Biobanking of human pancreas cancer tissue: impact of ex-vivo procurement times on RNA quality

Capillary electrophoresis based on the nucleic acid detection in the application of cancer diagnosis and therapy

This review focuses on capillary electrophoresis-based nucleic acid detection as it is applied to cancer diagnosis and therapy, and provides an introduction to the drawbacks and future developments of analysis with CE.

MicroRNAs cooperatively inhibit a network of tumor suppressor genes to promote pancreatic tumor growth and progression

BACKGROUND & AIMS

There has not been a broad analysis of the combined effects of altered activities of microRNAs (miRNAs) in pancreatic ductal adenocarcinoma (PDAC) cells, and it is unclear how these might affect tumor progression or patient outcomes.

METHODS

We combined data from miRNA and messenger RNA (mRNA) expression profiles and bioinformatic analyses to identify an miRNA-mRNA regulatory network in PDAC cell lines (PANC-1 and MIA PaCa-2) and in PDAC samples from patients. We used this information to identify miRNAs that contribute most to tumorigenesis.

RESULTS

We identified 3 miRNAs (MIR21, MIR23A, and MIR27A) that acted as cooperative repressors of a network of tumor suppressor genes that included PDCD4, BTG2, and NEDD4L. Inhibition of MIR21, MIR23A, and MIR27A had synergistic effects in reducing proliferation of PDAC cells in culture and growth of xenograft tumors in mice. The level of inhibition was greater than that of inhibition of MIR21 alone. In 91 PDAC samples from patients, high levels of a combination of MIR21, MIR23A, and MIR27A were associated with shorter survival times after surgical resection.

CONCLUSIONS

In an integrated data analysis, we identified functional miRNA-mRNA interactions that contribute to growth of PDACs. These findings indicate that miRNAs act together to promote tumor progression; therapeutic strategies might require inhibition of several miRNAs.

The association between the expression of solute carrier transporters and the prognosis of pancreatic cancer

OBJECTIVES

The aim of this study was to investigate the prognostic significance of fourteen anticancer drug-relevant solute carrier transporters (SLCs) in pancreatic cancer in the context of clinical-pathological characteristics and the KRAS mutation status of tumors.

METHODS

Tumors and non-neoplastic pancreatic tissues were obtained from 32 histologically verified patients with pancreatic ductal adenocarcinoma. The transcript profile of SLCs was assessed using quantitative real-time PCR. KRAS mutations in exon 2 were assessed by high-resolution melting analysis and confirmed by sequencing.

RESULTS

SLC22A3 and SLC22A18 were upregulated and SLC22A1, SLC22A2, SLC22A11, SLC28A1, SLC28A3 and SLC29A1 were downregulated when compared with non-neoplastic pancreatic tissues. Moreover, significantly lower levels of SLC22A1, SLC22A11 and SLC29A1 were found in tumors with angioinvasion. There was also a significantly higher transcript level of SLC28A1 in tumors with regional lymph nodes affected by metastasis. The study found that a high expression of SLC28A1 was significantly associated with poor overall survival in unselected patients. In contrast, a high expression of SLC22A3 or SLC29A3 was significantly associated with longer overall survival in patients treated with nucleoside analogs. Protein expression of SLC22A1, SLC22A3 and SLC29A3 in tumor tissues of patients with pancreatic carcinoma was observed by immunoblotting for the first time. Finally, SLC levels were not found to be associated with KRAS mutation status in exon 2.

CONCLUSIONS

This study identified a number of associations of transcript levels of SLCs with prognosis of pancreatic cancer patients.

Differences in transcript levels of ABC transporters between pancreatic adenocarcinoma and nonneoplastic tissues

OBJECTIVES

The aim of this study was to evaluate transcript levels of all 49 human ATP-binding cassette transporters (ABCs) in one of the most drug-resistant cancers, namely, the pancreatic ductal adenocarcinoma (PDAC). Association of ABCs levels with clinical-pathologic characteristics and KRAS mutation status was followed as well.

METHODS

Tumors and adjacent nonneoplastic tissues were obtained from 32 histologically verified PDAC patients. The transcript profile of ABCs was assessed using quantitative real-time polymerase chain reaction with a relative standard curve. KRAS mutations in exon 2 were assessed by high-resolution melting analysis and sequencing.

RESULTS

Most ABCs were deregulated in PDAC and 10 ABCs were associated with clinical-pathologic characteristics. KRAS mutations did not change the global expression profile of ABCs.

CONCLUSIONS

The expression of ABC transporters was significantly deregulated in PDAC tumors when compared to nonmalignant tissues. The observed up-regulation of ABCB4, ABCB11, ABCC1, ABCC3, ABCC5, ABCC10, and ABCG2 in tumors may contribute to the generally poor treatment response of PDAC. The up-regulation of ABCA1, ABCA7, and ABCG1 implicates a serious impairment of cellular cholesterol homeostasis in PDAC. On the other hand, the observed down-regulation of ABCA3, ABCC6, ABCC7, and ABCC8 suggests a possible role of stem cells in the development and progression of PDAC.

Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality

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.

The interference of cold ischemia time in the quality of total RNA from frozen tumor samples

Tumor Banks were created to organize the collection, storage and distribution of biological samples from oncological patients, facilitating its use in cancer research. To ensure the quality of the samples from our bank, we implemented standard operating procedures international. In order to evaluate the influence of cold ischemia time (time between surgical removal of the specimen and the snap freezing of the sample) on the quality of the samples (evaluated by measurement integrity of their RNA), collected during 10 months two tumor samples from each donor, one with up to 30 min of cold ischemia and other with exact 45 min, totaling 100 different donors and 200 samples, 40 from each of the following organs: breast, thyroid, stomach, lung and colorectum. We extracted total RNA from the samples and with the aid of a Bioanalyser, evaluate their quality, comparing it with cold ischemia times in different organs. Among the samples up to 30 min and the samples with exact 45 min, we respectively found 63 (64.3 %) and 36 (36 %) with intact RNA, 11 (11.2 %) and 17 (17 %) partially degraded and 24 (24.5 %) and 47 (47 %) degraded (p < 0.001). Thyroid and colorectal samples were more sensitive to variations in cold ischemia time (p = 0.006 and p = 0.03, respectively). Stomach and lungs were less sensitive (p = 0.919 and p = 0.384, respectively). We concluded that the cold ischemia time up to 30 min was more efficient to maintain the integrity of RNA in most samples, and that RNA degradation varied according to the different topographies.

Quality assurance of RNA expression profiling in clinical laboratories

RNA expression profiles are increasingly used to diagnose and classify disease, based on expression patterns of as many as several thousand RNAs. To ensure quality of expression profiling services in clinical settings, a standard operating procedure incorporates multiple quality indicators and controls, beginning with preanalytic specimen preparation and proceeding thorough analysis, interpretation, and reporting. Before testing, histopathological examination of each cellular specimen, along with optional cell enrichment procedures, ensures adequacy of the input tissue. Other tactics include endogenous controls to evaluate adequacy of RNA and exogenous or spiked controls to evaluate run- and patient-specific performance of the test system, respectively. Unique aspects of quality assurance for array-based tests include controls for the pertinent outcome signatures that often supersede controls for each individual analyte, built-in redundancy for critical analytes or biochemical pathways, and software-supported scrutiny of abundant data by a laboratory physician who interprets the findings in a manner facilitating appropriate medical intervention. Access to high-quality reagents, instruments, and software from commercial sources promotes standardization and adoption in clinical settings, once an assay is vetted in validation studies as being analytically sound and clinically useful. Careful attention to the well-honed principles of laboratory medicine, along with guidance from government and professional groups on strategies to preserve RNA and manage large data sets, promotes clinical-grade assay performance.

Clinical implementation of RNA signatures for pharmacogenomic decision-making

RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system.

Critical role of laser microdissection for genetic, epigenetic and proteomic analyses in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease, and molecular studies to unravel novel biomarkers and therapeutic targets are warranted. However, PDAC is characterized by different precursor lesions, as well as by an intense desmoplastic reaction, with islet of neoplastic cells often representing a minor population. Moreover, normal ductal cells, which are considered to be the normal counterpart of pancreatic adenocarcinoma cells, comprise approximately 5% of the total population of cells making up this organ. For all these reasons, molecular techniques to identify critical mutations, as well as the pattern of altered mRNA/microRNA/protein expression should be performed on selected pancreatic cell subpopulations. Therefore, the use of the newest laser microdissection techniques is critical for the analysis of PDAC biological characteristics. This article highlights the most recent and clinically relevant aspects of genetic, epigenetic and proteomic analyses of PDAC from the perspective of the application of laser microdissection.

Procurement of Human Tissues for Research Banking in the Surgical Pathology Laboratory: Prioritization Practices at Washington University Medical Center

Academic hospitals and medical schools with research tissue repositories often derive many of their internal human specimen acquisitions from their site's surgical pathology service. Typically, such acquisitions come from appropriately consented tissue discards sampled from surgical resections. Because the practice of surgical pathology has patient care as its primary mission, competing needs for tissue inevitably arise, with the requirement to preserve adequate tissue for clinical diagnosis being paramount. A set of best-practice gross pathology guidelines are summarized here, focused on the decision for tissue banking at the time specimens are macroscopically evaluated. These reflect our collective experience at Washington University School of Medicine, and are written from the point of view of our site biorepository. The involvement of trained pathology personnel in such procurements is very important. These guidelines reflect both good surgical pathology practice (including the pathologic features characteristic of various anatomic sites) and the typical objectives of research biorepositories. The guidelines should be helpful to tissue bank directors, and others charged with the procurement of tissues for general research purposes. We believe that appreciation of these principles will facilitate the partnership between surgical pathologists and biorepository directors, and promote both good patient care and strategic, value-added banking procurements.

Variation of Peripheral Blood Mononuclear Cell RNA Quality in Archived Samples

The Infectious Diseases BioBank (IDB) has consistently archived peripheral blood mononuclear cell (PBMNC) RNA for transcriptome analyses. RNA is particularly labile, and hence, these samples provide a sensitive indicator for assessing the IDB's quality-assurance measures. Independent analyses of 104 PBMNC RNA specimens from 26 volunteers revealed that the mean RNA integrity number (RIN) was high (9.02), although RIN ranged between scores of 7 and 10. This variation of RIN values was not associated with ischemic time, PBMNC quality, number of samples processed per day, self-medication after immunization, freezer location, donor characteristics, differential white blood cell counts, or daily variation in RNA extractions (all P>0.05). RIN values were related to the date of collection, with those processed during mid-summer having highest RIN scores (P=0.0001). Amongst specimens with the lowest RIN scores, no common feature could be identified. Thus, no technical explanation for the variation in RNA quality could be ascertained and these may represent normal physiological variations. These data provide strong evidence that current IDB protocols for the isolation and preservation PBMNC RNA are robust.

Biobanking after robotic-assisted radical prostatectomy: a quality assessment of providing prostate tissue for RNA studies

BACKGROUND

RNA quality is believed to decrease with ischaemia time, and therefore open radical prostatectomy has been advantageous in allowing the retrieval of the prostate immediately after its devascularization. In contrast, robotic-assisted laparoscopic radical prostatectomies (RALP) require the completion of several operative steps before the devascularized prostate can be extirpated, casting doubt on the validity of this technique as a source for obtaining prostatic tissue. We seek to establish the integrity of our biobanking process by measuring the RNA quality of specimens derived from robotic-assisted laparoscopic radical prostatectomy.

METHODS

We describe our biobanking process and report the RNA quality of prostate specimens using advanced electrophoretic techniques (RNA Integrity Numbers, RIN). Using multivariate regression analysis we consider the impact of various clinicopathological correlates on RNA integrity.

RESULTS

Our biobanking process has been used to acquire 1709 prostates, and allows us to retain approximately 40% of the prostate specimen, without compromising the histopathological evaluation of patients. We collected 186 samples from 142 biobanked prostates, and demonstrated a mean RIN of 7.25 (standard deviation 1.64) in 139 non-stromal samples, 73% of which had a RIN ≥ 7. Multivariate regression analysis revealed cell type--stromal/epithelial and benign/malignant--and prostate volume to be significant predictors of RIN, with unstandardized coefficients of 0.867(p = 0.001), 1.738(p < 0.001) and -0.690(p = 0.009) respectively. A mean warm ischaemia time of 120 min (standard deviation 30 min) was recorded, but multivariate regression analysis did not demonstrate a relationship with RIN within the timeframe of the RALP procedure.

CONCLUSIONS

We demonstrate the robustness of our protocol--representing the concerted efforts of dedicated urology and pathology departments--in generating RNA of sufficient concentration and quality, without compromising the histopathological evaluation and diagnosis of patients. The ischaemia time associated with our prostatectomy technique using a robotic platform does not negatively impact on biobanking for RNA studies.

Biobanking human endometrial tissue and blood specimens: standard operating procedure and importance to reproductive biology research and diagnostic development

OBJECTIVE

To develop a standard operating procedure (SOP) for collection, transport, storage of human endometrial tissue and blood samples, subject and specimen annotation, and establishing sample priorities.

DESIGN

The SOP synthesizes sound scientific procedures, the literature on ischemia research, sample collection and gene expression profiling, good laboratory practices, and the authors' experience of workflow and sample quality.

SETTING

The National Institutes of Health, University of California, San Francisco, Human Endometrial Tissue and DNA Bank.

PATIENT(S)

Women undergoing endometrial biopsy or hysterectomy for nonmalignant indications.

INTERVENTION(S)

Collecting, processing, storing, distributing endometrial tissue and blood samples under approved institutional review board protocols and written informed consent from participating subjects.

MAIN OUTCOME MEASURE(S)

Standard operating procedure.

RESULT(S)

The SOP addresses rigorous and consistent subject annotation, specimen processing and characterization, strict regulatory compliance, and a reference for researchers to track collection and storage times that may influence their research.

CONCLUSION(S)

The comprehensive and systematic approach to the procurement of human blood and endometrial tissue in this SOP ensures the high quality, reliability, and scientific usefulness of biospecimens made available to investigators by the National Institutes of Health, University of California, San Francisco, Human Endometrial Tissue and DNA Bank. The detail and perspective in this SOP also provides a blueprint for implementation of similar collection programs at other institutions.

Principles of Research Tissue Banking and Specimen Evaluation from the Pathologist's Perspective

Human tissue biorepositories have an increasingly visible and important role within industrial enterprises in supporting biomedical research, including the rapidly advancing fields of proteomics, pharmacogenomics, and molecular epidemiology. Pathologists play a vital but often underrecognized role in the operation of these tissue banks. Besides interpreting studies that arise from banked samples, pathologists are needed to characterize tissues for research, to conduct quality assurance programs, to assist with resource allocation decisions, and to serve an educational role for investigators using the tissues. This article describes these key principles and illustrates examples where pathologist involvement is crucial to biorepository management. Of overarching importance, pathologists play a critical role in helping biorepository users understand the principles of specimen evaluation (histologic and structural composition of tissues, and their limitations) so as to optimize the scientific benefit of the tissues. In conclusion, greater involvement of pathologists in research tissue banking will enhance the scientific utility of biorepositories.

Stabilizing the code-methods to preserve RNA prove their worth

Commercially available platforms to stabilize messenger RNA (mRNA) and microRNA are critically designed to optimize and ensure the quality and integrity of those nucleic acids. This is not only essential for gene expression analyses, but would provide technical utility in providing concordant standard operating procedures in preserving the structural integrity of RNA species in multicenter clinical research programs and biobanking of cells or tissues for subsequent isolation of intact RNA. The major challenge is that the presence of degraded samples may adversely influence the interpretation of expression levels on isolated mRNA or microRNA samples and that in the absence of a concordant operating procedure between multiple collaborating research centers would confound data analysis and interpretation. However, in this issue of Biomarker Insights, Weber et al provide a detailed and critical analysis of two common RNA preservation systems, PAXgene and RNAlater. Such studies are lacking in the literature. However, the authors provide compelling evidence that not all conservation platforms are created equal and only one system proves its worth.