Kenneth Lee - Academia.edu (original) (raw)

Papers by Kenneth Lee

Gastroenterology, Jun 1, 2018

Despite prognostic grading and staging systems, it is a challenge to predict outcomes for patient... more Despite prognostic grading and staging systems, it is a challenge to predict outcomes for patients with pancreatic neuroendocrine tumors (PanNETs). Sequencing studies of PanNETs have identified alterations in death domain-associated protein (DAXX) and alpha-thalassemia/mental retardation X-linked chromatin remodeler (ATRX). In tumors, mutations in DAXX or ATRX and corresponding loss of protein expression correlate with shorter times of disease-free survival and disease-specific survival of patients. However, DAXX or ATRX proteins were lost in only 50% of distant metastases analyzed. We performed whole-exome sequencing analyses of 20 distant metastases from 20 patients with a single nonsyndrome, nonfunctional PanNET. We found distant metastases contained alterations in multiple endocrine neoplasia type 1 (MEN1) (n = 8), ATRX (n = 5), DAXX (n = 5), TSC2 (n = 3), and DEP domain containing 5 (DEPDC5) (n = 3). We found copy number loss of cyclin dependent kinase inhibitor 2A (CDKN2A) in ...

Toxicology letters, Jan 14, 2017

Excess alcohol consumption during pregnancy could lead to fetal alcohol syndrome (FAS). However, ... more Excess alcohol consumption during pregnancy could lead to fetal alcohol syndrome (FAS). However, the molecular mechanism leading to craniofacial abnormality, a feature of FAS, is still poorly understood. The cranial neural crest cells (NCCs) contribute to the formation of the craniofacial bones. Therefore, NCCs exposed to ethanol was investigated - using chick embryos and in vitro explant culture as experimental models. We demonstrated that exposure to 2% ethanol induced craniofacial defects, which includes parietal defect, in the developing chick fetus. Immunofluorescent staining revealed that ethanol treatment downregulated Ap-2ɑ, Pax7 and HNK-1 expressions by cranial NCCs. Using double-immunofluorescent stainings for Ap-2ɑ/pHIS3 and Ap-2ɑ/c-Caspase3, we showed that ethanol treatment inhibited cranial NCC proliferation and increased NCC apoptosis, respectively. Moreover, ethanol treatment of the dorsal neuroepithelium increased Laminin, N-Cadherin and Cadherin 6B expressions while...

Cell death & disease, Mar 23, 2017

The BRE (brain and reproductive expression) gene, highly expressed in nervous and reproductive sy... more The BRE (brain and reproductive expression) gene, highly expressed in nervous and reproductive system organs, plays an important role in modulating DNA damage repair under stress response and pathological conditions. Folliculogenesis, a process that ovarian follicle develops into maturation, is closely associated with the interaction between somatic granulosa cell and oocyte. However, the regulatory role of BRE in follicular development remains undetermined. In this context, we found that BRE is normally expressed in the oocytes and granulosa cells from the primordial follicle stage. There was a reduction in follicles number of BRE mutant (BRE(-/-)) mice. It was attributed to increase the follicular atresia in ovaries, as a result of retarded follicular development. We established that cell proliferation was inhibited, while apoptosis was markedly increased in the granulosa cells in the absence of BRE. In addition, expressions of γ-H2AX (marker for showing DNA double-strand breaks) ...

Scientific reports, Oct 10, 2016

Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset or first recogni... more Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset or first recognition during pregnancy. It is associated with an increased risk of pregnancy complications. Susceptibility to GDM is partly determined by genetics and linked with type 1 diabetes-associated high risk HLA class II genes. However, the evidence for this relationship is still highly controversial. In this study, we assessed the relationship between HLA class II variants and GDM. We performed meta-analysis on all of literatures available in PubMed, Embase, Web of Science and China National Knowledge Infrastructure databases. The odds ratio and 95% confidence interval of each variant were estimated. All statistical analyses were conducted using the Comprehensive Meta Analysis 2.2.064 software. At the allelic analysis, DQB1*02, DQB1*0203, DQB1*0402, DQB1*0602, DRB1*03, DRB1*0301 and DRB1*1302 reached a nominal level of significance, and only DQB1*02, DQB1*0602 and DRB1*1302 were statistically si...

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 12, 2016

Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of neoplasms with increasing... more Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of neoplasms with increasing incidence and unpredictable behavior. Whole exome sequencing has identified recurrent mutations in the genes DAXX and ATRX, which correlate with loss of protein expression and alternative lengthening of telomeres (ALT). Both ALT and DAXX/ATRX loss were initially reported to be associated with a favorable prognosis; however, recent studies suggest the contrary. Our aims were to assess the prevalence and prognostic significance of ALT and DAXX/ATRX in both primary and metastatic PanNETs. Telomere-specific FISH and DAXX/ATRX immunohistochemistry were performed on a multi-institutional cohort of 321 patients with resected PanNET and 191 distant metastases from 52 patients. These results were correlated with clinicopathologic features including disease-free survival (DFS) and disease-specific survival (DSS). The prevalence of ALT and DAXX/ATRX loss in resected PanNETs was 31% and 26%, respec...

Molecular and Cellular Biology, 1997

The HIR/HPC (histone regulation/histone periodic control) negative regulators play important role... more The HIR/HPC (histone regulation/histone periodic control) negative regulators play important roles in the transcription of six of the eight core histone genes during the Saccharomyces cerevisiae cell cycle. The phenotypes of hir1 and hir2 mutants suggested that the wild-type HIR1 and HIR2 genes encode transcriptional repressors that function in the absence of direct DNA binding. When Hir1p and Hir2p were artificially tethered to yeast promoters, each protein repressed transcription, suggesting that they represent a new class of transcriptional corepressors. The two proteins might function as a complex in vivo: Hir2p required both Hir1p and another Hir protein, Hir3p, to repress transcription when it was tethered to an HTA1-lacZ reporter gene, and Hir1p and Hir2p could be coimmunoprecipitated from yeast cell extracts. Tethered Hir1p also directed the periodic transcription of the HTA1 gene and repressed HTA1 transcription in response to two cell cycle regulatory signals. Thus, it rep...

PLOS ONE, 2015

In mammals, cardiomyocytes rapidly proliferate in the fetus and continue to do so for a few more ... more In mammals, cardiomyocytes rapidly proliferate in the fetus and continue to do so for a few more days after birth. These cardiomyocytes then enter into growth arrest but the detailed molecular mechanisms involved have not been fully elucidated. We have addressed this issue by comparing the transcriptomes of 2-day-old (containing dividing cardiomyocytes) with 13-day-old (containing growth arrested cardiomyocytes) postnatal mouse hearts. We performed comparative microarray analysis on the heart tissues and then conducted Functional annotation, Gene ontology, KEGG pathway and Gene Set enrichment analyses on the differentially expressed genes. The bioinformatics analysis revealed that gene ontology categories associated with the "cell cycle", "DNA replication", "chromosome segregation" and "microtubule cytoskeleton" were down-regulated. Inversely, "immune response", "extracellular matrix", "cell differentiation" and "cell membrane" were up-regulated. Ingenuity Pathways Analysis (IPA) has revealed that GATA4, MYH7 and IGF1R were the key drivers of the gene interaction networks. In addition, Regulator Effects network analysis suggested that TASP1, TOB1, C1orf61, AIF1, ROCK1, TFF2 and miR503-5p may be acting on the cardiomyocytes in 13-day-old mouse hearts to inhibit cardiomyocyte proliferation and G1/S phase transition. RT-qPCR was used to validate genes which were differentially expressed and genes that play a prominent role in the pathways and interaction networks that we identified. In sum, our integrative analysis has provided more insights into the transcriptional regulation of cardiomyocyte exit from the cell cycle during postnatal heart development. The results also pinpoint potential regulators that could be used to induce growth arrested cardiomyocytes to proliferate in the infarcted heart.

F1000Research, 2014

Currently, there are genetic- and chemical-based methods for producing pluripotent stem cells fro... more Currently, there are genetic- and chemical-based methods for producing pluripotent stem cells from somatic cells, but all of them are extremely inefficient. However, a simple and efficient technique has recently been reported by Obokata et al (2014a, b) that creates pluripotent stem cells through acid-based treatment of somatic cells. These cells were named stimulus-triggered acquisition of pluripotency (STAP) stem cells. This would be a major game changer in regenerative medicine if the results could be independently replicated. Hence, we isolated CD45+ splenocytes from five-day-old Oct4-GFP mice and treated the cells with acidified (pH 5.7) Hank’s Balanced Salt Solution (HBSS) for 25 min, using the methods described by Obokata et al 2014c. However, we found that this method did not induce the splenocytes to express the stem cell marker Oct4-GFP when observed under a confocal microscope three to six days after acid treatment. qPCR analysis also confirmed that acid treatment did n...

International Oil Spill Conference Proceedings, 1999

Natural biodegradation rates of oil within the marine environment are partly controlled by surfac... more Natural biodegradation rates of oil within the marine environment are partly controlled by surface availability, as microbial attack primarily occurs at the oil-water interface. Therefore, increasing the surface area of residual oil by the addition of fine oleophilic particles may prove to be an effective bioremediation strategy. Considering commercial availability and cost, heat-treated peat was identified to be a promising particle source as it has high oil absorption properties and does not compete with oil as an alternative carbon source to oil-degrading bacteria. A preliminary laboratory experiment conducted with a respirometry system demonstrated the feasibility of nutrient and peat additions to enhance the metabolic activity of bacteria within oil-contaminated sand beach sediments. Field trials were conducted with similar peat and nutrient concentrations in a north-temperate beach environment with weathered Scotian Light crude oil over a 138-day period. The rates of microbial...

Spine, 2010

Study Design. This study evaluates the biomechanical characteristics of spinal instrumentation co... more Study Design. This study evaluates the biomechanical characteristics of spinal instrumentation constructs in a human unstable thoracolumbar burst fracture model simulated by corpectomy. Objective. To compare the biomechanical characteristics of short-segment posterior instrumentation, with and without crosslinks, in a human unstable burst fracture model simulated by corpectomy. Summary of Background Data. Unstable thoracolumbar burst fractures are serious injuries, and their management remains controversial. Some authors advocate the use of short-segment posterior instrumentation for certain burst fractures. Whether crosslinks contribute additional stability has not been determined. Methods. Six fresh frozen human spines (T10-L2) were potted to isolate the T11-L1 segments, and biomechanically tested in axial rotation, lateral bending, flexion, and extension. A custom spine testing system was used that allows motion with 6 degrees of freedom. After testing was completed on intact specimens, a corpectomy was performed at T12 to simulate an unstable burst fracture with loss of anterior and middle column support. Short-segment transpedicular instrumentation was then performed from T11 to L1. Each specimen was retested with 1, 2, or no crosslinks. Construct stiffness and motion data were analyzed with each intact specimen serving as its own internal control. Results. Torsional stiffness in axial rotation was significantly increased (P Ͻ 0.05) in short-segment fixation constructs with 1 and 2 crosslinks, but none was restored to the preinjury baseline level. Significant reductions in standardized motion were also achieved with 1 and 2 crosslinks compared to no crosslinks (P Ͻ 0.05), but they remained greater than baseline. Crosslinks significantly increased stiffness and decreased motion in lateral bending, beyond the baseline level (P Ͻ 0.05). In flexion, all constructs had significantly decreased stiffness and increased motion compared to the intact specimen (P Ͻ 0.05), with crosslinks providing no additional benefit. Conversely, none of the constructs demonstrated a significant change in extension compared to baseline (P Ͼ 0.05). When attempting to load the constructs to failure, screw pullout was seen in all specimens. Conclusion. Crosslinks, when added to short-segment posterior fixation, improve stiffness and decrease motion in axial rotation, but do not restore baseline stability in this corpectomy model. Short-segment posterior fixation is also inadequate in restoring stability in flexion with injuries of this severity. Short-segment posterior instrumentation alone can achieve baseline stability in lateral bending, and crosslinks provide even greater stiffness.

PLoS Genetics, 2012

Cohesin is a protein complex known for its essential role in chromosome segregation. However, coh... more Cohesin is a protein complex known for its essential role in chromosome segregation. However, cohesin and associated factors have additional functions in transcription, DNA damage repair, and chromosome condensation. The human cohesinopathy diseases are thought to stem not from defects in chromosome segregation but from gene expression. The role of cohesin in gene expression is not well understood. We used budding yeast strains bearing mutations analogous to the human cohesinopathy disease alleles under control of their native promoter to study gene expression. These mutations do not significantly affect chromosome segregation. Transcriptional profiling reveals that many targets of the transcriptional activator Gcn4 are induced in the eco1-W216G mutant background. The upregulation of Gcn4 was observed in many cohesin mutants, and this observation suggested protein translation was reduced. We demonstrate that the cohesinopathy mutations eco1-W216G and smc1-Q843D are associated with defects in ribosome biogenesis and a reduction in the actively translating fraction of ribosomes, eiF2a-phosphorylation, and 35 S-methionine incorporation, all of which indicate a deficit in protein translation. Metabolic labeling shows that the eco1-W216G and smc1-Q843D mutants produce less ribosomal RNA, which is expected to constrain ribosome biogenesis. Further analysis shows that the production of rRNA from an individual repeat is reduced while copy number remains unchanged. Similar defects in rRNA production and protein translation are observed in a human Roberts syndrome cell line. In addition, cohesion is defective specifically at the rDNA locus in the eco1-W216G mutant, as has been previously reported for Roberts syndrome. Collectively, our data suggest that cohesin proteins normally facilitate production of ribosomal RNA and protein translation, and this is one way they can influence gene expression. Reduced translational capacity could contribute to the human cohesinopathies.

Optics Letters, 2010

We optimize speckle variance optical coherence tomography (svOCT) imaging of microvasculature in ... more We optimize speckle variance optical coherence tomography (svOCT) imaging of microvasculature in high and low bulk tissue motion scenarios. To achieve a significant level of image contrast, frame rates must be optimized such that tissue displacement between frames is less than the beam radius. We demonstrate that higher accuracy estimates of speckle variance can enhance the detection of capillaries. These findings are illustrated in vivo by imaging the dorsal window chamber model (low bulk motion). We also show svOCT imaging of the nonstabilized finger (high bulk motion), using optimized imaging parameters, demonstrating better vessel detection than Doppler OCT.

Molecular Systems Biology, 2014

Despite the availability of several large-scale proteomics studies aiming to identify protein int... more Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive highresolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.

Marine Pollution Bulletin, 2007

The interaction of chemical dispersants and suspended sediments with crude oil influences the fat... more The interaction of chemical dispersants and suspended sediments with crude oil influences the fate and transport of oil spills in coastal waters. A wave tank study was conducted to investigate the effects of chemical dispersants and mineral fines on the dispersion of oil and the formation of oil-mineral-aggregates (OMAs) in natural seawater. Results of ultraviolet spectrofluorometry and gas chromatography flame ionized detection analysis indicated that dispersants and mineral fines, alone and in combination, enhanced the dispersion of oil into water column. Measurements taken with a laser in situ scattering and transmissometer (LISST-100X) showed that the presence of mineral fines increased the total concentration of the suspended particles from 4 to 10 ll l À1 , whereas the presence of dispersants decreased the particle size (mass mean diameter) of OMAs from 50 to 10 lm. Observation with an epifluorescence microscope indicated that the presence of dispersants, mineral fines, or both in combination significantly increased the number of particles dispersed into the water.

Marine Pollution Bulletin, 2008

Current chemical dispersant effectiveness tests for product selection are commonly performed with... more Current chemical dispersant effectiveness tests for product selection are commonly performed with bench-scale testing apparatus. However, for the assessment of oil dispersant effectiveness under real sea state conditions, test protocols are required to have hydrodynamic conditions closer to the natural environment, including transport and dilution effects. To achieve this goal, Fisheries and Oceans Canada and the US Environmental Protection Agency (EPA) designed and constructed a wave tank system to study chemical dispersant effectiveness under controlled mixing energy conditions (regular non-breaking, spilling breaking, and plunging breaking waves). Quantification of oil dispersant effectiveness was based on observed changes in dispersed oil concentrations and oil-droplet size distribution. The study results quantitatively demonstrated that total dispersed oil concentration and breakup kinetics of oil droplets in the water column were strongly dependent on the presence of chemical dispersants and the influence of breaking waves. These data on the effectiveness of dispersants as a function of sea state will have significant implications in the drafting of future operational guidelines for dispersant use at sea.

Journal of Nuclear Cardiology, 1995

Journal of Biomedical Optics, 2010

We demonstrate the potential of a forwardlooking Doppler optical coherence tomography ͑OCT͒ probe... more We demonstrate the potential of a forwardlooking Doppler optical coherence tomography ͑OCT͒ probe for color flow imaging in several commonly seen narrowed artery morphologies. As a proof of concept, we present imaging results of a surgically exposed thrombotic occlusion model that was imaged superficially to demonstrate that Doppler OCT can identify flow within the recanalization channels of a blocked artery. We present Doppler OCT images in which the flow is nearly antiparallel to the imaging direction. These images are acquired using a flexible 2.2-mm-diam catheter that used electrostatic actuation to scan up to 30 deg ahead of the distal end. Doppler OCT images of physiologically relevant flow phantoms consisting of small channels and tapered entrance geometries are demonstrated.

Environmental Engineering Science, 2009

Numerous laboratory test systems have been developed for the comparison of efficacy between vario... more Numerous laboratory test systems have been developed for the comparison of efficacy between various chemical oil dispersant formulations. However, for the assessment of chemical dispersant effectiveness under realistic sea state, test protocols are required to produce hydrodynamic conditions close to the mixing, transport, and dilution effects found in the natural environment. To this end, we have designed and constructed an experimental wave tank system capable of generating waves of different energy levels, ranging from regular nonbreaking waves to plunging breakers. The hydrodynamics of these wave conditions were characterized using an autocorrelation function method applied to in situ velocity measurements. We report here an investigation of the effectiveness of two chemical dispersants (Corexit 9500 and SPC 1000) on two crude oils (weathered MESA and fresh ANS) under three different wave conditions in the wave tank operated in batch mode. Corexit 9500 dispersed approximately 75% of the weathered MESA and more than 90% of the fresh ANS crude, and SPC 1000 dispersed about 53 and 64%, respectively. Under control conditions (absence of chemical dispersant), only 10 to 20% of the crude oils were dispersed. Quantitative relationships were established between dispersant effectiveness and energy dissipation rate under the different simulated wave conditions. These relationships are essential for the development of accurate predictive models on dispersant effectiveness and operational guidelines for dispersant use.

Cell, 2008

Ire1 is an ancient transmembrane sensor of ER stress with dual protein kinase and ribonuclease ac... more Ire1 is an ancient transmembrane sensor of ER stress with dual protein kinase and ribonuclease activities. In response to ER stress, Ire1 catalyzes the splicing of target mRNAs in a spliceosome-independent manner. We have determined the crystal structure of the dual catalytic region of Ire1at 2.4 Å resolution, revealing the fusion of a domain, which we term the KEN domain, to the protein kinase domain. Dimerization of the kinase domain composes a large catalytic surface on the KEN domain which carries out ribonuclease function. We further show that signal induced trans-autophosphorylation of the kinase domain permits unfettered binding of nucleotide, which in turn promotes dimerization to compose the ribonuclease active site. Comparison of Ire1 to a topologically disparate ribonuclease reveals the convergent evolution of their catalytic mechanism. These findings provide a basis for understanding the mechanism of action of RNaseL and other pseudokinases, which represent 10% of the human kinome.

Cell, 2010

Trimethyl-lysine (me3) modifications on histones are the most stable epigenetic marks and they co... more Trimethyl-lysine (me3) modifications on histones are the most stable epigenetic marks and they control chromatin-mediated regulation of gene expression. Here, we determine proteins that bind these marks by high-accuracy, quantitative mass spectrometry. These chromatin ''readers'' are assigned to complexes by interaction proteomics of full-length BAC-GFP-tagged proteins. ChIP-Seq profiling identifies their genomic binding sites, revealing functional properties. Among the main findings, the human SAGA complex binds to H3K4me3 via a double Tudor-domain in the C terminus of Sgf29, and the PWWP domain is identified as a putative H3K36me3 binding motif. The ORC complex, including LRWD1, binds to the three most prominent transcriptional repressive lysine methylation sites. Our data reveal a highly adapted interplay between chromatin marks and their associated protein complexes. Reading specific trimethyl-lysine sites by specialized complexes appears to be a widespread mechanism to mediate gene expression.