Of 38 gastric cancer cell lines, we found that NCI-N87 cells, the basis for most preclinical anti... more Of 38 gastric cancer cell lines, we found that NCI-N87 cells, the basis for most preclinical anti-ERBB2 studies, had the highest ERBB2 expression level. (DOC 152Â kb)
A recent hypothesis for cancer chemoresistance posits that cytotoxic survival of a subpopulation ... more A recent hypothesis for cancer chemoresistance posits that cytotoxic survival of a subpopulation of tumor progenitors drives the propagation of recurrent disease, underscoring the need for new therapeutics that target such primitive cells. To discover such novel compounds active against drug-resistant ovarian cancer, we identified a subset of chemoresistant ovarian tumor cells fulfilling current definitions of cancer-initiating cells from cell lines and patient tumors using multiple stemness phenotypes, including the expression of stem cell markers, membrane dye efflux, sphere formation, potent tumorigenicity, and serial tumor propa-gation. We then subjected such stem-like ovarian tumor-initiating cells (OTIC) to high-throughput drug screening using more than 1,200 clinically approved drugs. Of 61 potential compounds preliminarily identified, more stringent assessments showed that the antihelmintic niclosamide selectively targets OTICs in vitro and in vivo.Gene expression arrays fol...
Previously, we identified Ras homologous A (RHOA) as a major signaling hub in gastric cancer (GC)... more Previously, we identified Ras homologous A (RHOA) as a major signaling hub in gastric cancer (GC), the third most common cause of cancer death in the world, prompting us to rationally design an efficacious inhibitor of this oncogenic GTPase. Here, based on that previous work, we extend those computational analyses to further pharmacologically optimize anti-RHOA hydrazide derivatives for greater anti-GC potency. Two of these, JK-136 and JK-139, potently inhibited cell viability and migration/invasion of GC cell lines, and mouse xenografts, diversely expressing RHOA. Moreover, JK-136′s binding affinity for RHOA was >140-fold greater than Rhosin, a nonclinical RHOA inhibitor. Network analysis of JK-136/-139 vs. Rhosin treatments indicated downregulation of the sphingosine-1-phosphate, as an emerging cancer metabolic pathway in cell migration and motility. We assert that identifying and targeting oncogenic signaling hubs, such as RHOA, represents an emerging strategy for the design, characterization, and translation of new antineoplastics, against gastric and other cancers.
DNA hypermethylation is a driving force in carcinogenesis. However, the role of active DNA hypome... more DNA hypermethylation is a driving force in carcinogenesis. However, the role of active DNA hypomethylation in cancer remains largely unknown. This process, facilitated by ten-eleven translocation methylcytosine dioxygenase 1 (TET1), which oxidizes 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5hmC), has never been studied in cervical cancer. Here, we found that TET1 and 5hmC correlative increases from normal cervix to Low-grade squamous intraepithelial lesion (LSIL), maximizing in High-grade squamous intraepithelial lesion (HSIL), and decreasing in invasive cancer. Full-length HPV-immortalized HSIL cells demonstrated higher TET1/5hmC levels, and stemness properties, compared to invasive cancer cells. TET1 silencing promoted the epithelial-mesenchymal transition (EMT), to transform precancerous cells in vivo. TET1 increased 5hmC in the ZEB1 and VIM promoters, surprisingly, silencing both genes. TET1 interaction with the histone modifiers, LSD1 and EZH2, on the ZEB1 promoter, resulted in gene silencing, via loss of histone H3K4 trimethylation, and gain of histone H3K27 trimethylation. Taken together, TET1 promotes stemness properties, and inhibits EMT, in HSIL cells, through 5hmC-dependent and -independent mechanisms.
License, which permits unrestricted use, distribution, and reproduction in any medium, provided t... more License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A number of empirical Bayes models (each with different statistical distribution assumptions) have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e.g., enrichment of transcription factor-binding sites (TFBSs)), the sensitivity of such analyses, using various empirical Bayes models, remains unclear. In this paper, five empirical Bayes models were constructed, based on either a gamma distribution or a log-normal distribution, for the identification of differential methylated loci and their cell division—(1, 3, and 5) and drug-treatment-
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that regulate differentiation... more Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that regulate differentiation in primordial germ cells, found mainly in the nucleus and cytoplasm. However, despite the essentiality of mitochondria to intrinsic apoptosis and energy metabolism, the presence of piRNAs (and their associated Piwi proteins) in this organelle remains largely unknown. In this study, a public database comparison of mitochondrial RNA-seq data from human normal (HEK293) and cancer (HeLa and 143B) cells revealed the presence of 29 mature piRNA sequences, with 12 of those piRNA sequences perfectly matching 7 tRNAs (Phe, Val, Leu, His, Ser, Glu, and Thr), suggesting piRNAs and tRNAs derive from a common precursor mitochondrial polycistronic transcript. Consistent with their known interaction with piRNAs, further examination revealed the presence of PIWI proteins in mitochondria. Moreover, the majority of the 29 piRNA sequences overlapped multiple longer sequences (expressed sequence tags, ESTs) that uniquely mapped to the mitochondrial genome. To our knowledge, this is the first report of Piwi and piRNAs in the mitochondria of mammalian normal and cancer cells. Citation Format: ChangHyuk Kwon, Hyosun Tak, Mina Rho, Hae Ryung Chang, Yon Hui Km, Kyung Tae Kim, Eun Kyung Lee, Curt Balch, Seungyoon Nam. Detection of PIWI-piRNAS in the mitochondria of human normal and cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 523. doi:10.1158/1538-7445.AM2014-523
IEEE/ACM transactions on computational biology and bioinformatics, Jan 8, 2018
The "guardian of the genome," TP53, is one of the most frequently mutated genes of all ... more The "guardian of the genome," TP53, is one of the most frequently mutated genes of all cancers. Despite the important biological roles of TP53, the clinical relevance of TP53 mutations, in gastric cancer (GC), remains largely unknown. Here, we systematically assessed clinical relevance, in terms of TP53 mutation positions, finding substantial variability. Thus, we hypothesized that the position of the TP53 mutation might affect clinical outcomes in GC. We systematically inspected missense mutations in TP53, from a TCGA (The Cancer Genome Atlas) GC dataset in UCSC Xena repository. Specifically, we examined five aspects of each mutational position: (1) the whole gene body; (2) known hot-spots; (3) the DNA-binding domain; (4) the secondary structure of the domain; and (5) individual mutation positions. We then analyzed the clinical outcomes for each aspect. These results showed that, in terms of secondary structure, patients with mutations in turn regions showed poor prognosi...
Gastric cancer (GC) is a highly heterogeneous disease, in dire need of specific, biomarker-driven... more Gastric cancer (GC) is a highly heterogeneous disease, in dire need of specific, biomarker-driven cancer therapies. While the accumulation of cancer "Big Data" has propelled the search for novel molecular targets for GC, its specific subpathway and cellular functions vary from patient to patient. In particular, mutations in the small GTPase gene RHOA have been identified in recent genome-wide sequencing of GC tumors. Moreover, protein overexpression of RHOA was reported in Chinese populations, while RHOA mutations were found in Caucasian GC tumors. To develop evidence-based precision medicine for heterogeneous cancers, we established a systematic approach to integrate transcriptomic and genomic data. Predicted signaling subpathways were then laboratory-validated both in vitro and in vivo, resulting in the identification of new candidate therapeutic targets. Here, we show: i) differences in RHOA expression patterns, and its pathway activity, between Asian and Caucasian GC t...
Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular ... more Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal cells/bone-marrow derived mesenchymal stem cells (BMSCs) for repairing ischemic, injured tissue. In this study, we systematically evaluated the effects of LPS treatment on genome-wide splicing pattern changes in mouse BMSCs by comparing transcriptome sequencing data from control vs. LPS-treated samples, revealing 197 exons whose BMSC splicing patterns were altered by LPS. Functional analysis of these alternatively spliced genes demonstrated significant enrichment of phosphoproteins, zinc finger proteins, and proteins undergoing acetylation. Additional bioinformatics analysis strongly suggest that LPS-induced alternatively spliced exons could have major effects on protein functions by disrupting key protein functional domains, protein-protein interactions, and post-translational...
Resistance to chemotherapy remains a major impediment to the management of most types of cancer. ... more Resistance to chemotherapy remains a major impediment to the management of most types of cancer. Both intrinsic and acquired drug resistance are mediated by several cellular and molecular mechanisms, including alternative growth-signaling pathways unaffected by specific therapies, alterations in the tumor microenvironment (e.g., hypoxia and angiogenesis), and active transport of drugs out of the cell. Epidemiological studies have validated an inverse correlation between the consumption of dietary polyphenols and the risk of cancer, which has been attributed to polyphenol antioxidant capacity and their potential to inhibit activation of procarcinogens, cancer cell proliferation, metastasis, and angiogenesis, and inhibition or downregulation of active drug efflux transporters. Moreover, polyphenols can induce apoptosis in cancer cells and modulate immune responses and inflammatory cascades. Augmentation of the efficacy of chemotherapy and prevention of multidrug resistance are other important effects of dietary polyphenols that deserve further research, especially after the discovery of tight "crosstalk" between aberrant growth signaling and metabolic dysfunction in cancer cells. In this review, we cover what is currently known about the role of natural polyphenolic compounds in overcoming cancer drug resistance mediated by diverse primary and secondary resistance mechanisms.
Expert opinion on drug metabolism & toxicology, Jan 4, 2016
Expression of the multifunctional ATP-binding cassette (ABC) efflux transporter gene family is a ... more Expression of the multifunctional ATP-binding cassette (ABC) efflux transporter gene family is a well-established mechanism for protecting cancer stem cells (CSCs) from damage or death due to toxins. The outcome of such protection makes CSCs innately multidrug resistant (MDR) to conventional chemotherapy. Areas covered: While research has focused on gaining better insight into the role of ABC transporters in CSC drug resistance, various strategies to circumvent the function of these transporters have been proposed, including inhibition of transporter function through targeted tyrosine kinase inhibitors, competitive and allosteric modulators, shRNA-mediated inhibition, nanoparticle-mediated delivery of inhibitors, and modulating the regulation of transcriptional and signaling pathways involving ABC transporters. This review highlights the role of MDR mediated by ABC transporters, particularly in CSCs, and the current progress and pitfalls of strategies to circumvent MDR in CSCs. Expe...
Of 38 gastric cancer cell lines, we found that NCI-N87 cells, the basis for most preclinical anti... more Of 38 gastric cancer cell lines, we found that NCI-N87 cells, the basis for most preclinical anti-ERBB2 studies, had the highest ERBB2 expression level. (DOC 152Â kb)
A recent hypothesis for cancer chemoresistance posits that cytotoxic survival of a subpopulation ... more A recent hypothesis for cancer chemoresistance posits that cytotoxic survival of a subpopulation of tumor progenitors drives the propagation of recurrent disease, underscoring the need for new therapeutics that target such primitive cells. To discover such novel compounds active against drug-resistant ovarian cancer, we identified a subset of chemoresistant ovarian tumor cells fulfilling current definitions of cancer-initiating cells from cell lines and patient tumors using multiple stemness phenotypes, including the expression of stem cell markers, membrane dye efflux, sphere formation, potent tumorigenicity, and serial tumor propa-gation. We then subjected such stem-like ovarian tumor-initiating cells (OTIC) to high-throughput drug screening using more than 1,200 clinically approved drugs. Of 61 potential compounds preliminarily identified, more stringent assessments showed that the antihelmintic niclosamide selectively targets OTICs in vitro and in vivo.Gene expression arrays fol...
Previously, we identified Ras homologous A (RHOA) as a major signaling hub in gastric cancer (GC)... more Previously, we identified Ras homologous A (RHOA) as a major signaling hub in gastric cancer (GC), the third most common cause of cancer death in the world, prompting us to rationally design an efficacious inhibitor of this oncogenic GTPase. Here, based on that previous work, we extend those computational analyses to further pharmacologically optimize anti-RHOA hydrazide derivatives for greater anti-GC potency. Two of these, JK-136 and JK-139, potently inhibited cell viability and migration/invasion of GC cell lines, and mouse xenografts, diversely expressing RHOA. Moreover, JK-136′s binding affinity for RHOA was >140-fold greater than Rhosin, a nonclinical RHOA inhibitor. Network analysis of JK-136/-139 vs. Rhosin treatments indicated downregulation of the sphingosine-1-phosphate, as an emerging cancer metabolic pathway in cell migration and motility. We assert that identifying and targeting oncogenic signaling hubs, such as RHOA, represents an emerging strategy for the design, characterization, and translation of new antineoplastics, against gastric and other cancers.
DNA hypermethylation is a driving force in carcinogenesis. However, the role of active DNA hypome... more DNA hypermethylation is a driving force in carcinogenesis. However, the role of active DNA hypomethylation in cancer remains largely unknown. This process, facilitated by ten-eleven translocation methylcytosine dioxygenase 1 (TET1), which oxidizes 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5hmC), has never been studied in cervical cancer. Here, we found that TET1 and 5hmC correlative increases from normal cervix to Low-grade squamous intraepithelial lesion (LSIL), maximizing in High-grade squamous intraepithelial lesion (HSIL), and decreasing in invasive cancer. Full-length HPV-immortalized HSIL cells demonstrated higher TET1/5hmC levels, and stemness properties, compared to invasive cancer cells. TET1 silencing promoted the epithelial-mesenchymal transition (EMT), to transform precancerous cells in vivo. TET1 increased 5hmC in the ZEB1 and VIM promoters, surprisingly, silencing both genes. TET1 interaction with the histone modifiers, LSD1 and EZH2, on the ZEB1 promoter, resulted in gene silencing, via loss of histone H3K4 trimethylation, and gain of histone H3K27 trimethylation. Taken together, TET1 promotes stemness properties, and inhibits EMT, in HSIL cells, through 5hmC-dependent and -independent mechanisms.
License, which permits unrestricted use, distribution, and reproduction in any medium, provided t... more License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A number of empirical Bayes models (each with different statistical distribution assumptions) have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e.g., enrichment of transcription factor-binding sites (TFBSs)), the sensitivity of such analyses, using various empirical Bayes models, remains unclear. In this paper, five empirical Bayes models were constructed, based on either a gamma distribution or a log-normal distribution, for the identification of differential methylated loci and their cell division—(1, 3, and 5) and drug-treatment-
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that regulate differentiation... more Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that regulate differentiation in primordial germ cells, found mainly in the nucleus and cytoplasm. However, despite the essentiality of mitochondria to intrinsic apoptosis and energy metabolism, the presence of piRNAs (and their associated Piwi proteins) in this organelle remains largely unknown. In this study, a public database comparison of mitochondrial RNA-seq data from human normal (HEK293) and cancer (HeLa and 143B) cells revealed the presence of 29 mature piRNA sequences, with 12 of those piRNA sequences perfectly matching 7 tRNAs (Phe, Val, Leu, His, Ser, Glu, and Thr), suggesting piRNAs and tRNAs derive from a common precursor mitochondrial polycistronic transcript. Consistent with their known interaction with piRNAs, further examination revealed the presence of PIWI proteins in mitochondria. Moreover, the majority of the 29 piRNA sequences overlapped multiple longer sequences (expressed sequence tags, ESTs) that uniquely mapped to the mitochondrial genome. To our knowledge, this is the first report of Piwi and piRNAs in the mitochondria of mammalian normal and cancer cells. Citation Format: ChangHyuk Kwon, Hyosun Tak, Mina Rho, Hae Ryung Chang, Yon Hui Km, Kyung Tae Kim, Eun Kyung Lee, Curt Balch, Seungyoon Nam. Detection of PIWI-piRNAS in the mitochondria of human normal and cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 523. doi:10.1158/1538-7445.AM2014-523
IEEE/ACM transactions on computational biology and bioinformatics, Jan 8, 2018
The "guardian of the genome," TP53, is one of the most frequently mutated genes of all ... more The "guardian of the genome," TP53, is one of the most frequently mutated genes of all cancers. Despite the important biological roles of TP53, the clinical relevance of TP53 mutations, in gastric cancer (GC), remains largely unknown. Here, we systematically assessed clinical relevance, in terms of TP53 mutation positions, finding substantial variability. Thus, we hypothesized that the position of the TP53 mutation might affect clinical outcomes in GC. We systematically inspected missense mutations in TP53, from a TCGA (The Cancer Genome Atlas) GC dataset in UCSC Xena repository. Specifically, we examined five aspects of each mutational position: (1) the whole gene body; (2) known hot-spots; (3) the DNA-binding domain; (4) the secondary structure of the domain; and (5) individual mutation positions. We then analyzed the clinical outcomes for each aspect. These results showed that, in terms of secondary structure, patients with mutations in turn regions showed poor prognosi...
Gastric cancer (GC) is a highly heterogeneous disease, in dire need of specific, biomarker-driven... more Gastric cancer (GC) is a highly heterogeneous disease, in dire need of specific, biomarker-driven cancer therapies. While the accumulation of cancer "Big Data" has propelled the search for novel molecular targets for GC, its specific subpathway and cellular functions vary from patient to patient. In particular, mutations in the small GTPase gene RHOA have been identified in recent genome-wide sequencing of GC tumors. Moreover, protein overexpression of RHOA was reported in Chinese populations, while RHOA mutations were found in Caucasian GC tumors. To develop evidence-based precision medicine for heterogeneous cancers, we established a systematic approach to integrate transcriptomic and genomic data. Predicted signaling subpathways were then laboratory-validated both in vitro and in vivo, resulting in the identification of new candidate therapeutic targets. Here, we show: i) differences in RHOA expression patterns, and its pathway activity, between Asian and Caucasian GC t...
Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular ... more Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal cells/bone-marrow derived mesenchymal stem cells (BMSCs) for repairing ischemic, injured tissue. In this study, we systematically evaluated the effects of LPS treatment on genome-wide splicing pattern changes in mouse BMSCs by comparing transcriptome sequencing data from control vs. LPS-treated samples, revealing 197 exons whose BMSC splicing patterns were altered by LPS. Functional analysis of these alternatively spliced genes demonstrated significant enrichment of phosphoproteins, zinc finger proteins, and proteins undergoing acetylation. Additional bioinformatics analysis strongly suggest that LPS-induced alternatively spliced exons could have major effects on protein functions by disrupting key protein functional domains, protein-protein interactions, and post-translational...
Resistance to chemotherapy remains a major impediment to the management of most types of cancer. ... more Resistance to chemotherapy remains a major impediment to the management of most types of cancer. Both intrinsic and acquired drug resistance are mediated by several cellular and molecular mechanisms, including alternative growth-signaling pathways unaffected by specific therapies, alterations in the tumor microenvironment (e.g., hypoxia and angiogenesis), and active transport of drugs out of the cell. Epidemiological studies have validated an inverse correlation between the consumption of dietary polyphenols and the risk of cancer, which has been attributed to polyphenol antioxidant capacity and their potential to inhibit activation of procarcinogens, cancer cell proliferation, metastasis, and angiogenesis, and inhibition or downregulation of active drug efflux transporters. Moreover, polyphenols can induce apoptosis in cancer cells and modulate immune responses and inflammatory cascades. Augmentation of the efficacy of chemotherapy and prevention of multidrug resistance are other important effects of dietary polyphenols that deserve further research, especially after the discovery of tight "crosstalk" between aberrant growth signaling and metabolic dysfunction in cancer cells. In this review, we cover what is currently known about the role of natural polyphenolic compounds in overcoming cancer drug resistance mediated by diverse primary and secondary resistance mechanisms.
Expert opinion on drug metabolism & toxicology, Jan 4, 2016
Expression of the multifunctional ATP-binding cassette (ABC) efflux transporter gene family is a ... more Expression of the multifunctional ATP-binding cassette (ABC) efflux transporter gene family is a well-established mechanism for protecting cancer stem cells (CSCs) from damage or death due to toxins. The outcome of such protection makes CSCs innately multidrug resistant (MDR) to conventional chemotherapy. Areas covered: While research has focused on gaining better insight into the role of ABC transporters in CSC drug resistance, various strategies to circumvent the function of these transporters have been proposed, including inhibition of transporter function through targeted tyrosine kinase inhibitors, competitive and allosteric modulators, shRNA-mediated inhibition, nanoparticle-mediated delivery of inhibitors, and modulating the regulation of transcriptional and signaling pathways involving ABC transporters. This review highlights the role of MDR mediated by ABC transporters, particularly in CSCs, and the current progress and pitfalls of strategies to circumvent MDR in CSCs. Expe...
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