Deoxyadenosine has been implicated in the lymphocytopenia that occurs in immunodeficient children... more Deoxyadenosine has been implicated in the lymphocytopenia that occurs in immunodeficient children with an inherited deficiency of adenosine deaminase (ADA) and in leukemic patients treated with the ADA inhibitor deoxycoformycin. The recent reports of deoxyadenosine toxicity to nondividing lymphocytes indicates a challenge to the mechanism for deoxyadenosine toxicity, which involves the inhibition of ribonucleotide reductase by dATP, leading to the inhibition of DNA synthesis. This study provides evidence for the inhibition of transcription by deoxyadenosine as an alternative mechanism of toxicity. The incubation of resting peripheral blood lymphocytes with deoxyadenosine plus deoxycoformycin led to an inhibition of uridine incorporation. The extent of inhibition increased with the increasing time of incubation and concentration of deoxyadenosine. Replacement of deoxyadenosine with other nucleosides, adenosine or deoxyguanosine, had no effect, suggesting that deoxyadenosine-induced i...
BackgroundOral cavity squamous cell carcinoma (OSCC) is an aggressive malignant tumor with high r... more BackgroundOral cavity squamous cell carcinoma (OSCC) is an aggressive malignant tumor with high recurrence and poor prognosis in the advanced stage. Patient-derived xenografts (PDXs) serve as powerful preclinical platforms for drug testing and precision medicine for cancer therapy. We assess which molecular signatures affect tumor engraftment ability and tumor growth rate in OSCC PDXs.MethodsTreatment-naïve OSCC primary tumors were collected for PDX models establishment. Comprehensive genomic analysis, including whole-exome sequencing and RNA-seq, was performed on case-matched tumors and PDXs. Regulatory genes/pathways were analyzed to clarify which molecular signatures affect tumor engraftment ability and the tumor growth rate in OSCC PDXs.ResultsPerineural invasion was found as an important pathological feature related to engraftment ability. Tumor microenvironment with enriched hypoxia, PI3K-Akt, and epithelial–mesenchymal transition pathways and decreased inflammatory responses ...
Background The comparative evolutionary genomics analysis was used to study the functions of nove... more Background The comparative evolutionary genomics analysis was used to study the functions of novel Ka/Ks-predicted human exons in a zebrafish model. The Yulink (MIOS, Entrez Gene: 54,468), a conserved gene from zebrafish to human with WD40 repeats at N-terminus, was identified and found to encode an 875 amino acid in human. The biological function of this Yulink gene in cardiomyocytes remains unexplored. The purpose of this study is to determine the involvement of Yulink in the functions of cardiomyocytes and to investigate its molecular regulatory mechanism. Methods Knockdown of Yulink was performed using morpholino or shRNA in zebrafish, mouse HL-1 cardiomyocytes, and human iPSC-derived cardiomyocytes. The expression levels of mRNA and protein were quantified by qPCR and western blots. Other methods including DNA binding, ligand uptake, agonists treatment and Ca2+ imaging assays were used to study the molecular regulatory mechanism by Yulink. Statistical data were shown as mean ± ...
Anti-cancer glyco-peptides inhibit the thrombin-protease activated receptor-1 interaction in exos... more Anti-cancer glyco-peptides inhibit the thrombin-protease activated receptor-1 interaction in exosite I without affecting the active-site mediated coagulation activity.
Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects... more Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior m...
In this study, a simple type ofO-6 analogue of KRN7000 was synthesized starting from galactosyl i... more In this study, a simple type ofO-6 analogue of KRN7000 was synthesized starting from galactosyl iodide andd-lyxose.
Proceedings of the National Academy of Sciences, 2008
H5N1 influenza viruses have spread extensively among wild birds and domestic poultry. Cross-speci... more H5N1 influenza viruses have spread extensively among wild birds and domestic poultry. Cross-species transmission of these viruses to humans has been documented in over 380 cases, with a mortality rate of ≈60%. There is great concern that a H5N1 virus would acquire the ability to spread efficiently between humans, thereby becoming a pandemic threat. An H5N1 influenza vaccine must, therefore, be an integral part of any pandemic preparedness plan. However, traditional methods of making influenza vaccines have yet to produce a candidate that could induce potently neutralizing antibodies against divergent strains of H5N1 influenza viruses. To address this need, we generated a consensus H5N1 hemagglutinin (HA) sequence based on data available in early 2006. This sequence was then optimized for protein expression before being inserted into a DNA plasmid (pCHA5). Immunizing mice with pCHA5, delivered intramuscularly via electroporation, elicited antibodies that neutralized a panel of virion...
Proceedings of the National Academy of Sciences, 2006
In this study, we report a serum-free culture system for primary neonatal pulmonary cells that ca... more In this study, we report a serum-free culture system for primary neonatal pulmonary cells that can support the growth of octamer-binding transcription factor 4 + (Oct-4 + ) epithelial colonies with a surrounding mesenchymal stroma. In addition to Oct-4, these cells also express other stem cell markers such as stage-specific embryonic antigen 1 (SSEA-1), stem cell antigen 1 (Sca-1), and Clara cell secretion protein (CCSP) but not c-Kit, CD34, and p63, indicating that they represent a subpopulation of Clara cells that have been implicated as lung stem/progenitor cells in lung injury models. These colony cells can be kept for weeks in primary cultures and undergo terminal differentiation to alveolar type-2- and type-1-like pneumocytes sequentially when removed from the stroma. In addition, we have demonstrated the presence of Oct-4 + long-term BrdU label-retaining cells at the bronchoalveolar junction of neonatal lung, providing a link between the Oct-4 + cells in vivo and in vitro and...
Purpose: In 2010, a Children's Oncology Group (COG) phase III randomized trial for patients w... more Purpose: In 2010, a Children's Oncology Group (COG) phase III randomized trial for patients with high-risk neuroblastoma (ANBL0032) demonstrated improved event-free survival (EFS) and overall survival (OS) following treatment with an immunotherapy regimen of dinutuximab, GM-CSF, IL2, and isotretinoin compared with treatment with isotretinoin alone. Dinutuximab, a chimeric anti-GD2 monoclonal antibody, acts in part via natural killer (NK) cells. Killer immunoglobulin-like receptors (KIR) on NK cells and their interactions with KIR-ligands can influence NK cell function. We investigated whether KIR/KIR-ligand genotypes were associated with EFS or OS in this trial.Experimental Design: We genotyped patients from COG study ANBL0032 and evaluated the effect of KIR/KIR-ligand genotypes on clinical outcomes. Cox regression models and log-rank tests were used to evaluate associations of EFS and OS with KIR/KIR-ligand genotypes.Results: In this trial, patients with the “all KIR-ligands pr...
Background In endothelial cells, phospholipase C (PLC) β1-activated Ca2+ is a crucial second mess... more Background In endothelial cells, phospholipase C (PLC) β1-activated Ca2+ is a crucial second messenger for the signaling pathways governing angiogenesis. PLCβ1 is inactivated by complexing with an intracellular protein called translin-associated factor X (TRAX). This study demonstrates specific interactions between Globo H ceramide (GHCer) and TRAX, which highlight a new angiogenic control through PLCβ1 activation. Methods Globo-series glycosphingolipids (GSLs), including GHCer and stage-specific embryonic antigen-3 ceramide (SSEA3Cer), were analyzed using enzyme-linked immunosorbent assay (ELISA) and Biacore for their binding with TRAX. Angiogenic activities of GSLs in human umbilical vein endothelial cells (HUVECs) were evaluated. Molecular dynamics (MD) simulation was used to study conformations of GSLs and their molecular interactions with TRAX. Fluorescence resonance energy transfer (FRET) analysis of HUVECs by confocal microscopy was used to validate the release of PLCβ1 from ...
Thymus leukemia antigens and H-2a antigens were released in soluble form from ASL-1 leukemia cell... more Thymus leukemia antigens and H-2a antigens were released in soluble form from ASL-1 leukemia cells (H-2a; TL 1,2,3) during extraction with the nonionic detergent, NP-40. They were isolated by immunoprecipitation with specific antisera and rabbit anti-mouse IgG. Specific antigens were obtained by the procedure because: 1) increasing radioactivity in immunoprecipitates of the NP-40 extracts of 3H-fucose or 125I-labeled ASL-1 cells was obtained with increasing amounts of H-2a or TL 1,3 antisera, but no significant amounts of radioactivity above control precipitates were detected in extracts incubated with H-2b antiserum; 2) the complete removal of TL antigens from the NP-40 extract of ASL-1 cells by immunoprecipitation with excess TL antisera had little effect upon the subsequent immunoprecipitation of H-2a antisera; 3) immunoprecipitates of NP-40 extracts of ASL-1 cells with H-2a antisera yielded one radioactive peak on acrylamide gel electrophoresis whereas the control immunoprecipit...
Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer pr... more Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)–tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer; however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermo...
Previously, we identified Puf-A as a novel member of Puf-family RNA-binding proteins; however, it... more Previously, we identified Puf-A as a novel member of Puf-family RNA-binding proteins; however, its biological functions remain obscure. Analysis of tumor samples of non-small cell lung cancer (NSCLC) showed that high Puf-A expression correlated with high histology grade and abnormal p53 status. Kaplan–Meier curve for overall survival revealed high expression of Puf-A to predict poor prognosis in stage I NSCLC. Among patients with colorectal cancer, high Puf-A expression also showed an adverse impact on overall survival. In lung cancer cell lines, downregulation of p53 increased Puf-A expression, and upregulation of p53 dampened its expression. However, luciferase reporter assays indicated that PUF-A locus harbored the p53-response element, but regulated Puf-A transcription indirectly. In vivo suppression of p53 in CCSP-rtTA/TetO-Cre/LSL-KrasG12D/p53flox/flox conditional mutant mice accelerated the progression of the KrasG12D-driven lung cancer, along with enhanced expression of Puf-...
Deoxyadenosine has been implicated in the lymphocytopenia that occurs in immunodeficient children... more Deoxyadenosine has been implicated in the lymphocytopenia that occurs in immunodeficient children with an inherited deficiency of adenosine deaminase (ADA) and in leukemic patients treated with the ADA inhibitor deoxycoformycin. The recent reports of deoxyadenosine toxicity to nondividing lymphocytes indicates a challenge to the mechanism for deoxyadenosine toxicity, which involves the inhibition of ribonucleotide reductase by dATP, leading to the inhibition of DNA synthesis. This study provides evidence for the inhibition of transcription by deoxyadenosine as an alternative mechanism of toxicity. The incubation of resting peripheral blood lymphocytes with deoxyadenosine plus deoxycoformycin led to an inhibition of uridine incorporation. The extent of inhibition increased with the increasing time of incubation and concentration of deoxyadenosine. Replacement of deoxyadenosine with other nucleosides, adenosine or deoxyguanosine, had no effect, suggesting that deoxyadenosine-induced i...
BackgroundOral cavity squamous cell carcinoma (OSCC) is an aggressive malignant tumor with high r... more BackgroundOral cavity squamous cell carcinoma (OSCC) is an aggressive malignant tumor with high recurrence and poor prognosis in the advanced stage. Patient-derived xenografts (PDXs) serve as powerful preclinical platforms for drug testing and precision medicine for cancer therapy. We assess which molecular signatures affect tumor engraftment ability and tumor growth rate in OSCC PDXs.MethodsTreatment-naïve OSCC primary tumors were collected for PDX models establishment. Comprehensive genomic analysis, including whole-exome sequencing and RNA-seq, was performed on case-matched tumors and PDXs. Regulatory genes/pathways were analyzed to clarify which molecular signatures affect tumor engraftment ability and the tumor growth rate in OSCC PDXs.ResultsPerineural invasion was found as an important pathological feature related to engraftment ability. Tumor microenvironment with enriched hypoxia, PI3K-Akt, and epithelial–mesenchymal transition pathways and decreased inflammatory responses ...
Background The comparative evolutionary genomics analysis was used to study the functions of nove... more Background The comparative evolutionary genomics analysis was used to study the functions of novel Ka/Ks-predicted human exons in a zebrafish model. The Yulink (MIOS, Entrez Gene: 54,468), a conserved gene from zebrafish to human with WD40 repeats at N-terminus, was identified and found to encode an 875 amino acid in human. The biological function of this Yulink gene in cardiomyocytes remains unexplored. The purpose of this study is to determine the involvement of Yulink in the functions of cardiomyocytes and to investigate its molecular regulatory mechanism. Methods Knockdown of Yulink was performed using morpholino or shRNA in zebrafish, mouse HL-1 cardiomyocytes, and human iPSC-derived cardiomyocytes. The expression levels of mRNA and protein were quantified by qPCR and western blots. Other methods including DNA binding, ligand uptake, agonists treatment and Ca2+ imaging assays were used to study the molecular regulatory mechanism by Yulink. Statistical data were shown as mean ± ...
Anti-cancer glyco-peptides inhibit the thrombin-protease activated receptor-1 interaction in exos... more Anti-cancer glyco-peptides inhibit the thrombin-protease activated receptor-1 interaction in exosite I without affecting the active-site mediated coagulation activity.
Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects... more Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior m...
In this study, a simple type ofO-6 analogue of KRN7000 was synthesized starting from galactosyl i... more In this study, a simple type ofO-6 analogue of KRN7000 was synthesized starting from galactosyl iodide andd-lyxose.
Proceedings of the National Academy of Sciences, 2008
H5N1 influenza viruses have spread extensively among wild birds and domestic poultry. Cross-speci... more H5N1 influenza viruses have spread extensively among wild birds and domestic poultry. Cross-species transmission of these viruses to humans has been documented in over 380 cases, with a mortality rate of ≈60%. There is great concern that a H5N1 virus would acquire the ability to spread efficiently between humans, thereby becoming a pandemic threat. An H5N1 influenza vaccine must, therefore, be an integral part of any pandemic preparedness plan. However, traditional methods of making influenza vaccines have yet to produce a candidate that could induce potently neutralizing antibodies against divergent strains of H5N1 influenza viruses. To address this need, we generated a consensus H5N1 hemagglutinin (HA) sequence based on data available in early 2006. This sequence was then optimized for protein expression before being inserted into a DNA plasmid (pCHA5). Immunizing mice with pCHA5, delivered intramuscularly via electroporation, elicited antibodies that neutralized a panel of virion...
Proceedings of the National Academy of Sciences, 2006
In this study, we report a serum-free culture system for primary neonatal pulmonary cells that ca... more In this study, we report a serum-free culture system for primary neonatal pulmonary cells that can support the growth of octamer-binding transcription factor 4 + (Oct-4 + ) epithelial colonies with a surrounding mesenchymal stroma. In addition to Oct-4, these cells also express other stem cell markers such as stage-specific embryonic antigen 1 (SSEA-1), stem cell antigen 1 (Sca-1), and Clara cell secretion protein (CCSP) but not c-Kit, CD34, and p63, indicating that they represent a subpopulation of Clara cells that have been implicated as lung stem/progenitor cells in lung injury models. These colony cells can be kept for weeks in primary cultures and undergo terminal differentiation to alveolar type-2- and type-1-like pneumocytes sequentially when removed from the stroma. In addition, we have demonstrated the presence of Oct-4 + long-term BrdU label-retaining cells at the bronchoalveolar junction of neonatal lung, providing a link between the Oct-4 + cells in vivo and in vitro and...
Purpose: In 2010, a Children's Oncology Group (COG) phase III randomized trial for patients w... more Purpose: In 2010, a Children's Oncology Group (COG) phase III randomized trial for patients with high-risk neuroblastoma (ANBL0032) demonstrated improved event-free survival (EFS) and overall survival (OS) following treatment with an immunotherapy regimen of dinutuximab, GM-CSF, IL2, and isotretinoin compared with treatment with isotretinoin alone. Dinutuximab, a chimeric anti-GD2 monoclonal antibody, acts in part via natural killer (NK) cells. Killer immunoglobulin-like receptors (KIR) on NK cells and their interactions with KIR-ligands can influence NK cell function. We investigated whether KIR/KIR-ligand genotypes were associated with EFS or OS in this trial.Experimental Design: We genotyped patients from COG study ANBL0032 and evaluated the effect of KIR/KIR-ligand genotypes on clinical outcomes. Cox regression models and log-rank tests were used to evaluate associations of EFS and OS with KIR/KIR-ligand genotypes.Results: In this trial, patients with the “all KIR-ligands pr...
Background In endothelial cells, phospholipase C (PLC) β1-activated Ca2+ is a crucial second mess... more Background In endothelial cells, phospholipase C (PLC) β1-activated Ca2+ is a crucial second messenger for the signaling pathways governing angiogenesis. PLCβ1 is inactivated by complexing with an intracellular protein called translin-associated factor X (TRAX). This study demonstrates specific interactions between Globo H ceramide (GHCer) and TRAX, which highlight a new angiogenic control through PLCβ1 activation. Methods Globo-series glycosphingolipids (GSLs), including GHCer and stage-specific embryonic antigen-3 ceramide (SSEA3Cer), were analyzed using enzyme-linked immunosorbent assay (ELISA) and Biacore for their binding with TRAX. Angiogenic activities of GSLs in human umbilical vein endothelial cells (HUVECs) were evaluated. Molecular dynamics (MD) simulation was used to study conformations of GSLs and their molecular interactions with TRAX. Fluorescence resonance energy transfer (FRET) analysis of HUVECs by confocal microscopy was used to validate the release of PLCβ1 from ...
Thymus leukemia antigens and H-2a antigens were released in soluble form from ASL-1 leukemia cell... more Thymus leukemia antigens and H-2a antigens were released in soluble form from ASL-1 leukemia cells (H-2a; TL 1,2,3) during extraction with the nonionic detergent, NP-40. They were isolated by immunoprecipitation with specific antisera and rabbit anti-mouse IgG. Specific antigens were obtained by the procedure because: 1) increasing radioactivity in immunoprecipitates of the NP-40 extracts of 3H-fucose or 125I-labeled ASL-1 cells was obtained with increasing amounts of H-2a or TL 1,3 antisera, but no significant amounts of radioactivity above control precipitates were detected in extracts incubated with H-2b antiserum; 2) the complete removal of TL antigens from the NP-40 extract of ASL-1 cells by immunoprecipitation with excess TL antisera had little effect upon the subsequent immunoprecipitation of H-2a antisera; 3) immunoprecipitates of NP-40 extracts of ASL-1 cells with H-2a antisera yielded one radioactive peak on acrylamide gel electrophoresis whereas the control immunoprecipit...
Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer pr... more Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)–tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer; however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermo...
Previously, we identified Puf-A as a novel member of Puf-family RNA-binding proteins; however, it... more Previously, we identified Puf-A as a novel member of Puf-family RNA-binding proteins; however, its biological functions remain obscure. Analysis of tumor samples of non-small cell lung cancer (NSCLC) showed that high Puf-A expression correlated with high histology grade and abnormal p53 status. Kaplan–Meier curve for overall survival revealed high expression of Puf-A to predict poor prognosis in stage I NSCLC. Among patients with colorectal cancer, high Puf-A expression also showed an adverse impact on overall survival. In lung cancer cell lines, downregulation of p53 increased Puf-A expression, and upregulation of p53 dampened its expression. However, luciferase reporter assays indicated that PUF-A locus harbored the p53-response element, but regulated Puf-A transcription indirectly. In vivo suppression of p53 in CCSP-rtTA/TetO-Cre/LSL-KrasG12D/p53flox/flox conditional mutant mice accelerated the progression of the KrasG12D-driven lung cancer, along with enhanced expression of Puf-...
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