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Abstract 1377: Impact of biospecimen pre-analytical factors on molecular analysis. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Biospecimen Pre-analytical Variables (BPV) Program of the Biorepositories and Biospecimen Research Branch (BBRB) at the National Cancer Institute (NCI) is designed to systematically investigate the effects of preanalytical factors on the molecular integrity of biospecimens. Specific parameters related to formalin fixation and paraffin embedding (FFPE) of cancer tissues were examined, including the effects of cold ischemic time (delay to fixation (DTF)) and time in fixative (TIF). Additional preanalytical studies focus on snap freezing method for tissue specimens (dry Ice vs. LN2 vapor), storage temperature (-80°C vs. LN2 vapor), and duration of storage for frozen specimens.
Biospecimens for the BPV program were collected at four medical centers, within a tightly regulated infrastructure and strict adherence to SOPs, to enable consistent collection and handling across all sites. Biospecimens were collected from research participants undergoing surgical treatment for renal cell carcinoma; ovarian, fallopian tube, and peritoneal carcinoma; lung adenocarcinoma and squamous cell carcinoma; and colorectal adenocarcinoma. Biospecimens were subjected to specific experimental protocols to systematically vary the preanalytical factors of interest. Extensive annotation was performed with 300+ data elements that include steps in the collection, handling, and processing of the biospecimens, pathological evaluation of the tumor, and clinical information collected from donors. Biospecimen collections concluded in April 2015 with a total of 364 tumor tissue cases collected.
The BPV program has conducted multiple, simultaneous molecular analyses to understand the impact of FFPE preanalytical factors on the expression and detection of various molecular analytes. Initial efforts were focused on evaluating the impact of DTF and TIF on the quality of DNA and RNA from FFPE samples using multiple methods and approaches such as NanoDrop 8000 UV-Vis spectrophotometer, Qubit 2.0 Fluorometer, Agilent Bioanalyzer and KAPA Human Genomic DNA Quantification.
The QC data from both RIN and Kappa assays showed that FFPE samples have a significant drop in RNA and DNA quality compared with matched frozen samples. 72 hr TIF samples showed a significant drop in both RNA and DNA quality compared to shorter time points (6, 12, or 23 hr TIF), as measured by DV200 and Kappa assays. No significant differences were observed in RNA/DNA quality between the shorter TIF time points or between the DTF time points (1, 2, 3, 12 hr DTF).
Further studies are now underway to evaluate additional preanalytical factors. The data from BPV studies will be widely shared with the research community through publication and deposition at a public data repository. The results from these studies will be used to develop evidence-based protocols and best practices for fit-for-purpose collection, processing, and storage of biospecimens.
This project is funded by NCI Contract No. HHSN261200800001E.
Citation Format: Rachana Agarwal, Ping Guan, Mary Barcus, Jasmin Bavarva, Robin Burges, Philip Branton, Latarsha Carithers, Corinne Camalier, Biswajit Das, Jason Lih, Hana Odeh, Nancy Roche, Dan Rohrer, Michael Sachs, Leslie Sobin, Jewell Scott, Anna Smith, Conrado Soria, Kimberly Valentino, Dana Valley, Mickey Williams, Helen Moore. Impact of biospecimen pre-analytical factors on molecular analysis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1377.
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Abstract
Pattern recognition receptors are preferentially expressed on APCs allowing selective uptake of pathogens for the initiation of antimicrobial immunity. In particular, C-type lectin receptors, including the mannose receptor (MR), facilitate APC-mediated adsorptive endocytosis of microbial glyconjugates. We have investigated the potential of antigenic targeting to the MR as a means to induce Ag-specific humoral and cellular immunity. hMR transgenic (hMR Tg) mice were generated to allow specific targeting with the anti-hMR Ab, B11. We show that hMR targeting induced both humoral and cellular antigenic specific immunity. Immunization of hMR Tg mice with B11 mAbs induced potent humoral responses independent of adjuvant. Injection of hMR Tg mice with mouse anti-hMR Ab clone 19.2 elicited anti-Id-specific humoral immunity while non-Tg mice were unresponsive. B11-OVA fusion proteins (B11-OVA) were efficiently presented to OVA-specific CD4 and CD8 T cells in MR Tg, but not in non-Tg, mice. Effector differentiation of responding T cells in MR Tg mice was significantly enhanced with concomitant immunization with the TLR agonist, CpG. Administration of both CpG and B11-OVA to hMR Tg mice induced OVA-specific tumor immunity while WT mice remained unprotected. These studies support the clinical development of immunotherapeutic approaches in cancer using pattern recognition receptor targeting systems for the selective delivery of tumor Ags to APCs.
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MESH Headings
- Animals
- Antibodies, Monoclonal/metabolism
- Antibodies, Neoplasm/biosynthesis
- Antigens/immunology
- Antigens/metabolism
- Cross-Priming/genetics
- Cross-Priming/immunology
- Humans
- Immunoglobulin G/biosynthesis
- Insulin-Like Growth Factor II/metabolism
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Lectins, C-Type/metabolism
- Mannose Receptor
- Mannose-Binding Lectins/biosynthesis
- Mannose-Binding Lectins/genetics
- Mannose-Binding Lectins/immunology
- Mannose-Binding Lectins/metabolism
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/prevention & control
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/immunology
- Receptors, Cell Surface/metabolism
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Efficacy of a green tea extract rich in catechin polyphenols and caffeine in increasing 24-h energy expenditure and fat oxidation in humans. Am J Clin Nutr 1999; 70:1040-5. [PMID: 10584049 DOI: 10.1093/ajcn/70.6.1040] [Citation(s) in RCA: 538] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Current interest in the role of functional foods in weight control has focused on plant ingredients capable of interfering with the sympathoadrenal system. OBJECTIVE We investigated whether a green tea extract, by virtue of its high content of caffeine and catechin polyphenols, could increase 24-h energy expenditure (EE) and fat oxidation in humans. DESIGN Twenty-four-hour EE, the respiratory quotient (RQ), and the urinary excretion of nitrogen and catecholamines were measured in a respiratory chamber in 10 healthy men. On 3 separate occasions, subjects were randomly assigned among 3 treatments: green tea extract (50 mg caffeine and 90 mg epigallocatechin gallate), caffeine (50 mg), and placebo, which they ingested at breakfast, lunch, and dinner. RESULTS Relative to placebo, treatment with the green tea extract resulted in a significant increase in 24-h EE (4%; P < 0.01) and a significant decrease in 24-h RQ (from 0.88 to 0.85; P < 0.001) without any change in urinary nitrogen. Twenty-four-hour urinary norepinephrine excretion was higher during treatment with the green tea extract than with the placebo (40%, P < 0.05). Treatment with caffeine in amounts equivalent to those found in the green tea extract had no effect on EE and RQ nor on urinary nitrogen or catecholamines. CONCLUSIONS Green tea has thermogenic properties and promotes fat oxidation beyond that explained by its caffeine content per se. The green tea extract may play a role in the control of body composition via sympathetic activation of thermogenesis, fat oxidation, or both.
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ERK plays a regulatory role in induction of LTP by theta frequency stimulation and its modulation by beta-adrenergic receptors. Neuron 1999; 24:715-26. [PMID: 10595521 DOI: 10.1016/s0896-6273(00)81124-1] [Citation(s) in RCA: 262] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MAP kinase (ERK) translates cell surface signals into alterations in transcription. We have found that ERK also regulates hippocampal neuronal excitability during 5 Hz stimulation and thereby regulates forms of long-term potentiation (LTP) that do not require macromolecular synthesis. Moreover, ERK-mediated changes in excitability are selectively required for some forms of LTP but not others. ERK is required for the early phase of LTP elicited by brief 5 Hz stimulation, as well as for LTP elicited by more prolonged 5 Hz stimulation when paired with beta1-adrenergic receptor activation. By contrast, ERK plays no role in LTP elicited by a single 1 s 100 Hz train. Consistent with these results, we find that ERK is activated by beta-adrenergic receptors in CA1 pyramidal cell somas and dendrites.
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The disparate effects of Alzheimer's disease and Huntington's disease on semantic memory. Neuropsychology 1999. [PMID: 10447299 DOI: 10.1037//0894-4105.13.3.381] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Alzheimer's disease (AD) and Huntington's disease (HD) impair performance on semantic memory tasks, but researchers disagree on whether AD and HD cause these impairments in the same manner. According to one view, AD disrupts the storage of semantic memories, whereas HD disrupts the retrieval of semantic memories. Dissenters argue that AD, like HD, disrupts retrieval. In this study, participants generated category exemplars (e.g., kinds of fruits) for 1 min, and response latencies were examined. Relative to healthy controls, the 12 AD patients produced a larger proportion of responses earlier in the recall period, consistent with the view that AD patients quickly exhaust their limited supply of items in storage. By contrast, the 12 HD patients produced a larger proportion of their responses late in the recall period, consistent with the view that HD slows retrieval.
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Abstract
Genetic transfer approaches have received recent consideration as potential treatment modalities for human central and peripheral nervous system (CNS and PNS, respectively) neurodegenerative disorders, including Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis. Transplantation of genetically modified cells into the brain represents a promising strategy for the delivery and expression of specific neurotrophic factors, neurotransmitter-synthesizing enzymes, and cellular regulatory proteins for intervention in neurodegenerative diseases. The use of specific regulatable promoters may also provide potential control of gene expression required for dose-specific or time-specific therapeutic strategies. In this article, we review the potential use of activated promoters in ex vivo systems for the potential genetic therapy of neurodegenerative disorders, and then describe our own studies using the zinc-inducible metallothionein promoter for the regulated expression of nerve growth factor (NGF) in rodent brain transplants.
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Abstract
Alzheimer's disease (AD) and Huntington's disease (HD) impair performance on semantic memory tasks, but researchers disagree on whether AD and HD cause these impairments in the same manner. According to one view, AD disrupts the storage of semantic memories, whereas HD disrupts the retrieval of semantic memories. Dissenters argue that AD, like HD, disrupts retrieval. In this study, participants generated category exemplars (e.g., kinds of fruits) for 1 min, and response latencies were examined. Relative to healthy controls, the 12 AD patients produced a larger proportion of responses earlier in the recall period, consistent with the view that AD patients quickly exhaust their limited supply of items in storage. By contrast, the 12 HD patients produced a larger proportion of their responses late in the recall period, consistent with the view that HD slows retrieval.
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Abstract
Ten percent of head injuries quality as "severe," requiring prompt diagnosis and treatment. This level I trauma center uses an aggressive approach to treatment of severe head injuries and, when indicated, intervenes with decompressive craniectomy. This article explains decompressive craniectomy, including indications, procedures, and protocols. The case studies presented highlight two patients with profound head injuries. Additionally, cranioplasty replacement of autograft flap is explained and discussed.
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Abstract
We examined whether two memories can be retrieved concurrently from long-term memory. In Experiment 1, the subjects recalled words, either from two categories--alternating between the two--or from just one category. In Experiment 2, the subjects recalled two words belonging to either the same category or different categories, and the category prompts for these two responses appeared either simultaneously or successively. The results of both studies are consistent with the view that two items from different categories must be retrieved serially, whereas two items from the same category can be retrieved in parallel.
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Retrieval from semantic memory and its implications for Alzheimer's disease. J Exp Psychol Learn Mem Cogn 1996. [PMID: 8744958 DOI: 10.1037//0278-7393.21.5.1127] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In 3 experiments, participants generated category exemplars (e.g., kinds of fruits) while a voice key and computer recorded each response latency relative to the onset of responding. In Experiment 1, mean response latency was faster when participants generated exemplars from smaller categories, suggesting that smaller mental search sets result in faster mean latencies. In Experiment 2, a concurrent secondary task increased mean response latency, suggesting that slowed mental processing results in slower mean latencies. In Experiment 3, the mean response latency of Alzheimer's participants was faster than that of elderly controls, which is consistent with the idea that the semantic memory impairments of Alzheimer's disease patients stem primarily from a reduction in available items (as in Experiment 1) rather than retrieval slowing (as in Experiment 2).
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Abstract
Subjects studied either an 8- or 16-word list and later recalled the items while a voice key recorded each response latency. The trials were partitioned by recall total in order to examine the means and distributions of both latencies and interresponse times as a function of recall total. Each analysis was consistent with the view that an item's absolute strength determines whether it is recalled whereas an item's relative strength determines when it is recalled. In addition, mean latency was effectively proportional to study list length yet independent of recall total. All of the analyses were consistent with the view that the set of study items is sampled according to a relative-strength rule until all items are found and that a sampled item is recovered into consciousness only when its absolute strength exceeds a fixed threshold.
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Abstract
In 3 experiments, participants generated category exemplars (e.g., kinds of fruits) while a voice key and computer recorded each response latency relative to the onset of responding. In Experiment 1, mean response latency was faster when participants generated exemplars from smaller categories, suggesting that smaller mental search sets result in faster mean latencies. In Experiment 2, a concurrent secondary task increased mean response latency, suggesting that slowed mental processing results in slower mean latencies. In Experiment 3, the mean response latency of Alzheimer's participants was faster than that of elderly controls, which is consistent with the idea that the semantic memory impairments of Alzheimer's disease patients stem primarily from a reduction in available items (as in Experiment 1) rather than retrieval slowing (as in Experiment 2).
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Abstract
In four experiments, subjects freely recalled previously studied items while a voice key and computer recorded each item's recall latency relative to the onset of the recall period. The measures of recall probability and mean recall latency were shown to be empirically independent, demonstrating that there exists no a priori relationship between the two. In all four experiments, latency distributions were fit well by the ex-Gaussian, suggesting that retrieval includes a brief normally distributed initiation stage followed by a longer exponentially distributed search stage. Further, the variation in mean latency stemmed from the variation in the duration of the search stage, not the initiation stage. Interresponse times (IRTs), the time elapsed between two successive item recalls, were analyzed as well. The growth of mean IRTs, plotted as a function of output position, was shown to be a simple function of the number of items not yet recalled. Finally, the mathematical nature of both free recall latency and IRT growth are shown to be consistent with a simple theoretical account of retrieval that depicts mean recall latency as a measure of the breadth of search.
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Abstract
In demonstrations of part-list cuing inhibition, subjects who are shown a subset of studied list words recall fewer noncue words than subjects not shown such part-list cues. We propose that part-list inhibition is governed in part by an incongruency principle: Inhibition occurs to the extent that part-list cues induce a retrieval framework different from that used to encode list items. In Experiment 1, word lists were studied followed by a test of free recall either without cues, or with cue words serially organized to be either congruent or incongruent with the order of studied items. In Experiments 2-4, cues consisted of every second study item in the original presentation order (congruent ones) or reordered to form famous names or familiar idioms that had been hidden in the study list (incongruent cues). More part-list inhibition was observed with incongruent cues than congruent cues in all 4 experiments.
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Abstract
Age-associated slowing of cardiac relaxation related to the decline in the Ca2+ pump function of cardiac sarcoplasmic reticulum (SR) has been previously described. It is unclear if the decreased Ca2+ pump function results from a lower amount of Ca2(+)-ATPase protein or a decreased pumping activity of the enzyme. To determine if these alterations could be mediated by changes in the amount of the protein itself, the level of the messenger RNA (mRNA) coding for the Ca2(+)-ATPase of the SR of Fischer rat hearts (4- and 30-month-old rats) were quantitated with a Northern blotting technique. We observed that the levels of SR Ca2(+)-ATPase mRNA were 60% lower in old rats as compared with young rats, suggesting that a quantitative reduction in the levels of the corresponding protein could occur during aging to explain the delayed diastolic relaxation documented in old animals as opposed to a change in the specific activity of this enzyme. The thyroid hormone responsiveness of SR Ca2(+)-ATPase mRNA has been previously established. We have found in this study that the thyroxine levels were consistently lower in old rats; however, this difference was relatively small (4.3 +/- 0.7 and 3.1 +/- 0.8 micrograms/dl [mean +/- SD), respectively, in young and old rats). In addition, no age-induced decrease in 3,5,3'-triiodothyronine levels was observed, suggesting that the aging process itself may be responsible for the changes in SR Ca2(+)-ATPase mRNA levels.
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Thyroid hormone markedly increases the mRNA coding for sarcoplasmic reticulum Ca2+-ATPase in the rat heart. J Biol Chem 1988; 263:6941-4. [PMID: 2966798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previous findings have shown that thyroid hormone markedly increases the speed of diastolic relaxation in the heart. This thyroid hormone-dependent change is also accompanied by an increased Ca2+ pumping ability in the sarcoplasmic reticulum. In an effort to determine the underlying cause of improved Ca2+ transport, mRNA levels of the slow Ca2+-ATPase of the sarcoplasmic reticulum were quantified on Northern blots. In hypothyroid rat hearts, the steady state level of Ca2+-ATPase mRNA was only 36% of control levels, whereas hyperthyroid rat heart mRNA levels were 136% of control. Ca2+-ATPase mRNA responded rapidly to T3, as the mRNA level was significantly increased by 2 h and normalized by 5 h after T3 injection into hypothyroid rats. The well established effect of thyroid hormone on improved myocardial contractility and increased speed of diastolic relaxation may in part relate to specific alterations in the level of the mRNA coding for Ca2+-ATPase, resulting in increased pump units.
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Thyroid hormone markedly increases the mRNA coding for sarcoplasmic reticulum Ca2+-ATPase in the rat heart. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68584-9] [Citation(s) in RCA: 157] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Letter: Reassignment of the absolute configuration of 19-substituted 19-hydroxysteroids and stereomechanism of estrogen biosynthesis. J Am Chem Soc 1975; 97:4400-2. [PMID: 1141602 DOI: 10.1021/ja00848a046] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Additions and Corrections - Stereochemistry of Nucleic Acids and Their Constituents. XI. The Molecular Structure and Conformation of α-Pseudouridine Monohydrate, an Unusual Nucleoside with a "Glycoside" Carbon-Carbon Bond. Stereochemistry of Nucleic Acids and Their Constituents. XII. The Crystal and Molecular Structure of α-D-2'-Amino-2'-deoxyadenosine Monohydrate. J Am Chem Soc 1971. [DOI: 10.1021/ja00730a604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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