored treatment regimens for this disorder. However, no molecular marker has yet made it into daily practice. In this review we will discuss some of the potential molecular markers, focus on the lessons learnt from marker development and identify strategies for the future.
Collapse
Affiliation(s)
- Sabine Tejpar
- Digestive Oncology Unit, Centre for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
| |
Collapse
|