Publications by authors named "Kyu-Tae Kim"

41 Publications

Comparison of the Radiologic, Morphometric, and Clinical Outcomes between Kinematically and Mechanically Aligned Total Knee Arthroplasty: A Propensity Matching Study.

J Knee Surg 2021 Mar 3. Epub 2021 Mar 3.

Department of Orthopedic Surgery, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, The Republic of Korea.

The purpose of this study was to compare radiologic, morphometric, and clinical outcomes between kinematically aligned (KA) and mechanically aligned (MA) total knee arthroplasty (TKA) in Korean patients. Overall, 168 patients who underwent primary TKA were retrospectively reviewed, and propensity matching (age, sex, and body mass index) was performed as 1:3 ration (KA TKAs [ = 42]: MA TKAs [ = 126]). Joint-line orientation angle (JLOA), coronal and axial alignments of implants, hip-knee-ankle (HKA) angle, and patellar tilt angle were assessed using full-length standing radiograph, axial computed tomography (CT) scan, and plain radiographs. Morphometric assessment was performed by analyzing the intraoperative measurement of the femoral cut surface and femoral components fitting in five zones. Clinical outcomes more than 2 years of follow-up were evaluated with the Knee Society (KS) knee and functional scores, Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores, and the Short-Form Health Survey (SF-36). In radiologic results, JLOA was more parallel to the floor in KA TKAs (KA: medial tilt 0.9 ± 1.5 degrees; MA: lateral tilt 1.7 ± 1.5 degrees, < 0.05), and patellar tilt angle was closer to preoperative status after KA TKA (KA: 2.0 ± 1.6 degrees; MA;0.3 ± 1.2 degrees, < 0.05). HKA angle and rotational mismatch were similar between two groups. In morphometric analysis, entire overhang of anterior femoral cutting surface was reduced in KA TKA compared with MA TKA (KA: 11.7 ± 6.2 mm; MA: 14.4 ± 5.9 mm, < 0.05). However, both of MA and KA TKAs showed underhang in mediolateral dimension without difference. There were no significant differences in clinical scores between two groups. KA TKA showed more parallel JLOA to floor, closer patellar tilt to preoperative status, and better anterior flange fitting that can reproduce more natural knee kinematics compared with MA TKA. Although clinical outcomes assessed by conventional evaluating tools were similar between two groups, further evaluation focusing on the patellofemoral symptoms or unawareness of TKA is necessary to clarify the clinical benefit of KA TKA.
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http://dx.doi.org/10.1055/s-0041-1725006DOI Listing
March 2021

DNA methylation disruption reshapes the hematopoietic differentiation landscape.

Nat Genet 2020 04 23;52(4):378-387. Epub 2020 Mar 23.

New York Genome Center, New York, NY, USA.

Mutations in genes involved in DNA methylation (DNAme; for example, TET2 and DNMT3A) are frequently observed in hematological malignancies and clonal hematopoiesis. Applying single-cell sequencing to murine hematopoietic stem and progenitor cells, we observed that these mutations disrupt hematopoietic differentiation, causing opposite shifts in the frequencies of erythroid versus myelomonocytic progenitors following Tet2 or Dnmt3a loss. Notably, these shifts trace back to transcriptional priming skews in uncommitted hematopoietic stem cells. To reconcile genome-wide DNAme changes with specific erythroid versus myelomonocytic skews, we provide evidence in support of differential sensitivity of transcription factors due to biases in CpG enrichment in their binding motif. Single-cell transcriptomes with targeted genotyping showed similar skews in transcriptional priming of DNMT3A-mutated human clonal hematopoiesis bone marrow progenitors. These data show that DNAme shapes the topography of hematopoietic differentiation, and support a model in which genome-wide methylation changes are transduced to differentiation skews through biases in CpG enrichment of the transcription factor binding motif.
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http://dx.doi.org/10.1038/s41588-020-0595-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216752PMC
April 2020

Mutual synchronization of two flame-driven thermoacoustic oscillators: Dissipative and time-delayed coupling effects.

Chaos 2020 Feb;30(2):023110

Department of Aerospace Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea.

Low-emissions can-annular gas turbines are prone to develop low-frequency self-excited thermoacoustic oscillations. Such oscillations arise from the coupling between adjacent combustors and can increase wear and thermal stresses. In this experimental study, we explore the mutual synchronization of two thermoacoustic oscillators (i.e., two model combustors) interacting via dissipative and time-delayed coupling, as introduced via a cross-talk section. Unlike most previous studies, our study makes use of a turbulent lean-premixed flame in each combustor, bringing the system configuration closer to that of practical gas turbines. Using stationary and transient measurements, we examine the effect of the cross-talk diameter and length so as to gain insight into the effect of dissipative and time-delayed coupling. We find that strengthening the dissipative coupling promotes mutual synchronization, but that weakening the dissipative coupling leads to weakly coupled or desynchronized oscillations. On operating the two combustors at different conditions, we find a significant reduction in their overall oscillation amplitude for some coupling conditions. On varying the combustor length and examining the transient response, we find elaborate changes in the pressure-heat-release-rate coupling, spontaneous mode transitions between coupled thermoacoustic modes, and the emergence of a rhomboid structure in the phase plane owing to the coexistence of in-phase and out-of-phase synchronization. In the combustion community, these two types of synchronization are known to be associated with push-push modes and push-pull modes. These findings offer new insight into the mutual synchronization of low-frequency, self-excited thermoacoustic oscillations in can-annular gas turbines, paving the way for the development of improved control strategies.
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http://dx.doi.org/10.1063/1.5126765DOI Listing
February 2020

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation.

Genome Biol 2019 11 21;20(1):248. Epub 2019 Nov 21.

New York University Langone Health, New York, NY, USA.

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.
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http://dx.doi.org/10.1186/s13059-019-1853-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868874PMC
November 2019

Impedance spectroscopy for in situ and real-time observations of the effects of hydrogen on nitrile butadiene rubber polymer under high pressure.

Sci Rep 2019 Sep 10;9(1):13035. Epub 2019 Sep 10.

Department of Physics, and The Research Institute of Natural Science, Gyeongsang National University, Jinju, 52828, Korea.

Nondestructive impedance spectroscopy (IS) was developed and demonstrated to detect the effects of hydrogen on nitrile butadiene rubber exposed to hydrogen gas (H) at high pressures up to 10 MPa. IS was applied to obtain an in situ and real-time quantification of H penetration into and its desorption out of rubber under high pressure. The diffusion coefficients of H were also obtained from the time evolution of the capacitance, which were compared with those obtained by thermal desorption gas analysis. The in situ measurements of the capacitance and the dissipation factor under various pressures during cyclic stepwise pressurization and decompression demonstrated the diffusion behaviour of H, the phase of the rubber under high pressure, the transport properties of H gas, and the physicochemical interaction between H and the rubber. These phenomena were supported by a COMSOL simulation based on the electric current conservation equation and scanning electron microscopy (SEM) observations.
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http://dx.doi.org/10.1038/s41598-019-49692-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736861PMC
September 2019

Somatic mutations and cell identity linked by Genotyping of Transcriptomes.

Nature 2019 07 3;571(7765):355-360. Epub 2019 Jul 3.

New York Genome Center, New York, NY, USA.

Defining the transcriptomic identity of malignant cells is challenging in the absence of surface markers that distinguish cancer clones from one another, or from admixed non-neoplastic cells. To address this challenge, here we developed Genotyping of Transcriptomes (GoT), a method to integrate genotyping with high-throughput droplet-based single-cell RNA sequencing. We apply GoT to profile 38,290 CD34 cells from patients with CALR-mutated myeloproliferative neoplasms to study how somatic mutations corrupt the complex process of human haematopoiesis. High-resolution mapping of malignant versus normal haematopoietic progenitors revealed an increasing fitness advantage with myeloid differentiation of cells with mutated CALR. We identified the unfolded protein response as a predominant outcome of CALR mutations, with a considerable dependency on cell identity, as well as upregulation of the NF-κB pathway specifically in uncommitted stem cells. We further extended the GoT toolkit to genotype multiple targets and loci that are distant from transcript ends. Together, these findings reveal that the transcriptional output of somatic mutations in myeloproliferative neoplasms is dependent on the native cell identity.
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http://dx.doi.org/10.1038/s41586-019-1367-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782071PMC
July 2019

Chaos, synchronization, and desynchronization in a liquid-fueled diffusion-flame combustor with an intrinsic hydrodynamic mode.

Chaos 2019 May;29(5):053124

Department of Aerospace Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.

We experimentally investigate the nonlinear dynamics of a thermoacoustically self-excited aero-engine combustion system featuring a turbulent swirling liquid-fueled diffusion flame in a variable-length combustor. We focus on the steady-state dynamics via simultaneous measurements of the acoustic pressure in the combustor and the heat release rate (HRR) from the flame. When the combustor length is increased following the onset of thermoacoustic instability, we find that the pressure signal transitions from a period-1 limit cycle to chaos, whereas the HRR signal remains chaotic owing to the presence of an intrinsic hydrodynamic mode in the flame. When the hydrodynamic mode is filtered out of the data, we find that the pressure and HRR signals are in generalized synchronization. However, when the hydrodynamic mode is retained in the data, we find that the pressure and HRR signals are either weakly phase synchronized or desynchronized. This study has two main contributions: (i) it shows that a liquid-fueled diffusion-flame combustor can exhibit dynamics as complex as those of its gaseous-fueled premixed-flame counterparts and (ii) it highlights the need to be exceptionally careful when selecting a diagnostic signal from which to calculate nonlinear measures of self-excited thermoacoustic oscillations, because our experiments show that the pressure and HRR signals can be desynchronized by the presence of a hydrodynamic mode in the flame at a frequency different from that of the dominant thermoacoustic mode.
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http://dx.doi.org/10.1063/1.5088735DOI Listing
May 2019

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia.

Nature 2019 05 15;569(7757):576-580. Epub 2019 May 15.

New York Genome Center, New York, NY, USA.

Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy. The CLL epigenome is also an important disease-defining feature, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy.
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http://dx.doi.org/10.1038/s41586-019-1198-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533116PMC
May 2019

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL.

Nat Commun 2019 04 23;10(1):1874. Epub 2019 Apr 23.

New York Genome Center, New York, 10013, NY, USA.

Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively study the epigenetic dimension of cancer evolution, we integrate DNAme analysis with histone modification mapping and single cell analyses of RNA expression and DNAme in 22 primary CLL and 13 healthy donor B lymphocyte samples. Our data reveal corrupted coherence across different layers of the CLL epigenome. This manifests in decreased mutual information across epigenetic modifications and gene expression attributed to cell-to-cell heterogeneity. Disrupted epigenetic-transcriptional coordination in CLL is also reflected in the dysregulation of the transcriptional output as a function of the combinatorial chromatin states, including incomplete Polycomb-mediated gene silencing. Notably, we observe unexpected co-mapping of typically mutually exclusive activating and repressing histone modifications, suggestive of intra-tumoral epigenetic diversity. Thus, CLL epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging cellular identities.
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http://dx.doi.org/10.1038/s41467-019-09645-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478836PMC
April 2019

Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator.

Sci Rep 2019 03 14;9(1):4542. Epub 2019 Mar 14.

Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.

Tumor genetic heterogeneity may underlie poor clinical outcomes because diverse subclones could be comprised of metastatic and drug resistant cells. Targeted deep sequencing has been used widely as a diagnostic tool to identify actionable mutations in cancer patients. In this study, we evaluated the clinical utility of estimating tumor heterogeneity using targeted panel sequencing data. We investigated the prognostic impact of a tumor heterogeneity (TH) index on clinical outcomes, using mutational profiles from targeted deep sequencing data acquired from 1,352 patients across 8 cancer types. The TH index tended to be increased in high pathological stage disease in several cancer types, indicating clonal expansion of cancer cells as tumor progression proceeds. In colorectal cancer patients, TH index values also correlated significantly with clinical prognosis. Integration of the TH index with genomic and clinical features could improve the power of risk prediction for clinical outcomes. In conclusion, deep sequencing to determine the TH index could serve as a promising prognostic indicator in cancer patients.
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http://dx.doi.org/10.1038/s41598-019-41098-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418103PMC
March 2019

Establishment of a Patient-derived Xenograft for Development of Personalized HER2-targeting Therapy in Gastric Cancer.

Anticancer Res 2018 01;38(1):287-293

Institute for Innovative Cancer Research, ASAN Medical Center, Seoul, Republic of Korea

Background/aim: To maximize success rate for development of HER2-targeted therapeutics, patient-derived xenograft (PDX) models reflecting HER2-positive gastric cancer (HER2 GC) patients were established.

Materials And Methods: GC tissues obtained from surgery of GC patients were implanted into immune-deficient mice, and tumor tissue of HER2 PDXs were verified of the patient-mimic HER2 expression by immunohistochemistry and explored for the feasibility by testing with Herceptin, the approved therapeutics and novel HER2 antibody therapeutics being developed.

Results: We obtained 5 cases of HER2 GC PDX models reflecting patient's GC tumor, consisting of 2 cases of HER2 3+ and 2 cases of HER2 2+. Novel HER2 antibody displayed significantly improved anti-cancer efficacy in combination with Herceptin.

Conclusion: The HER2 GC PDX models were successfully established to be utilized for preclinical evaluation of HER2-targeting drugs and combined therapies for GC treatment, as an ideal platform of personalized tools for precision therapy.
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http://dx.doi.org/10.21873/anticanres.12220DOI Listing
January 2018

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells.

Genome Res 2018 01 5;28(1):75-87. Epub 2017 Dec 5.

Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.

Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level.
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http://dx.doi.org/10.1101/gr.223263.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749184PMC
January 2018

Clinical Application of Targeted Deep Sequencing in Solid-Cancer Patients and Utility for Biomarker-Selected Clinical Trials.

Oncologist 2017 10 12;22(10):1169-1177. Epub 2017 Jul 12.

Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

Molecular profiling of actionable mutations in refractory cancer patients has the potential to enable "precision medicine," wherein individualized therapies are guided based on genomic profiling. The molecular-screening program was intended to route participants to different candidate drugs in trials based on clinical-sequencing reports. In this screening program, we used a custom target-enrichment panel consisting of cancer-related genes to interrogate single-nucleotide variants, insertions and deletions, copy number variants, and a subset of gene fusions. From August 2014 through April 2015, 654 patients consented to participate in the program at Samsung Medical Center. Of these patients, 588 passed the quality control process for the 381-gene cancer-panel test, and 418 patients were included in the final analysis as being eligible for any anticancer treatment (127 gastric cancer, 122 colorectal cancer, 62 pancreatic/biliary tract cancer, 67 sarcoma/other cancer, and 40 genitourinary cancer patients). Of the 418 patients, 55 (12%) harbored a biomarker that guided them to a biomarker-selected clinical trial, and 184 (44%) patients harbored at least one genomic alteration that was potentially targetable. This study demonstrated that the panel-based sequencing program resulted in an increased rate of trial enrollment of metastatic cancer patients into biomarker-selected clinical trials. Given the expanding list of biomarker-selected trials, the guidance percentage to matched trials is anticipated to increase.

Implications For Practice: This study demonstrated that the panel-based sequencing program resulted in an increased rate of trial enrollment of metastatic cancer patients into biomarker-selected clinical trials. Given the expanding list of biomarker-selected trials, the guidance percentage to matched trials is anticipated to increase.
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http://dx.doi.org/10.1634/theoncologist.2017-0020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634774PMC
October 2017

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer.

Nat Commun 2017 05 5;8:15081. Epub 2017 May 5.

Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.

Single-cell transcriptome profiling of tumour tissue isolates allows the characterization of heterogeneous tumour cells along with neighbouring stromal and immune cells. Here we adopt this powerful approach to breast cancer and analyse 515 cells from 11 patients. Inferred copy number variations from the single-cell RNA-seq data separate carcinoma cells from non-cancer cells. At a single-cell resolution, carcinoma cells display common signatures within the tumour as well as intratumoral heterogeneity regarding breast cancer subtype and crucial cancer-related pathways. Most of the non-cancer cells are immune cells, with three distinct clusters of T lymphocytes, B lymphocytes and macrophages. T lymphocytes and macrophages both display immunosuppressive characteristics: T cells with a regulatory or an exhausted phenotype and macrophages with an M2 phenotype. These results illustrate that the breast cancer transcriptome has a wide range of intratumoral heterogeneity, which is shaped by the tumour cells and immune cells in the surrounding microenvironment.
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http://dx.doi.org/10.1038/ncomms15081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424158PMC
May 2017

Affibody molecules as engineered protein drugs.

Exp Mol Med 2017 03 24;49(3):e306. Epub 2017 Mar 24.

AbClon Inc., Guro-gu, Seoul, Republic of Korea.

Affibody molecules can be used as tools for molecular recognition in diagnostic and therapeutic applications. There are several preclinical studies reported on diagnostic and therapeutic use of this molecular class of alternative scaffolds, and early clinical evidence is now beginning to accumulate that suggests the Affibody molecules to be efficacious and safe in man. The small size and ease of engineering make Affibody molecules suitable for use in multispecific constructs where AffiMabs is one such that offers the option to potentiate antibodies for use in complex disease.
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http://dx.doi.org/10.1038/emm.2017.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382565PMC
March 2017

Spatiotemporal genomic architecture informs precision oncology in glioblastoma.

Nat Genet 2017 Apr 6;49(4):594-599. Epub 2017 Mar 6.

Institute for Refractory Cancer Research, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.

Precision medicine in cancer proposes that genomic characterization of tumors can inform personalized targeted therapies. However, this proposition is complicated by spatial and temporal heterogeneity. Here we study genomic and expression profiles across 127 multisector or longitudinal specimens from 52 individuals with glioblastoma (GBM). Using bulk and single-cell data, we find that samples from the same tumor mass share genomic and expression signatures, whereas geographically separated, multifocal tumors and/or long-term recurrent tumors are seeded from different clones. Chemical screening of patient-derived glioma cells (PDCs) shows that therapeutic response is associated with genetic similarity, and multifocal tumors that are enriched with PIK3CA mutations have a heterogeneous drug-response pattern. We show that targeting truncal events is more efficacious than targeting private events in reducing the tumor burden. In summary, this work demonstrates that evolutionary inference from integrated genomic analysis in multisector biopsies can inform targeted therapeutic interventions for patients with GBM.
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http://dx.doi.org/10.1038/ng.3806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627771PMC
April 2017

Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer.

Cancer Res 2016 11 13;76(22):6568-6576. Epub 2016 Sep 13.

Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.

Tumor heterogeneity influences the clinical outcome of patients with cancer, and the diagnostic method to measure the tumor heterogeneity needs to be developed. We analyzed genomic features on pairs of primary and multiple metastatic lymph nodes from six patients with lung cancer using whole-exome sequencing and RNA sequencing. Although somatic single-nucleotide variants were shared in primary lung cancer and metastases, tumor evolution predicted by the pattern of genomic alterations was matched to anatomic location of the tumors. Four of six cases exhibited a branched clonal evolution pattern. Lymph nodes with acquired somatic variants demonstrated resistance to the cancer treatment. In this study, we demonstrated that multiple biopsies and sequencing strategies for different tumor regions are required for a comprehensive understanding of the landscape of genetic alteration and for guiding targeted therapy in advanced primary lung cancer. Cancer Res; 76(22); 6568-76. ©2016 AACR.
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http://dx.doi.org/10.1158/0008-5472.CAN-16-0873DOI Listing
November 2016

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.

Genome Biol 2016 Apr 29;17:80. Epub 2016 Apr 29.

Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.

Background: Intratumoral heterogeneity hampers the success of marker-based anticancer treatment because the targeted therapy may eliminate a specific subpopulation of tumor cells while leaving others unharmed. Accordingly, a rational strategy minimizing survival of the drug-resistant subpopulation is essential to achieve long-term therapeutic efficacy.

Results: Using single-cell RNA sequencing (RNA-seq), we examine the intratumoral heterogeneity of a pair of primary renal cell carcinoma and its lung metastasis. Activation of drug target pathways demonstrates considerable variability between the primary and metastatic sites, as well as among individual cancer cells within each site. Based on the prediction of multiple drug target pathway activation, we derive a combinatorial regimen co-targeting two mutually exclusive pathways for the metastatic cancer cells. This combinatorial strategy shows significant increase in the treatment efficacy over monotherapy in the experimental validation using patient-derived xenograft platforms in vitro and in vivo.

Conclusions: Our findings demonstrate the investigational application of single-cell RNA-seq in the design of an anticancer regimen. The approach may overcome intratumoral heterogeneity which hampers the success of precision medicine.
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http://dx.doi.org/10.1186/s13059-016-0945-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852434PMC
April 2016

Deciphering intratumor heterogeneity using cancer genome analysis.

Hum Genet 2016 06 28;135(6):635-42. Epub 2016 Apr 28.

Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.

Intratumor heterogeneity within individual cancer tissues underlies the numerous phenotypes of cancer. Tumor subclones ultimately affect therapeutic outcomes due to their distinct molecular features. Drug-resistant subclones are present at a low frequency in tissues at the time of biopsy, but can also arise as a result of acquired somatic mutations. A number of different approaches have been utilized to understand the nature of intratumor heterogeneity. Clonal analysis using whole exome or genome sequencing data can help monitor subclones in the context of tumor progression. Multiregional biopsies permit the molecular characterization of subclones within tumors. Deep sequencing has also provided researchers with the ability to measure the low allele fraction variant within a small number of cells. Ultimately, single-cell sequencing will enable the identification of every minor population within a tumor microenvironment. In the clinical context, the ability to identify and monitor the subclonal architecture of a tumor is valuable for the development of precise cancer therapeutic methods.
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http://dx.doi.org/10.1007/s00439-016-1670-xDOI Listing
June 2016

Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq.

PLoS One 2015 25;10(8):e0135817. Epub 2015 Aug 25.

Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, 200-701, Korea.

Single-cell sequencing, which is used to detect clinically important tumor subpopulations, is necessary for understanding tumor heterogeneity. Here, we analyzed transcriptomic data obtained from 34 single cells from human lung adenocarcinoma (LADC) patient-derived xenografts (PDXs). To focus on the intrinsic transcriptomic signatures of these tumors, we filtered out genes that displayed extensive expression changes following xenografting and cell culture. Then, we performed clustering analysis using co-regulated gene modules rather than individual genes to minimize read drop-out errors associated with single-cell sequencing. This combined approach revealed two distinct intra-tumoral subgroups that were primarily distinguished by the gene module G64. The G64 module was predominantly composed of cell-cycle genes. E2F1 was found to be the transcription factor that most likely mediates the expression of the G64 module in single LADC cells. Interestingly, the G64 module also indicated inter-tumoral heterogeneity based on its association with patient survival and other clinical variables such as smoking status and tumor stage. Taken together, these results demonstrate the feasibility of single-cell RNA sequencing and the strength of our analytical pipeline for the identification of tumor subpopulations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135817PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549254PMC
May 2016

Affinity Maturation of Monoclonal Antibody 1E11 by Targeted Randomization in CDR3 Regions Optimizes Therapeutic Antibody Targeting of HER2-Positive Gastric Cancer.

PLoS One 2015 30;10(7):e0134600. Epub 2015 Jul 30.

Therapeutic antibody research center, AbClon Inc., Seoul, Korea.

Anti-HER2 murine monoclonal antibody 1E11 has strong and synergistic anti-tumor activity in HER2-overexpressing gastric cancer cells when used in combination with trastuzumab. We presently optimized this antibody for human therapeutics. First, the complementarity determining regions (CDRs) of the murine antibody were grafted onto human germline immunoglobulin variable genes. No difference in affinity and biological activity was observed between chimeric 1E11 (ch1E11) and humanized 1E11 (hz1E11). Next, affinity maturation of hz1E11 was performed by the randomization of CDR-L3 and H3 residues followed by stringent biopanning selection. Milder selection pressure favored the selection of more diverse clones, whereas higher selection stringency resulted in the convergence of the panning output to a smaller number of clones with improved affinity. Clone 1A12 had four amino acid substitutions in CDR-L3, and showed a 10-fold increase in affinity compared to the parental clone and increased potency in an in vitro anti-proliferative activity assay with HER2-overepxressing gastric cancer cells. Clone 1A12 inhibited tumor growth of NCI-N87 xenograft model with similar efficacy to trastuzumab alone, and the combination treatment of 1A12 and trastuzumab completely removed the established tumors. These results suggest that humanized and affinity matured monoclonal antibody 1A12 is a highly optimized molecule for future therapeutic development against HER2-positive tumors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134600PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520604PMC
May 2016

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.

Genome Biol 2015 Jun 19;16:127. Epub 2015 Jun 19.

Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.

Background: Intra-tumoral genetic and functional heterogeneity correlates with cancer clinical prognoses. However, the mechanisms by which intra-tumoral heterogeneity impacts therapeutic outcome remain poorly understood. RNA sequencing (RNA-seq) of single tumor cells can provide comprehensive information about gene expression and single-nucleotide variations in individual tumor cells, which may allow for the translation of heterogeneous tumor cell functional responses into customized anti-cancer treatments.

Results: We isolated 34 patient-derived xenograft (PDX) tumor cells from a lung adenocarcinoma patient tumor xenograft. Individual tumor cells were subjected to single cell RNA-seq for gene expression profiling and expressed mutation profiling. Fifty tumor-specific single-nucleotide variations, including KRAS(G12D), were observed to be heterogeneous in individual PDX cells. Semi-supervised clustering, based on KRAS(G12D) mutant expression and a risk score representing expression of 69 lung adenocarcinoma-prognostic genes, classified PDX cells into four groups. PDX cells that survived in vitro anti-cancer drug treatment displayed transcriptome signatures consistent with the group characterized by KRAS(G12D) and low risk score.

Conclusions: Single-cell RNA-seq on viable PDX cells identified a candidate tumor cell subgroup associated with anti-cancer drug resistance. Thus, single-cell RNA-seq is a powerful approach for identifying unique tumor cell-specific gene expression profiles which could facilitate the development of optimized clinical anti-cancer strategies.
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http://dx.doi.org/10.1186/s13059-015-0692-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506401PMC
June 2015

Combination of novel HER2-targeting antibody 1E11 with trastuzumab shows synergistic antitumor activity in HER2-positive gastric cancer.

Mol Oncol 2015 Feb 28;9(2):398-408. Epub 2014 Sep 28.

AbClon Inc., #1403, Ace Twin Tower 1, 212-1, Guro-dong, Guro-gu, Seoul 152-779, Republic of Korea.

The synergistic interaction of two antibodies targeting the same protein could be developed as an effective anti-cancer therapy. Human epidermal growth factor receptor 2 (HER2) is overexpressed in 20-25% of breast and gastric cancer patients, and HER2-targeted antibody therapy using trastuzumab is effective in many of these patients. Nonetheless, improving therapeutic efficacy and patient survival is important, particularly in patients with HER2-positive gastric cancer. Here, we describe the development of 1E11, a HER2-targeted humanized monoclonal antibody showing increased efficacy in a highly synergistic manner in combination with trastuzumab in the HER2-overexpressing gastric cancer cell lines NCI-N87 and OE-19. The two antibodies bind to sub-domain IV of the receptor, but have non-overlapping epitopes, allowing them to simultaneously bind HER2. Treatment with 1E11 alone induced apoptosis in HER2-positive cancer cells, and this effect was enhanced by combination treatment with trastuzumab. Combination treatment with 1E11 and trastuzumab reduced the levels of total HER2 protein and those of aberrant HER2 signaling molecules including phosphorylated HER3 and EGFR. The synergistic antitumor activity of 1E11 in combination with trastuzumab indicates that it could be a novel potent therapeutic antibody for the treatment of HER2-overexpressing gastric cancers.
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http://dx.doi.org/10.1016/j.molonc.2014.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528653PMC
February 2015

Biological effects of femtosecond-terahertz pulses on C57BL/6 mouse skin.

Ann Dermatol 2014 Feb 17;26(1):129-32. Epub 2014 Feb 17.

Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea. ; Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea.

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http://dx.doi.org/10.5021/ad.2014.26.1.129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956785PMC
February 2014

High-power femtosecond-terahertz pulse induces a wound response in mouse skin.

Sci Rep 2013 ;3:2296

Departments of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 110-799, Korea.

Terahertz (THz) technology has emerged for biomedical applications such as scanning, molecular spectroscopy, and medical imaging. Although a thorough assessment to predict potential concerns has to precede before practical utilization of THz source, the biological effect of THz radiation is not yet fully understood with scant related investigations. Here, we applied a femtosecond-terahertz (fs-THz) pulse to mouse skin to evaluate non-thermal effects of THz radiation. Analysis of the genome-wide expression profile in fs-THz-irradiated skin indicated that wound responses were predominantly mediated by transforming growth factor-beta (TGF-β) signaling pathways. We validated NFκB1- and Smad3/4-mediated transcriptional activation in fs-THz-irradiated skin by chromatin immunoprecipitation assay. Repeated fs-THz radiation delayed the closure of mouse skin punch wounds due to up-regulation of TGF-β. These findings suggest that fs-THz radiation initiate a wound-like signal in skin with increased expression of TGF-β and activation of its downstream target genes, which perturbs the wound healing process in vivo.
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http://dx.doi.org/10.1038/srep02296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731731PMC
February 2014

MicroRNA-16 is down-regulated in mutated FLT3 expressing murine myeloid FDC-P1 cells and interacts with Pim-1.

PLoS One 2012 6;7(9):e44546. Epub 2012 Sep 6.

School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.

Activating mutations in the receptor tyrosine kinase FLT3 are one of the most frequent somatic mutations in acute myeloid leukemia (AML). Internal tandem duplications of the juxtamembrane region of FLT3 (FLT3/ITD) constitutively activate survival and proliferation pathways, and are associated with a poor prognosis in AML. We suspected that alteration of small non-coding microRNA (miRNA) expression in these leukemia cells is involved in the transformation process and used miRNA microarrays to determine the miRNA signature from total RNA harvested from FLT3/ITD expressing FDC-P1 cells (FD-FLT3/ITD). This revealed that a limited set of miRNAs appeared to be affected by expression of FLT3/ITD compared to the control group consisting of FDC-P1 parental cells transfected with an empty vector (FD-EV). Among differentially expressed miRNAs, we selected miR-16, miR-21 and miR-223 to validate the microarray data by quantitative real-time RT-PCR showing a high degree of correlation. We further analyzed miR-16 expression with FLT3 inhibitors in FLT3/ITD expressing cells. MiR-16 was found to be one of most significantly down-regulated miRNAs in FLT3/ITD expressing cells and was up-regulated upon FLT3 inhibition. The data suggests that miR-16 is acting as a tumour suppressor gene in FLT3/ITD-mediated leukemic transformation. Whilst miR-16 has been reported to target multiple mRNAs, computer models from public bioinformatic resources predicted a potential regulatory mechanism between miR-16 and Pim-1 mRNA. In support of this interaction, miR-16 was shown to suppress Pim-1 reporter gene expression. Further, our data demonstrated that over-expression of miR-16 mimics suppressed Pim-1 expression in FD-FLT3/ITD cells suggesting that increased miR-16 expression contributes to depletion of Pim-1 after FLT3 inhibition and that miR-16 repression may be associated with up-regulated Pim-1 in FLT3/ITD expressing cells.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044546PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435263PMC
March 2013

Induction of hair growth by insulin-like growth factor-1 in 1,763 MHz radiofrequency-irradiated hair follicle cells.

PLoS One 2011 2;6(12):e28474. Epub 2011 Dec 2.

Department of Dermatology, College of Medicine, Seoul National University, Seoul, Korea.

Radiofrequency (RF) radiation does not transfer high energy to break the covalent bonds of macromolecules, but these low energy stimuli might be sufficient to induce molecular responses in a specific manner. We monitored the effect of 1,763 MHz RF radiation on cultured human dermal papilla cells (hDPCs) by evaluating changes in the expression of cytokines related to hair growth. The expression of insulin-like growth factor-1 (IGF-1) mRNA in hDPCs was significantly induced upon RF radiation at the specific absorption rate of 10 W/kg, which resulted in increased expression of B-cell chronic lymphocytic leukemia/lymphoma 2 (BCL-2) and cyclin D1 (CCND1) proteins and increased phosphorylation of MAPK1 protein. Exposure to 10 W/kg RF radiation 1 h per day for 7 days significantly enhanced hair shaft elongation in ex vivo hair organ cultures. In RF-exposed follicular matrix keratinocytes in the hair bulb, the expression of Ki-67 was increased, while the signal for terminal deoxynucleotidyl transferase dUTP nick end labeling was reduced. From these results, we suggest that 1,763 MHz RF exposure stimulates hair growth in vitro through the induction of IGF-1 in hDPCs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028474PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229574PMC
July 2012

Demethylation by 5-aza-2'-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists.

BMC Cancer 2010 Jul 12;10:366. Epub 2010 Jul 12.

Discipline of Medical Genetics, School of Biomedical Sciences, Faculty of Health, University of Newcastle, Australia.

Background: DNA methylation and histone acetylation are epigenetic modifications that act as regulators of gene expression. Aberrant epigenetic gene silencing in tumours is a frequent event, yet the factors which dictate which genes are targeted for inactivation are unknown. DNA methylation and histone acetylation can be modified with the chemical agents 5-aza-2'-deoxycytidine (5-aza-dC) and Trichostatin A (TSA) respectively. The aim of this study was to analyse de-methylation and re-methylation and its affect on gene expression in colorectal cancer cell lines treated with 5-aza-dC alone and in combination with TSA. We also sought to identify methylation patterns associated with long term reactivation of previously silenced genes.

Method: Colorectal cancer cell lines were treated with 5-aza-dC, with and without TSA, to analyse global methylation decreases by High Performance Liquid Chromatography (HPLC). Re-methylation was observed with removal of drug treatments. Expression arrays identified silenced genes with differing patterns of expression after treatment, such as short term reactivation or long term reactivation. Sodium bisulfite sequencing was performed on the CpG island associated with these genes and expression was verified with real time PCR.

Results: Treatment with 5-aza-dC was found to affect genomic methylation and to a lesser extent gene specific methylation. Reactivated genes which remained expressed 10 days post 5-aza-dC treatment featured hypomethylated CpG sites adjacent to the transcription start site (TSS). In contrast, genes with uniformly hypermethylated CpG islands were only temporarily reactivated.

Conclusion: These results imply that 5-aza-dC induces strong de-methylation of the genome and initiates reactivation of transcriptionally inactive genes, but this does not require gene associated CpG island de-methylation to occur. In addition, for three of our selected genes, hypomethylation at the TSS of an epigenetically silenced gene is associated with the long term reversion of gene expression level brought about by alterations in the epigenetic status following 5-aza-dC treatment.
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http://dx.doi.org/10.1186/1471-2407-10-366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912869PMC
July 2010

Noise characteristics of single-walled carbon nanotube network transistors.

Nanotechnology 2008 Jul 3;19(28):285705. Epub 2008 Jun 3.

Frontier Research Laboratory, Samsung Advanced Institute of Technology, Yongin, Korea.

The noise characteristics of randomly networked single-walled carbon nanotubes grown directly by plasma enhanced chemical vapor deposition (PECVD) are studied with field effect transistors (FETs). Due to the geometrical complexity of nanotube networks in the channel area and the large number of tube-tube/tube-metal junctions, the inverse frequency, 1/f, dependence of the noise shows a similar level to that of a single single-walled carbon nanotube transistor. Detailed analysis is performed with the parameters of number of mobile carriers and mobility in the different environment. This shows that the change in the number of mobile carriers resulting in the mobility change due to adsorption and desorption of gas molecules (mostly oxygen molecules) to the tube surface is a key factor in the 1/f noise level for carbon nanotube network transistors.
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http://dx.doi.org/10.1088/0957-4484/19/28/285705DOI Listing
July 2008

Internal tandem duplication of FLT3 (FLT3/ITD) induces increased ROS production, DNA damage, and misrepair: implications for poor prognosis in AML.

Blood 2008 Mar 11;111(6):3173-82. Epub 2008 Jan 11.

Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

Activating mutations of the FMS-like tyrosine kinase-3 (FLT3) receptor occur in approximately 30% of acute myeloid leukemia (AML) patients and, at least for internal tandem duplication (ITD) mutations, are associated with poor prognosis. FLT3 mutations trigger downstream signaling pathways including RAS-MAP/AKT kinases and signal transducer and activator of transcription-5 (STAT5). We find that FLT3/ITD mutations start a cycle of genomic instability whereby increased reactive oxygen species (ROS) production leads to increased DNA double-strand breaks (DSBs) and repair errors that may explain aggressive AML in FLT3/ITD patients. Cell lines transfected with FLT3/ITD and FLT3/ITD-positive AML cell lines and primary cells demonstrate increased ROS. Increased ROS levels appear to be produced via STAT5 signaling and activation of RAC1, an essential component of ROS-producing NADPH oxidases. A direct association of RAC1-GTP binding to phosphorylated STAT5 (pSTAT5) provides a possible mechanism for ROS generation. A FLT3 inhibitor blocked increased ROS in FLT3/ITD cells resulting in decreased DSB and increased repair efficiency and fidelity. Our study suggests that the aggressiveness of the disease and poor prognosis of AML patients with FLT3/ITD mutations could be the result of increased genomic instability that is driven by higher endogenous ROS, increased DNA damage, and decreased end-joining fidelity.
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http://dx.doi.org/10.1182/blood-2007-05-092510DOI Listing
March 2008