Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
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Published Erratum↗
Biomedical subjects
Young Kim
Publications and source records attributed to Young Kim.
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.
Humans↗
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.
Journal Article↗
In vivo imaging of tumor response to therapy using a dual-modality imaging strategy.
In vivo assessment of the outcome of cancer therapy is hampered by the paucity of imaging probes that target tumors specifically and noninvasively. The importance of such probes increases with the continuous development of chemotherapeutics and the necessity to evaluate their effectiveness in a clinical setting. We have recently reported on a dual-modality imaging probe specifically targeting the underglycosylated mucin-1 tumor-specific antigen (uMUC-1), which is one of the early hallmarks of tumorigenesis in a wide variety of tumors. This probe consists of crosslinked superparamagnetic iron oxide nanoparticles (CLIO) for MR imaging, modified with Cy5.5 dye (for near infrared optical fluorescence imaging (NIRF)), and has peptides (EPPT), specifically recognizing uMUC-1, attached to the nanoparticle's dextran coat. In the present study, we demonstrated that this probe could not only detect orthotopically implanted preclinical models of adenocarcinomas but could also track tumor response to chemotherapy in vivo in real time. Considering the high cost associated with the development and testing of new cancer therapeutics and the need for accurate, noninvasive assessment of their effectiveness, we believe that the developed probe represents a valuable research tool relevant to clinical discovery.
Adenocarcinoma↗
Push-pull tests evaluating in situ aerobic cometabolism of ethylene, propylene, and cis-1,2-dichloroethylene.
In situ aerobic cometabolic transformations of ethylene, propylene, and cis-1,2-dichloroethylene (c-DCE), by microorganisms stimulated on propane, were examined in groundwater contaminated with c-DCE and trichloroethylene (TCE). In situ measurements were performed by conducting field push-pull tests, which consisted of injecting site groundwater amended with a bromide tracer and combinations of propane, dissolved oxygen (DO), nitrate, ethylene, propylene, c-DCE, and TCE into existing monitoring wells and sampling the same wells over time. Mass balance and transformation rate calculations were performed after adjusting for dilution losses using measured tracer concentrations. Initial rates of propane utilization were very low; rates increased substantially following sequential additions of propane and DO. Evidence that propane and DO additions had stimulated organisms expressing a propane monoxygenase enzyme system and that had the capability to transform chlorinated aliphatic hydrocarbons (CAHs) included: (1) the transformation of injected ethylene and propylene to the cometabolic byproducts ethylene oxide and propylene oxide, (2) the transformation of c-DCE, and (3) the inhibition of these transformations in the presence of coinjected acetylene, a known monoxygenase mechanism-based inactivator. These results suggest that a series of push-pull tests performed with nontoxic chemical probes can be useful for detecting and monitoring in situ aerobic cometabolism of CAHs.
Alkenes↗
Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines.
BACKGROUND: The aim of this study was to characterize gene expression and DNA copy number profiles in androgen sensitive (AS) and androgen insensitive (AI) prostate cancer cell lines on a genome-wide scale. METHODS: Gene expression profiles and DNA copy number changes were examined using DNA microarrays in eight commonly used prostate cancer cell lines. Chromosomal regions with DNA copy number changes were identified using cluster along chromosome (CLAC). RESULTS: There were discrete differences in gene expression patterns between AS and AI cells that were not limited to androgen-responsive genes. AI cells displayed more DNA copy number changes, especially amplifications, than AS cells. The gene expression profiles of cell lines showed limited similarities to prostate tumors harvested at surgery. CONCLUSIONS: AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers.
Cell Line, Tumor↗
Evaluation of right ventricular volume and mass using retrospective ECG-gated cardiac multidetector computed tomography: comparison with first-pass radionuclide angiography.
The purposes of this study were to evaluate the right ventricular (RV) volume and mass using cardiac multidetector computed tomography (MDCT) and to compare the cardiac MDCT results with those from first-pass radionuclide angiography (FPRA). Twenty patients were evaluated for the RV end-diastolic volume (RVEDV), the RV end-systolic volume (RVESV), the RV ejection fraction (RVEF), and RV mass using cardiac MDCT with a two-phase reconstruction method based on ECG. The end-diastolic phase was reconstructed at the starting point of the QRS complex on ECG, and the end-systolic phase was reconstructed at the halfway point of the ascending T-wave on ECG. The RV mass was measured for the end-systole. The RVEF was also obtained by FPRA. The mean RVEF (47+/-7%) measured by cardiac MDCT was well correlated with that (44+/-6%) measured by FPRA (r=0.854). A significant difference in the mean RVEF was found between cardiac MDCT and FPRA (p=0.001), with an overestimation of 2.9+/-5.3% by cardiac MDCT versus FPRA. The interobserver variability was 4.4% for the RVEDV, 6.8% for the RVESV, and 7.9% for the RV mass, respectively. Cardiac MDCT is relatively simple and allows the RV volume and mass to be assessed, and the RVEF obtained by cardiac MDCT correlates well with that measured by FPRA.
Adult↗
Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.
Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalin-fixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens.
Chromosome Aberrations↗
A method for calling gains and losses in array CGH data.
Array CGH is a powerful technique for genomic studies of cancer. It enables one to carry out genome-wide screening for regions of genetic alterations, such as chromosome gains and losses, or localized amplifications and deletions. In this paper, we propose a new algorithm 'Cluster along chromosomes' (CLAC) for the analysis of array CGH data. CLAC builds hierarchical clustering-style trees along each chromosome arm (or chromosome), and then selects the 'interesting' clusters by controlling the False Discovery Rate (FDR) at a certain level. In addition, it provides a consensus summary across a set of arrays, as well as an estimate of the corresponding FDR. We illustrate the method using an application of CLAC on a lung cancer microarray CGH data set as well as a BAC array CGH data set of aneuploid cell strains.
Algorithms↗
Immortalization of human bronchial epithelial cells in the absence of viral oncoproteins.
By expressing two genes (hTERT and Cdk4), we have developed a method to reproducibly generate continuously replicating human bronchial epithelial cell (HBEC) lines that provide a novel resource to study the molecular pathogenesis of lung cancer and the differentiation of bronchial epithelial cells. Twelve human bronchial epithelial biopsy specimens obtained from persons with and without lung cancer were placed into short-term culture and serially transfected with retroviral constructs containing cyclin-dependent kinase (Cdk) 4 and human telomerase reverse transcriptase (hTERT), resulting in continuously growing cultures. The order of introduction of Cdk4 and hTERT did not appear to be important; however, transfection of either gene alone did not result in immortalization. Although they could be cloned, the immortalized bronchial cells did not form colonies in soft agar or tumors in nude mice. The immortalized HBECs have epithelial morphology; express epithelial markers cytokeratins 7, 14, 17, and 19, the stem cell marker p63, and high levels of p16(INK4a); and have an intact p53 checkpoint pathway. Cytogenetic analysis and array comparative genomic hybridization profiling show immortalized HBECs to have duplication of parts of chromosomes 5 and 20. Microarray gene expression profiling demonstrates that the Cdk4/hTERT-immortalized bronchial cell lines clustered together and with nonimmortalized bronchial cells, distinct from lung cancer cell lines. We also immortalized several parental cultures with viral oncoproteins human papilloma virus type 16 E6/E7 with and without hTERT, and these cells exhibited loss of the p53 checkpoint and significantly different gene expression profiles compared with Cdk4/hTERT-immortalized HBECs. These HBEC lines are a valuable new tool for studying of the pathogenesis of lung cancer.
Cell Growth Processes↗
Lineage-specific gene duplication and loss in human and great ape evolution.
Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
Animals↗
Cord-blood transplants from unrelated donors in patients with Hurler's syndrome.
BACKGROUND: Hurler's syndrome (the most severe form of mucopolysaccharidosis type I) causes progressive deterioration of the central nervous system and death in childhood. Allogeneic bone marrow transplantation before the age of two years halts disease progression and prolongs life, but many children lack a bone marrow donor. We investigated the feasibility of using cord-blood transplants from unrelated donors and a myeloablative preparative regimen that did not involve total-body irradiation in young children with Hurler's syndrome. METHODS: Between December 1995 and October 2002, 20 consecutive children with Hurler's syndrome received busulfan, cyclophosphamide, and antithymocyte globulin before receiving cord-blood transplants from unrelated donors. The children were subsequently evaluated for engraftment, adverse effects, and effects on disease symptoms. RESULTS: Cord-blood donors had normal alpha-L-iduronidase activity (mean number of cells, 10.53x10(7) per kilogram of body weight) and were discordant for up to three of six HLA markers. Neutrophil engraftment occurred a median of 24 days after transplantation. Five patients had grade II or grade III acute graft-versus-host disease; none had extensive chronic graft-versus-host disease. Seventeen of the 20 children were alive a median of 905 days after transplantation, with complete donor chimerism and normal peripheral-blood alpha-L-iduronidase activity (event-free survival rate, 85 percent). Transplantation improved neurocognitive performance and decreased somatic features of Hurler's syndrome. CONCLUSIONS: Cord blood from unrelated donors appears to be an excellent source of stem cells for transplantation in patients with Hurler's syndrome. Sustained engraftment can be achieved without total-body irradiation. Cord-blood transplantation favorably altered the natural history of Hurler's syndrome and thus may be important to consider in young children with this form of the disease.
Blood Donors↗
Numerical deconvolution of cDNA microarray signal: simulation study.
A computational model for simulation of the cDNA microarray experiments has been created. The simulation allows one to foresee the statistical properties of replicated experiments without actually performing them. We introduce a new concept, the so-called bio-weight, which allows for reconciliation between conflicting meanings of biological and statistical significance in microarray experiments. It is shown that, for a small sample size, the bio-weight is a more powerful criterion of the presence of a signal in microarray data as compared to the standard approach based on t test. Joint simulation of microarray and quantitative PCR data shows that the genes recovered by using the bio-weight have better chances to be confirmed by PCR than those obtained by the t test technique. We also employ extreme value considerations to derive plausible cutoff levels for hypothesis testing.
Cell Line, Tumor↗
Two cases of post transplant lymphoproliferative disorder in lung transplant recipients.
Post-transplant lymphoproliferative disease (PTLD) is a serious, often fatal complication after solid organ transplantation. The incidence of PTLD is greater among heart (2 approximately 13%), lung (12%) and heart/lung (5 approximately 9%) transplant recipients than among liver (2%), renal (1 approximately 3%) and bone marrow (1 approximately 2%) transplants recipients. The difference in the incidence of PTLD may be partly attributed to the higher dose of immunosuppressant therapy used for heart and lung transplantation. The Epstein-Barr virus (EBV) infection status of the donor and recipient before a transplant, and high dose of immunosuppressive drugs are considered major risk factors. Recently, 2 cases of PTLD in a single lung and a heart-lung transplantation recipient were encountered. Both patients presented with multiple pulmonary nodules in the transplanted lung, which developed 6 months and 2 years after the transplantation, respectively. Following a transthoracic lung biopsy for diagnostic confirmation, one patient underwent chemotherapy for PTLD and the other conservative care for an accompanying viral infection. Both patients showed rapid clinical deterioration, without response to treatment, and then rapidly succumbed. Herein, our experiences are reported, with a review of the literature.
Adult↗
Down-regulation of SNAIL suppresses MIN mouse tumorigenesis: modulation of apoptosis, proliferation, and fractal dimension.
OBJECTIVES: Emerging evidence implicates the SNAIL family of transcriptional repressors in cancer development; however, the role of SNAIL in colorectal cancer has not been established. To investigate the importance of SNAIL in colorectal carcinogenesis, we examined the phenotypic and cellular consequences of SNAIL down-regulation in the MIN mouse. METHODS: Twenty-eight male MIN mice were randomized to treatment with an antisense phosphorodiamidate morpholino oligomer (AS-PMO) to SNAIL, saline, or a scrambled sequence control for 6 weeks. Tumors were scored and the molecular/cellular effects of anti-SNAIL treatment were evaluated through immunohistochemical analysis of the uninvolved intestinal mucosa for SNAIL and E-cadherin levels along with rates of apoptosis and proliferation. Furthermore, microarchitectural alterations were determined through measurement of fractal dimension. RESULTS: In the uninvolved mucosa, SNAIL AS-PMO treatment moderately decreased SNAIL protein when compared with saline-treated animals (immunohistochemistry scores 3.0 +/- 0.8 versus 2.1 +/- 0.6, respectively; P=0.01) with a concomitant increase in E-cadherin expression (1.8 +/- 0.6 versus 2.4 +/- 0.5; P < 0.05). Anti-SNAIL PMO, but not scramble control, resulted in a significant decrease in both total tumor number and incidence of tumors >2 mm (22% and 54%, respectively; P < 0.05). Furthermore, this was accompanied by an increased apoptosis rate (2-fold), decreased proliferation (3-fold), and normalization of the fractal dimension in the uninvolved intestinal mucosa. CONCLUSIONS: We show, for the first time, that SNAIL overexpression is important in intestinal tumorigenesis. While this PMO regimen afforded modest SNAIL suppression and hence tumor reduction, this provides compelling evidence for the role of SNAIL overexpression in colonic neoplasia.
Animals↗
On the nature of cardiovascular activation at an arousal from sleep.
STUDY OBJECTIVES: The intent of the study was to explore the nature and function of the cardiovascular activation response that occurs at an arousal from sleep. DESIGN: Four experiments were conducted. The first compared the pattern of physiologic response to orienting and startle stimuli and arousal from sleep. The second and third measured the amplitude of the cardiovascular arousal response as a function of the trait of fearfulness and the threat value of the arousing stimulus, respectively. The final experiment assessed the effect of arousal duration. SETTING: The experiments were conducted in the sleep laboratory of the Department of Psychology, University of Melbourne. PARTICIPANTS: A total of 42 (24 women and 18 men) healthy individuals between the ages of 18 and 24 participated in the experiments. INTERVENTIONS: The experiments manipulated the stimuli to which participants were exposed (orienting and startle stimuli and arousal from sleep), the threat value of stimuli used to arouse participants from sleep, and individual differences in fearfulness. MEASUREMENTS AND RESULTS: The major dependent variables were heart rate, blood pressure, and a measure of peripheral vasoconstriction (digital pulse volume). In addition, in the first study, the galvanic skin response and orbicularis oculi electromyographic activity were measured. Experiment 1 showed that the pattern of physiologic response at an arousal from sleep differed, with a substantially larger cardiovascular component, from responses to orienting and startle stimuli. Experiments 2a and 2b indicated that the magnitude of the cardiovascular response at an arousal was unrelated to either individual differences in fearfulness or differences in the threat value of arousing stimuli. The final experiment showed that the cardiovascular response at an arousal was not a return to waking levels of activity but, rather, was a transient activation response. CONCLUSIONS: The study supported the view that the cardiovascular activation response at an arousal from sleep is a transient, reflex-like response that is different from the response that occurs during normal wakefulness.
Adult↗
Effects of ankle exercise combined with deep breathing on blood flow velocity in the femoral vein.
Ankle exercises are commonly used to facilitate venous return in the lower extremity and to prevent deep vein thrombosis. Moreover, the respiratory cycle affects venous return. This study examined the effects of ankle exercise combined with deep breathing on the blood flow velocity in the femoral vein. Twenty healthy males (mean age 21.3 years), who had no medical history of lower extremity disease, were recruited for this study. The blood flow velocity in the femoral vein was measured while performing four exercise protocols: quiet breathing while resting (QR), deep breathing (DB), ankle exercise with quiet breathing (AQB), and ankle exercising combined with deep breathing (ADB). Using a Doppler ultrasound with an 8 MHz probe, peak blood flow velocities were collected for a 20 second period at the start of the inspiration phase in each protocol, three times. There were statistically significant differences in the peak blood flow velocity in the femoral vein with the four protocols (p lt 0.001). The mean (SD) peak blood flow velocity in the femoral vein was as follows: QR 10.1 (4.2) cm/sec, DB 15.5 (3.9) cm/sec, AQB 20.7 (6.6) cm/sec, and ADB 26.5 (9.4) cm/sec. Post hoc analyses revealed significant differences between each of the four protocols (p(adj) lt 0.01). The mean peak blood flow velocity in the femoral vein was greatest with the ADB protocol, which implies that the ADB protocol may be useful to prevent the blood stasis in patients at risk of deep vein thrombosis.
Adult↗
Phase I trial of docetaxel, carboplatin, and gemcitabine as first-line therapy for patients with high-risk epithelial tumors of müllerian origin.
OBJECTIVES: The aim of this study was to assess the feasibility of combining docetaxel, carboplatin, and gemcitabine (DoCaGem) as first-line treatment of ovarian and other müllerian origin tumors. METHODS: Four dose levels were planned for this phase I trial. Treatment consisted of carboplatin on day 1 only, docetaxel on days 1 and 8, and gemcitabine on days 1 and 8, every 21 days. RESULTS: Nineteen patients were enrolled, of whom 18 were evaluable for toxicity. The first 5 patients enrolled at dose level I (carboplatin AUC 5, 30 mg/m(2) docetaxel, 800 mg/m(2) gemcitabine) experienced no dose-limiting toxicity. At dose level II, 4/4 evaluable patients experienced significant bone marrow suppression that required dose reduction and/or dose delay. Further dose escalation was not attempted, and 9 additional patients were enrolled in dose level I. Of the 67 cycles administered on dose level I, day 8 treatment could not be administered due to bone marrow suppression in 16 cycles (24%), and prolongation of the cycle length from day 22 to day 29 was required in 13 cycles (19%). There were no episodes of febrile neutropenia in evaluable patients and no treatment-related deaths. Grade 3 nonhematologic toxicity (fatigue) occurred in 1 cycle. Response was determined in the 14 evaluable patients who tolerated 4 or more cycles of therapy, with 11 obtaining a complete clinical response and 3 obtaining a partial clinical response. CONCLUSIONS: The DoCaGem regimen is highly active, but myelosuppression at dose level I prevents full dose delivery. Other strategies to combine these three active agents are reasonable to explore.
Adult↗