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Cho SY, Kim Z, Chung DR, Cho BH, Chung MJ, Kim JH, Jeong J. Development of machine learning models for the surveillance of colon surgical site infections. J Hosp Infect 2024; 146:224-231. [PMID: 37094715 DOI: 10.1016/j.jhin.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Conventional surgical site infection (SSI) surveillance is labour-intensive. We aimed to develop machine learning (ML) models for the surveillance of SSIs for colon surgery and to assess whether the ML could improve surveillance process efficiency. METHODS This study included cases who underwent colon surgery at a tertiary center between 2013 and 2014. Logistic regression and four ML algorithms including random forest (RF), gradient boosting (GB), and neural networks (NNs) with or without recursive feature elimination (RFE) were first trained on the entire cohort, and then re-trained on cases selected based on a previous rule-based algorithm. We assessed model performance based on the area under the curve (AUC), sensitivity, and positive predictive value (PPV). The estimated proportion of reduction in workload for chart review based on the ML models was evaluated and compared with the conventional method. RESULTS At a sensitivity of 95%, the NN with RFE using 29 variables had the best performance with an AUC of 0.963 and PPV of 21.1%. When combining both the rule-based algorithm and ML algorithms, the NN with RFE using 19 variables had a higher PPV (28.9%) than with the ML algorithm alone, which could decrease the number of cases requiring chart review by 83.9% compared with the conventional method. CONCLUSION We demonstrated that ML can improve the efficiency of SSI surveillance for colon surgery by decreasing the burden of chart review while providing high sensitivity. In particular, the hybrid approach of ML with a rule-based algorithm showed the best performance in terms of PPV.
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Affiliation(s)
- S Y Cho
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Z Kim
- Medical AI Research Center, Samsung Medical Center, Seoul, Republic of Korea; Department of Data Convergence and Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - D R Chung
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - B H Cho
- Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam, Republic of Korea; Institute of Biomedical Informatics, School of Medicine, CHA University, Seongnam, Republic of Korea
| | - M J Chung
- Medical AI Research Center, Samsung Medical Center, Seoul, Republic of Korea; Department of Data Convergence and Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - J H Kim
- Department of Biomedical Science, Korea University College of Medicine, Seoul, Republic of Korea
| | - J Jeong
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Republic of Korea
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Kim KH, Park D, Cho SY, Cho Y, Lee B, Jeong H, Lee Y, Lee Y, Nam KT. Role of histamine-mediated macrophage differentiation in clearance of metastatic bacterial infection. Front Immunol 2023; 14:1290191. [PMID: 38035074 PMCID: PMC10682073 DOI: 10.3389/fimmu.2023.1290191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Macrophages are highly heterogeneous immune cells with a role in maintaining tissue homeostasis, especially in activating the defense response to bacterial infection. Using flow cytometric and single-cell RNA-sequencing analyses of peritoneal cells, we here show that small peritoneal macrophage and immature macrophage populations are enriched in histamine-deficient (Hdc -/-) mice, characterized by a CD11bmiF4/80loCCR2+MHCIIhi and CD11bloF4/80miTHBS1+IL-1α+ phenotype, respectively. Molecular characterization revealed that immature macrophages represent an abnormally differentiated form of large peritoneal macrophages with strong inflammatory properties. Furthermore, deficiency in histamine signaling resulted in significant impairment of the phagocytic activity of peritoneal macrophage populations, conferring high susceptibility to bacterial infection. Collectively, this study reveals the importance of histamine signaling in macrophage differentiation at the molecular level to maintain tissue homeostasis, offering a potential therapeutic target for bacterial infection-mediated diseases.
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Affiliation(s)
- Kwang H. Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Donghwan Park
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Cho
- Department of Molecular and Life Science, Hanyang University College of Science and Convergence Technology, Ansan, Republic of Korea
| | - Yejin Cho
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Buhyun Lee
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Haengdueng Jeong
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yura Lee
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yourim Lee
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ki Taek Nam
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
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Kim JY, Hyun DY, Nam D, Shin HJ, Jung J, Cho SY, Jung K, Hwang D, Lee SW, Kim JY. Proteogenomic Analysis of Human Uterine Cervical Cancer (UCC) Reveals Treatment-Resistant Subtypes of UCC. Int J Radiat Oncol Biol Phys 2023; 117:S22. [PMID: 37784455 DOI: 10.1016/j.ijrobp.2023.06.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Locally advanced uterine cervical cancer (UCC) is treated by radiotherapy with concurrent chemotherapy, but heterogenous treatment responses are frequently observed. To better optimize therapeutic options based on molecular signatures, we performed proteogenomic analysis of UCC. MATERIALS/METHODS UCC tissue and blood samples were collected from patients who underwent primary radiotherapy ± chemotherapy at the National Cancer Center (NCC) in Korea from July 2004 to March 2020. Most samples were obtained via biopsy. Genomic DNA for WES was isolated from frozen biopsy tumor tissues and peripheral blood buffy-coat of patients. Both global proteome and phosphoproteome were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Whole exome sequencing, RNA sequencing, global proteomics and phosphoproteomics were performed using 253, 337, and 147 cervical cancer samples, respectively. Patient-derived xenograft were established using intratongue implantation using 2 primary cell lines from sub3 and sub5, and flow cytometric analysis was performed. RESULTS Fourteen significantly mutated genes (SMG) were found in our study cohort which include 5 newly identified SMGs. Mutation-phosphorylation analysis revealed association with apoptosis and actin cytoskeleton pathway. Proteogenomic analysis defined 6 molecular subtypes of UCC. Of those, 3 subtypes (i.e., Sub3, Sub5 and Sub6) were associated with treatment-resistant phenotypes. The cell-type deconvolution analysis suggested activated stroma with activation of cancer-associated fibroblast in Sub 3, while Sub5 showed low levels of activated stroma and high levels of myeloid immune cells. FACS analysis of UCC mouse models established from these 2 radio-resistant primary cell lines showed high component of PDGFRA+CAF infiltration in Sub 3, and high level of PVR+CD45+ immune cells mainly composed of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) in Sub5. For Sub6, genes and/or protein signatures represented mucin-related processes (e.g., mucin glycosylation/sugar metabolism), which are linked to metastasis-associated Tn antigen production. CONCLUSION The proteogenomic analysis thus suggests potential targets for radiotherapy-resistant subtypes of UCC; secretory factors from activated stroma and cancer-associated fibroblast (Sub3); RHOA signaling, PVR, and PMN-MDSCs (Sub5), and keratin/chondroitin sulfate proteoglycan and Tn antigen production (Sub6). Our study shows the importance of proteogenomic analysis in unveiling the subtype specific molecular pathways of UCC that are beyond reach by genomic data alone. The validity of our molecular pathway and cellular signatures linking these pathways should be further validated through detailed functional experiments and in larger UCC cohorts.
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Affiliation(s)
- J Y Kim
- National Cancer Center, Goyang, Korea, Republic of (South) Korea
| | - D Y Hyun
- School of Biological Sciences, Seoul National University, Seoul, Korea, Republic of (South) Korea
| | - D Nam
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Korea, Republic of (South) Korea
| | - H J Shin
- Research Institute and Hospital, National Cancer Center, Korea, Goyang, Korea, Republic of (South) Korea
| | - J Jung
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - S Y Cho
- Research Institute and Hospital, National Cancer Center, Korea, Goyang-si, Korea, Republic of (South) Korea
| | - K Jung
- Department of Anatomy and Cell Biology and Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - D Hwang
- School of Biological Sciences, Seoul National University, Seoul, Korea, Republic of (South) Korea
| | - S W Lee
- Department of Chemistry and Center for Proteogenome Research, Korea University, Seoul, Korea, Republic of (South) Korea
| | - J Y Kim
- Research Institute and Hospital, National Cancer Center, Korea, Goyang-si, Korea, Republic of (South) Korea
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Hoppe BS, Castellino S, Pei Q, Charpentier AM, Keller F, Vega RM, Roberts KB, Parikh RR, Punnett A, Parsons S, McCarten KM, Flampouri S, Kessel S, Wu Y, Cho SY, Kelly KM, Hodgson D. Radiotherapy Utilization and Outcomes on a Contemporary Trial for Pediatric High-Risk Hodgkin Lymphoma Study. Int J Radiat Oncol Biol Phys 2023; 117:S62-S63. [PMID: 37784541 DOI: 10.1016/j.ijrobp.2023.06.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Contemporary trials in pediatric Hodgkin lymphoma (cHL) evaluate strategies to reduce radiotherapy (RT) utilization while maintaining excellent progression-free survival (PFS). An alternative strategy is to irradiate selective sites at higher risk of relapse, and/or use proton therapy (PT) to minimize exposure to healthy tissue. We investigated the use of PT and photon therapy (XRT) and associated early outcomes among patients receiving involved site RT (ISRT) to high-risk sites on the Children's Oncology Group (COG) trial AHOD1331 (NCT021664643). MATERIALS/METHODS This multicenter randomized, open-label phase 3 study enrolled patients 2-21 years (yrs) with previously untreated cHL: stages IIB + bulk, IIIB, IVA, IVB. Patients were randomized to 5 cycles of either ABVE-PC (doxorubicin, bleomycin, vincristine, etoposide, prednisone, cyclophosphamide) or the brentuximab vedotin (BV) containing regimen BV-AVE-PC given every 21 days. ISRT to 21 Gy was given to bulky mediastinal adenopathy and slow responding lesions (SRL) defined by 5-point score 4 or 5 on PET-CT after 2 cycles. ISRT could be delivered as 3D conformal XRT (3D), intensity modulated XRT (IMRT), or proton therapy (PT). Utilization of RT was compared by mode and by study enrollment midpoint among irradiated patients. Severe acute toxicity assessment included any incident grade 3 or higher toxicity during the ISRT period, except for neuropathy. RESULTS Among 587 eligible patients who were enrolled across 153 institutions between March 2015 and August 2019 with a median follow up of 43.1 months, the 3-yr PFS was 82.5% (90% CI, 78.3%-85.9%) with ABVE-PC and 92.5% (90% CI 89.5%-94.6%) with BV-AVE-PC (p = 0.0002). There was no difference in ISRT receipt or modality by study arm (p = 0.33). Among those who received RT 69.7% received it due to bulky mediastinal adenopathy, 6.6% due to SRL, and 23.7% for both. Overall, 317 (54.0%) patients received protocol RT of which 28.7% received 3D, 44.8% received IMRT, and 26.5% received PT. PT utilization increased over the course of the study from 21.5% among the first 50% of irradiated patients to 31.5% in the second half of irradiated patients (p = 0.045). The 3-yr progression-free survival rates overall by RT were comparable: PT (88.0%, 90% CI 80.6% - 92.7%%); XRT (87.1%, 90% CI 82.9%-90.4%) (p = 0.85). No difference in PFS was observed between 3D versus IMRT (p = 0.65). No differences were observed in severe acute toxicities (8.33% vs. 8.15%, p = 0.96) between PT and XRT. CONCLUSION Selective use of RT results in excellent outcomes for pediatric patients with high-risk HL and combination chemotherapy inclusive of the novel agent BV. Over the course of the study, PT utilization increased as an RT modality. Early results suggest that PT does not compromise disease control and has similar acute toxicity as XRT. Long term follow-up (>10 years) is needed to evaluate for secondary malignancies and cardiac toxicity among the different RT modalities.
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Affiliation(s)
- B S Hoppe
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL
| | | | - Q Pei
- University of Florida, Gainesville, FL
| | - A M Charpentier
- Centre hospitalier de l'Universite de Montreal, Montreal, QC, Canada
| | - F Keller
- Children Hospital of Atlanta, Atlanta, GA
| | | | | | - R R Parikh
- Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, New Brunswick, NJ
| | - A Punnett
- University of Toronto, Toronto, ON, Canada
| | | | | | - S Flampouri
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - S Kessel
- Imaging and Radiation Oncology Core, Lincoln, RI
| | - Y Wu
- University of Florida, Gainesville, FL
| | - S Y Cho
- Department of Radiology, University of Wisconsin Hospitals and Clinics, Madison, WI
| | - K M Kelly
- Roswell Park Cancer Institute, Buffalo, NY
| | - D Hodgson
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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Campbell G, Wells S, Huang W, Cooley GM, Jarrard D, Kyriakopoulos C, Cho SY, Lang J, Floberg JM. Disease and Toxicity Outcomes after Salvage Radiotherapy (SRT) for Biochemically Recurrent Prostate Cancer (PC) for Patients Enrolled in a Phase II, Open Label Trial Investigating Neoadjuvant Chemohormonal Therapy Followed by Radical Prostatectomy (RP). Int J Radiat Oncol Biol Phys 2023; 117:e369. [PMID: 37785259 DOI: 10.1016/j.ijrobp.2023.06.2466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Men with metastatic hormone sensitive prostate cancer have improved progression free and overall survival (PFS/OS) when treated with docetaxel and androgen deprivation therapy (ADT). Our institution conducted a phase II trial (UW17009) investigating the addition of three cycles of neoadjuvant docetaxel and ADT to RP in men with high-risk prostate cancer. Here we report toxicity and freedom from biochemical recurrence (FFBCR) for patients treated with SRT following participation in this trial. MATERIALS/METHODS Between January 17, 2018 and August 10, 2021, 28 patients enrolled on UW17009. Patients who had a recurrence and received SRT were identified. Toxicity was assessed using modified LENT (Late Effects of Normal Tissues)/RTOG (Radiation Therapy Oncology Group) criteria, and time to recurrence following SRT was determined for each patient. Additionally, the months of ADT received by each patient was recorded. FFBCR was then determined for this cohort using the method of Kaplan and Meier. RESULTS Of 28 patients enrolled on UW17009, 20 (71%) had BCR after RP. Of these, 19 received SRT, representing 68% of the patients enrolled on the trial. The rates of acute grade 1 and grade 2 GU toxicity with SRT were 37% (7) and 53% (10), respectively. The rates of acute grade 1 and grade 2 GI toxicity with SRT were 32% (6) and 37% (7), respectively. On patient experienced a grade 4 genitourinary toxicity during SRT. There were no acute grade 3 or grade 5 toxicities. The rates of late grade 1 and grade 2 GU toxicity were 16% (3) and 11% (2), respectively. The rates of late grade 1 and grade 2 GI toxicity were 11% (2) and 5% (1), respectively. There was 1 (5%) late grade 3 GU toxicity. There were no late grade 3-5 GI toxicities, or late grade 4-5 GU toxicities. The average duration of ADT after prostatectomy was 15 months (range: 0-37 months). According to the method of Kaplan and Meier, mean FFBCR after SRT was 34.0 months at a median of 37.8 months. Median FFBCR had not yet been reached. At the time of analysis, 13 patients remained free from biochemical recurrence after SRT. CONCLUSION Rates of biochemical recurrence and SRT following neoadjuvant docetaxel and ADT and then RP were consistent with historical data, as was the rate of successful SRT. Toxicities were also consistent with historical data, though there was notably one acute grade 4 GU toxicity.
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Affiliation(s)
- G Campbell
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - S Wells
- Department of Radiology, University of Wisconsin Hospitals & Clinics, Madison, WI
| | - W Huang
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - G M Cooley
- Department of Human Oncology, University of Wisconsin Hospital and Clinics, Madison, WI
| | - D Jarrard
- Department of Urology, University of Wisconsin Hospitals and Clinics, Madison, WI
| | - C Kyriakopoulos
- Department of Human Oncology, University of Wisconsin Hospital and Clinics, Madison, WI
| | - S Y Cho
- Department of Radiology, University of Wisconsin Hospitals and Clinics, Madison, WI
| | - J Lang
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - J M Floberg
- University of Wisconsin School of Medicine and Public Health, Madison, WI
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Cho SY, Hwang H, Kim YH, Yoo BC, Han N, Kong SY, Baek MJ, Kim KH, Lee MR, Park JG, Han SS, Lee WJ, Park C, Park JB, Kim JY, Park SJ, Woo SM. Refining Classification of Cholangiocarcinoma Subtypes via Proteogenomic Integration Reveals New Therapeutic Prospects. Gastroenterology 2023; 164:1293-1309. [PMID: 36898552 DOI: 10.1053/j.gastro.2023.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND & AIMS Intrahepatic cholangiocarcinomas (iCCs) are characterized by their rarity, difficult diagnosis, and overall poor prognosis. The iCC molecular classification for developing precision medicine strategies was investigated. METHODS Comprehensive genomic, transcriptomic, proteomic, and phosphoproteomic analyses were performed on treatment-naïve tumor samples from 102 patients with iCC who underwent surgical resection with curative intent. An organoid model was constructed for testing therapeutic potential. RESULTS Three clinically supported subtypes (stem-like, poorly immunogenic, and metabolism) were identified. NCT-501 (aldehyde dehydrogenase 1 family member A1 [ALDH1A1] inhibitor) exhibited synergism with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. The oncometabolite dysregulations were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype harbors the non-T-cell tumor infiltration. Integrated multiomics analysis not only reproduced the 3 subtypes but also showed heterogeneity in iCC. CONCLUSIONS This large-scale proteogenomic analysis provides information beyond that obtained with genomic analysis, allowing the functional impact of genomic alterations to be discerned. These findings may assist in the stratification of patients with iCC and in developing rational therapeutic strategies.
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Affiliation(s)
- Soo Young Cho
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea; Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yun-Hee Kim
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Byong Chul Yoo
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Nayoung Han
- Department of Pathology, National Cancer Center, Goyang, Republic of Korea
| | - Sun-Young Kong
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea; Deparment of Laboratory Medicine, National Cancer Center, Goyang, Republic of Korea
| | - Min-Jeong Baek
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Kyung-Hee Kim
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Mi Rim Lee
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Jae Gwang Park
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Sung-Sik Han
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Woo Jin Lee
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Charny Park
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jong Bae Park
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea; Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
| | - Sang-Jae Park
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea.
| | - Sang Myung Woo
- Research Institute, National Cancer Center, Goyang, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea; Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea.
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Lee K, Hyung D, Cho SY, Yu N, Hong S, Kim J, Kim S, Han JY, Park C. Splicing signature database development to delineate cancer pathways using literature mining and transcriptome machine learning. Comput Struct Biotechnol J 2023; 21:1978-1988. [PMID: 36942103 PMCID: PMC10023904 DOI: 10.1016/j.csbj.2023.02.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Alternative splicing (AS) events modulate certain pathways and phenotypic plasticity in cancer. Although previous studies have computationally analyzed splicing events, it is still a challenge to uncover biological functions induced by reliable AS events from tremendous candidates. To provide essential splicing event signatures to assess pathway regulation, we developed a database by collecting two datasets: (i) reported literature and (ii) cancer transcriptome profile. The former includes knowledge-based splicing signatures collected from 63,229 PubMed abstracts using natural language processing, extracted for 202 pathways. The latter is the machine learning-based splicing signatures identified from pan-cancer transcriptome for 16 cancer types and 42 pathways. We established six different learning models to classify pathway activities from splicing profiles as a learning dataset. Top-ranked AS events by learning model feature importance became the signature for each pathway. To validate our learning results, we performed evaluations by (i) performance metrics, (ii) differential AS sets acquired from external datasets, and (iii) our knowledge-based signatures. The area under the receiver operating characteristic values of the learning models did not exhibit any drastic difference. However, random-forest distinctly presented the best performance to compare with the AS sets identified from external datasets and our knowledge-based signatures. Therefore, we used the signatures obtained from the random-forest model. Our database provided the clinical characteristics of the AS signatures, including survival test, molecular subtype, and tumor microenvironment. The regulation by splicing factors was additionally investigated. Our database for developed signatures supported retrieval and visualization system.
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Key Words
- AS, Alternative splicing
- AUCPR, the area under the precision-recall curve
- AUROC, the area under the receiver operating characteristic
- Alternative splicing
- DAS, differential alternative splicing
- Database
- EMT, epithelial mesenchymal transition
- Gene signature
- ML, machine learning
- Machine-learning
- NER, named entity recognition
- NLP, natural language process
- PCA, principal component analysis
- PSI, percent spliced in index
- RF, random-forest
- SF, splicing factor
- TCGA, The Cancer Genome Atlas
- Text-mining
- Tumor transcriptome
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Affiliation(s)
- Kyubin Lee
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Daejin Hyung
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Soo Young Cho
- Department of Molecular & Life Science, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan-si, Gyeonggi-do 15588, Republic of Korea
| | - Namhee Yu
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Sewha Hong
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Jihyun Kim
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Department of Precision Medicine, National Institute of Health, Korea Disease Control and Prevention Agency, Osong Health Technology Administration Complex, 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159, Republic of Korea
| | - Sunshin Kim
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Ji-Youn Han
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Charny Park
- Research Institute, National Cancer Center, 232 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
- Correspondence to: 323 Ilsan-ro, Ilsandonggu, Goyang-si, Gyeonggi-do 10408, Republic of Korea.
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Kim SH, Cho SY. Single-cell transcriptomics to understand the cellular heterogeneity in toxicology. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Background
Identification of molecular signatures from omics studies is widely applied in toxicological studies, and the evaluation of potential toxic effects provides novel insights into molecular resolution.
Objective
The prediction of toxic effects and drug tolerance provides important clues regarding the mode of action of target compounds. However, heterogeneity within samples makes toxicology studies challenging because the purity of the target cell in the samples remains unknown until their actual utilization.
Result
Single-cell resolution studies have been suggested in toxicogenomics, and several studies have explained toxic effects and drug tolerance using heterogeneous cells in both in vivo and in vitro conditions. In this review, we presented an understanding of single-cell transcriptomes and their applications in toxicogenomics.
Conclusion
The most toxicological mechanism in organisms occurs through intramolecular combinations, and heterogeneity issues have reached a surmountable level. We hope this review provides insights to successfully conduct future studies on toxicology.
Purpose of the review
Toxicogenomics is an interdisciplinary field between toxicology and genomics that was successfully applied to construct molecular profiles in a broad spectrum of toxicology. However, heterogeneity within samples makes toxicology studies challenging because the purity of target cell in the samples remains unknown until their actual utilisation. In this review, we presented an understanding of single-cell transcriptomes and their applications in toxicogenomics.
Recent findings
A high-throughput techniques have been used to understand cellular heterogeneity and molecular mechanisms at toxicogenomics. Single-cell resolution analysis is required to identify biomarkers of explain toxic effect and in order to understand drug tolerance.
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Kim KH, Park J, Cho Y, Cho SY, Lee B, Jeong H, Lee Y, Yi JW, Oh Y, Lee JJ, Wang TC, Lim KM, Nam KT. Histamine Signaling Is Essential for Tissue Macrophage Differentiation and Suppression of Bacterial Overgrowth in the Stomach. Cell Mol Gastroenterol Hepatol 2022; 15:213-236. [PMID: 36167263 PMCID: PMC9672892 DOI: 10.1016/j.jcmgh.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND & AIMS Histamine in the stomach traditionally is considered to regulate acid secretion but also has been reported to participate in macrophage differentiation, which plays an important role in tissue homeostasis. Therefore, this study aimed to uncover the precise role of histamine in mediating macrophage differentiation and in maintaining stomach homeostasis. METHODS Here, we expand on this role using histidine decarboxylase knockout (Hdc-/-) mice with hypertrophic gastropathy. In-depth in vivo studies were performed in Hdc-/- mice, germ-free Hdc-/- mice, and bone-marrow-transplanted Hdc-/- mice. The stomach macrophage populations and function were characterized by flow cytometry. To identify stomach macrophages and find the new macrophage population, we performed single-cell RNA sequencing analysis on Hdc+/+ and Hdc-/- stomach tissues. RESULTS Single-cell RNA sequencing and flow cytometry of the stomach cells of Hdc-/- mice showed alterations in the ratios of 3 distinct tissue macrophage populations (F4/80+Il1bhigh, F4/80+CD93+, and F4/80-MHC class IIhighCD74high). Tissue macrophages of the stomachs of Hdc-/- mice showed impaired phagocytic activity, increasing the bacterial burden of the stomach and attenuating hypertrophic gastropathy in germ-free Hdc-/- mice. The transplantation of bone marrow cells of Hdc+/+ mice to Hdc-/- mice recovered the normal differentiation of stomach macrophages and relieved the hypertrophic gastropathy of Hdc-/- mice. CONCLUSIONS This study showed the importance of histamine signaling in tissue macrophage differentiation and maintenance of gastric homeostasis through the suppression of bacterial overgrowth in the stomach.
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Affiliation(s)
- Kwang H. Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Yejin Cho
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Cho
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Buhyun Lee
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Haengdueng Jeong
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yura Lee
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ja-Woon Yi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Yeseul Oh
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin-Jae Lee
- Department of Life Science, Hallym University, Chuncheon, Republic of Korea
| | - Timothy C. Wang
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Center, Columbia University, New York, New York
| | - Kyung-Min Lim
- College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea.
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.
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10
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Kang H, Cho SY, Suk EH, Ju W, Choi JY. Massive hemothorax following internal jugular vein catheterization under ultrasound guidance: A case report. World J Clin Cases 2022; 10:5776-5782. [PMID: 35979121 PMCID: PMC9258369 DOI: 10.12998/wjcc.v10.i17.5776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/22/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hemothorax is a rare but life-threatening complication of central venous catheterization. Recent reports suggest that ultrasound guidance may reduce complications however, it does not guarantee safety
CASE SUMMARY A 75-year-old male patient was admitted for laparoscopic radical nephrectomy. Under ultrasound guidance, right internal jugular vein catheterization was successfully achieved after failure to aspirate blood from the catheter in the first attempt. Sudden hypotension developed after surgical positioning and persisted until the end of the operation, lasting for about 4 h. In the recovery room, a massive hemothorax was identified on chest radiography and computed tomography. The patient recovered following chest tube drainage of 1.6 L blood.
CONCLUSION Hemothorax must be suspected when unexplained hemodynamic instability develops after central venous catheterization despite ultrasound guidance. So the proper use of ultrasound is important
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Affiliation(s)
- Hyun Kang
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Soo Young Cho
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Eun Ha Suk
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Wan Ju
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Joon Yong Choi
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
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11
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Lee K, Yu D, Hyung D, Cho SY, Park C. ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. Genomics Proteomics Bioinformatics 2022; 20:466-482. [PMID: 35085775 PMCID: PMC9801047 DOI: 10.1016/j.gpb.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 01/26/2023]
Abstract
Alternative splicing (AS) regulates biological processes governing phenotypes and diseases. Differential AS (DAS) gene test methods have been developed to investigate important exonic expression from high-throughput datasets. However, the DAS events extracted using statistical tests are insufficient to delineate relevant biological processes. In this study, we developed a novel application, Alternative Splicing Encyclopedia: Functional Interaction (ASpediaFI), to systemically identify DAS events and co-regulated genes and pathways. ASpediaFI establishes a heterogeneous interaction network of genes and their feature nodes (i.e., AS events and pathways) connected by co-expression or pathway gene set knowledge. Next, ASpediaFI explores the interaction network using the random walk with restart algorithm and interrogates the proximity from a query gene set. Finally, ASpediaFI extracts significant AS events, genes, and pathways. To evaluate the performance of our method, we simulated RNA sequencing (RNA-seq) datasets to consider various conditions of sequencing depth and sample size. The performance was compared with that of other methods. Additionally, we analyzed three public datasets of cancer patients or cell lines to evaluate how well ASpediaFI detects biologically relevant candidates. ASpediaFI exhibits strong performance in both simulated and public datasets. Our integrative approach reveals that DAS events that recognize a global co-expression network and relevant pathways determine the functional importance of spliced genes in the subnetwork. ASpediaFI is publicly available at https://bioconductor.org/packages/ASpediaFI.
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12
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Park JW, Seo MJ, Cho KS, Kook MC, Jeong JM, Roh SG, Cho SY, Cheon JH, Kim HK. Smad4 and p53 synergize in suppressing autochthonous intestinal cancer. Cancer Med 2022; 11:1925-1936. [PMID: 35274815 PMCID: PMC9089223 DOI: 10.1002/cam4.4533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022] Open
Abstract
Background Smad4 and p53 mutations are the most common mutations in human colorectal cancers (CRCs). We evaluated whether and how they are synergistic in intestinal carcinogenesis using novel autochthonous mouse models. Method To recapitulate human CRCs, we generated Villin‐Cre;Smad4F/F;Trp53F/F mice. We then compared the intestinal phenotype of Villin‐Cre;Smad4F/F;Trp53F/F mice (n = 40) with Villin‐Cre;Smad4F/F (n = 30) and Villin‐Cre;Trp53F/F mice (n = 45). Results Twenty‐week‐old Villin‐Cre;Smad4F/F;Trp53F/F mice displayed spontaneous highly proliferative intestinal tumors, and 85% of mice developed adenocarcinomas. p21 was downregulated in the intestinal mucosa in Villin‐Cre;Smad4F/F;Trp53F/F mice than in Villin‐Cre;Smad4F/F and Villin‐Cre;Trp53F/F mice. Villin‐Cre;Smad4F/F;Trp53F/F mice displayed multistep intestinal tumorigenesis and Wnt activation. Long‐term CWP232291 (small‐molecule Wnt inhibitor) treatment of Villin‐Cre;Smad4F/F;Trp53F/F mice suppressed intestinal tumorigenesis and progression. CWP232291 treatment downregulated cancer stem cell (CSC) tumor markers including CD133, Lgr‐5, and Sca‐1. CWP232291 treatment reduced the CSC frequency. Small‐molecule Wnt inhibitors reduced intestinal CSC populations and inhibited their growth, along with Bcl‐XL downregulation. Furthermore, BH3I‐1, a Bcl‐XL antagonist, increasingly inhibited intestinal CSCs than bulk tumor cells. Conclusion Smad4 loss and p53 loss are synergistic in autochthonous intestinal carcinogenesis, by downregulating p21 and activating Wnt/β‐catenin pathway.
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Affiliation(s)
- Jun Won Park
- National Cancer Center, Goyang, Republic of Korea.,Department of Biomedical Convergence, Kangwon National University, Kangwon, Republic of Korea
| | - Min-Jung Seo
- National Cancer Center, Goyang, Republic of Korea
| | - Kye Soo Cho
- National Cancer Center, Goyang, Republic of Korea.,Department of Infectious Disease & Immunobiology, Yonsei University College of Medical Science, Seoul, Republic of Korea
| | | | | | - Seul-Gi Roh
- National Cancer Center, Goyang, Republic of Korea.,Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | | | - Jae Hee Cheon
- Department of Infectious Disease & Immunobiology, Yonsei University College of Medical Science, Seoul, Republic of Korea
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13
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Cho SY, Ho DH, Choi YY, Lim S, Lee S, Suk JW, Jo SB, Cho JH. A general fruit acid chelation route for eco-friendly and ambient 3D printing of metals. Nat Commun 2022; 13:104. [PMID: 35256609 PMCID: PMC8901924 DOI: 10.1038/s41467-021-27730-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
AbstractRecent advances in metal additive manufacturing (AM) have provided new opportunities for prompt designs of prototypes and facile personalization of products befitting the fourth industrial revolution. In this regard, its feasibility of becoming a green technology, which is not an inherent aspect of AM, is gaining more interests. A particular interest in adapting and understanding of eco-friendly ingredients can set its important groundworks. Here, we demonstrate a water-based solid-phase binding agent suitable for binder jetting 3D printing of metals. Sodium salts of common fruit acid chelators form stable metal-chelate bridges between metal particles, enabling elaborate 3D printing of metals with improved strengths. Even further reductions in the porosity between the metal particles are possible through post-treatments. A compatibility of this chelation chemistry with variety of metals is also demonstrated. The proposed mechanism for metal 3D printing can open up new avenues for consumer-level personalized 3D printing of metals.
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14
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Kim J, Park C, Kim KH, Kim EH, Kim H, Woo JK, Seong JK, Nam KT, Lee YC, Cho SY. Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity. NPJ Precis Oncol 2022; 6:9. [PMID: 35087207 PMCID: PMC8795238 DOI: 10.1038/s41698-022-00251-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023] Open
Abstract
Single-cell transcriptomic profiles analysis has proposed new insights for understanding the behavior of human gastric cancer (GC). GC offers a unique model of intratumoral heterogeneity. However, the specific classes of cells involved in carcinogenetic passage, and the tumor microenvironment of stromal cells was poorly understood. We characterized the heterogeneous cell population of precancerous lesions and gastric cancer at the single-cell resolution by RNA sequencing. We identified 10 gastric cell subtypes and showed the intestinal and diffuse-type cancer were characterized by different cell population. We found that the intestinal and diffuse-type cancer cells have the differential metaplastic cell lineages: intestinal-type cancer cells differentiated along the intestinal metaplasia lineage while diffuse-type cancer cells resemble de novo pathway. We observed an enriched CCND1 mutation in premalignant disease state and discovered cancer-associated fibroblast cells harboring pro-stemness properties. In particular, tumor cells could be categorized into previously proposed molecular subtypes and harbored specific subtype of malignant cell with high expression level of epithelial-myofibroblast transition which was correlated with poor clinical prognosis. In addition to intratumoral heterogeneity, the analysis revealed different cellular lineages were responsible for potential carcinogenetic pathways. Single-cell transcriptomes analysis of gastric pre-cancerous lesions and cancer may provide insights for understanding GC cell behavior, suggesting potential targets for the diagnosis and treatment of GC.
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Affiliation(s)
- Jihyun Kim
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do, 10408, Republic of Korea
| | - Charny Park
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do, 10408, Republic of Korea
| | - Kwang H Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eun Hye Kim
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Kyu Woo
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea. .,Laboratory of Developmental Biology and Genomics, Research Institute of Veterinary Science, BK21 Program Plus for Advanced Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Yong Chan Lee
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Severance Hospital, Seoul, Republic of Korea.
| | - Soo Young Cho
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do, 10408, Republic of Korea. .,Department of Molecular and Life Science, Hanyang University, Ansan, 15588, Republic of Korea.
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15
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Lee JJ, Kang HY, Lee WI, Cho SY, Kim YJ, Lee HJ. Efflux pump gene expression study using RNA-seq in multidrug-resistant TB. Int J Tuberc Lung Dis 2021; 25:974-981. [PMID: 34886926 DOI: 10.5588/ijtld.21.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: The mechanism underlying kanamycin (KM) resistance in Mycobacterium tuberculosis is not well understood, although efflux pump proteins are thought to play a role. This study used RNA-seq data to investigate changes in the expression levels of efflux pump genes following exposure to KM.METHODS: RNA expression of efflux pump and regulatory genes following exposure to different concentrations of KM (minimum inhibitory concentration MIC 25 and MIC50) in rrs wild-type strain and rrs A1401G mutated strain were compared with the control group.RESULTS: The selected strains had differential RNA expression patterns. Among the 71 putative efflux pump and regulatory genes, 46 had significant fold changes, and 12 genes (Rv0842, Rv1146, Rv1258c, Rv1473, Rv1686c, Rv1687c, Rv1877, Rv2038c, Rv3065, Rv3197a, Rv3728 and Rv3789) that were overexpressed following exposure to KM were thought to contribute to drug resistance. Rv3197A (whiB7) showed a distinct fold change based on the concentration of KM.CONCLUSION: The significant changes in the expression of the efflux pump and regulatory genes following exposure to KM may provide insights into the identification of a new resistance mechanism.
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Affiliation(s)
- J J Lee
- Department of Laboratory Medicine, Graduate School, Kyung Hee University, Seoul, Korea, Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - H Y Kang
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - W-I Lee
- Department of Laboratory Medicine, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, Seoul, Korea
| | - S Y Cho
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - Y J Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - H J Lee
- Korean National Tuberculosis Association, Seoul, Korea
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16
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Yun D, Cho SY, Ju W, Seo EH. Transverse myelitis after infection with varicella zoster virus in patient with normal immunity: A case report. World J Clin Cases 2021; 9:10308-10314. [PMID: 34904104 PMCID: PMC8638050 DOI: 10.12998/wjcc.v9.i33.10308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/21/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Varicella zoster virus (VZV) is a human neurotropic and double-stranded DNA alpha-herpes virus. Primary infection with VZV usually occurs during childhood, manifesting as chickenpox. Reactivation of latent VZV can lead to various neurological complications, including transverse myelitis (TM); although cases of the latter are very rare, particularly in newly active VZV infection.
CASE SUMMARY We report here an unusual case of TM in a middle-aged adult immunocompetent patient that developed concomitant to an active VZV infection. The 46-year-old male presented with painful vesicular eruption on his left chest that had steadily progressed to involvement of his back over a 3-d period. Cerebrospinal fluid testing was denied, but findings from magnetic resonance imaging and collective symptomology indicated TM. He was administered antiviral drugs and corticosteroids immediately but his symptom improvement waxed and waned, necessitating multiple hospital admissions. After about a month of repeated treatments, he was deemed sufficiently improved for hospital discharge to home.
CONCLUSION VZV myelitis should be suspected when a patient visits the outpatient pain clinic with herpes zoster showing neurological symptoms.
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Affiliation(s)
- Daehun Yun
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Soo Young Cho
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Wan Ju
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
| | - Eun Hyoung Seo
- Department of Anesthesiology and Pain Medicine, Kwangju Christian Hospital, Gwangju 61661, South Korea
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17
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Hyung D, Baek MJ, Lee J, Cho J, Kim HS, Park C, Cho SY. Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis. Comput Struct Biotechnol J 2021; 19:4759-4769. [PMID: 34504668 PMCID: PMC8405889 DOI: 10.1016/j.csbj.2021.08.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/30/2022] Open
Abstract
Researchers have gained new therapeutic insights using multi-omics platform approaches to study DNA, RNA, and proteins of comprehensively characterized human cancer cell lines. To improve our understanding of the molecular features associated with oncogenic modulation in cancer, we proposed a proteogenomic database for human cancer cell lines, called Protein-gene Expression Nexus (PEN). We have expanded the characterization of cancer cell lines to include genetic, mRNA, and protein data of 145 cancer cell lines from various public studies. PEN contains proteomic and phosphoproteomic data on 4,129,728 peptides, 13,862 proteins, 7,138 phosphorylation site-associated genomic variations, 117 studies, and 12 cancer. We analyzed functional characterizations along with the integrated datasets, such as cis/trans association for copy number alteration (CNA), single amino acid variation for coding genes, post-translation modification site variation for Single Amino Acid Variation, and novel peptide expression for noncoding regions and fusion genes. PEN provides a user-friendly interface for searching, browsing, and downloading data and also supports the visualization of genome-wide association between CNA and expression, novel peptide landscape, mRNA-protein abundance, and functional annotation. Together, this dataset and PEN data portal provide a resource to accelerate cancer research using model cancer cell lines. PEN is freely accessible at http://combio.snu.ac.kr/pen.
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Affiliation(s)
- Daejin Hyung
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Min-Jeong Baek
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Jongkeun Lee
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Juyeon Cho
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Hyoun Sook Kim
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Charny Park
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Soo Young Cho
- National Cancer Center, 323 Ilsan-ro, Goyang-si, Gyeonggi-do 10408, Republic of Korea.,Department of Molecular and Life Science, Hanyang University, Ansan 15588, Republic of Korea
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18
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Jeong H, Lee B, Kim KH, Cho SY, Cho Y, Park J, Lee Y, Oh Y, Hwang BR, Jang AR, Park JH, Park JH, Jeong SH, Lee D, Lee YC, Lim KM, Goldenring JR, Nam KT. WFDC2 Promotes Spasmolytic Polypeptide-Expressing Metaplasia Through the Up-Regulation of IL33 in Response to Injury. Gastroenterology 2021; 161:953-967.e15. [PMID: 34116028 PMCID: PMC8380710 DOI: 10.1053/j.gastro.2021.05.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS WAP 4-disulfide core domain protein 2 (WFDC2), also known as human epididymis protein 4, is a small secretory protein that is highly expressed in fibrosis and human cancers, particularly in the ovaries, lungs, and stomach. However, the role of WFDC2 in carcinogenesis is not fully understood. The present study aimed to investigate the role of WFDC2 in gastric carcinogenesis with the use of preneoplastic metaplasia models. METHODS Three spasmolytic polypeptide-expressing metaplasia (SPEM) models were established in both wild-type and Wfdc2-knockout mice with DMP-777, L635, and high-dose tamoxifen, respectively. To reveal the functional role of WFDC2, we performed transcriptomic analysis with DMP-777-treated gastric corpus specimens. RESULTS Wfdc2-knockout mice exhibited remarkable resistance against oxyntic atrophy, SPEM emergence, and accumulation of M2-type macrophages in all 3 SPEM models. Transcriptomic analysis revealed that Wfdc2-knockout prevented the up-regulation of interleukin-33 (IL33) expression in the injured mucosal region of SPEM models. Notably, supplementation of recombinant WFDC2 induced IL33 production and M2 macrophage polarization, and ultimately promoted SPEM development. Moreover, long-term treatment with recombinant WFDC2 was able to induce SPEM development. CONCLUSIONS WFDC2 expressed in response to gastric injury promotes SPEM through the up-regulation of IL33 expression. These findings provide novel insights into the role of WFDC2 in gastric carcinogenesis.
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Affiliation(s)
- Haengdueng Jeong
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Buhyun Lee
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang H Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | | | - Yejin Cho
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jeongeun Park
- Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yura Lee
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yeseul Oh
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Bo Ram Hwang
- Department of Internal Medicine, Graduate School, Yonsei University College of Medicine, Seoul, Korea
| | - Ah-Ra Jang
- Laboratory of Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Korea
| | - Jong-Hwan Park
- Laboratory of Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, Korea
| | - Ji-Ho Park
- Department of Surgery, Gyeongsang National University Hospital, Jinju, Korea
| | - Sang-Ho Jeong
- Department of Surgery, Gyeongsang National University Hospital, Jinju, Korea
| | - Daekee Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yong Chan Lee
- Department of Internal Medicine, Graduate School, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-Min Lim
- College of Pharmacy, Ewha Womans University, Seoul, Korea.
| | - James R Goldenring
- Epithelial Biology Center and Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee; Nashville VA Medical Center, Nashville, Tennessee.
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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19
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Park JW, Jeong JM, Cho KS, Cho SY, Cheon JH, Choi DH, Park SJ, Kim HK. MiR-30a and miR-200c differentiate cholangiocarcinomas from gastrointestinal cancer liver metastases. PLoS One 2021; 16:e0250083. [PMID: 33852640 PMCID: PMC8046207 DOI: 10.1371/journal.pone.0250083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Prior studies have demonstrated the utility of microRNA assays for predicting some cancer tissue origins, but these assays need to be further optimized for predicting the tissue origins of adenocarcinomas of the liver. We performed microRNA profiling on 195 frozen primary tumor samples using 14 types of tumors that were either adenocarcinomas or differentiated from adenocarcinomas. The 1-nearest neighbor method predicted tissue-of-origin in 33 samples of a test set, with an accuracy of 93.9% at feature selection p values ranging from 10-4 to 10-10. According to binary decision tree analyses, the overexpression of miR-30a and the underexpression of miR-200 family members (miR-200c and miR-141) differentiated intrahepatic cholangiocarcinomas from extrahepatic adenocarcinomas. When binary decision tree analyses were performed using the test set, the prediction accuracy was 84.8%. The overexpression of miR-30a and the reduced expressions of miR-200c, miR-141, and miR-425 could distinguish intrahepatic cholangiocarcinomas from liver metastases from the gastrointestinal tract.
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Affiliation(s)
- Jun Won Park
- National Cancer Center of Korea, Goyang, Republic of Korea
- Department of Biomedical Convergence, Kangwon National University, Kangwon, Republic of Korea
| | - Jong Min Jeong
- National Cancer Center of Korea, Goyang, Republic of Korea
| | - Kye Soo Cho
- National Cancer Center of Korea, Goyang, Republic of Korea
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Cho
- National Cancer Center of Korea, Goyang, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dong Ho Choi
- Departments of Surgery, Hanyang University School of Medicine, Seoul, Republic of Korea
| | - Sang Jae Park
- National Cancer Center of Korea, Goyang, Republic of Korea
| | - Hark Kyun Kim
- National Cancer Center of Korea, Goyang, Republic of Korea
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20
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Romano C, Cho SY, Marino S, Raucci U, Fiumara A, Falsaperla R, Massimino CR, Taibi R, Greco F, Venti V, Sullo F, Fontana A, Rizzo R, Pustorino E, Jin DK, Pavone P. Primary headache in childhood associated with psychiatric disturbances: an update. Eur Rev Med Pharmacol Sci 2020; 24:6893-6898. [PMID: 32633382 DOI: 10.26355/eurrev_202006_21680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Primary headache disorders in children are one of the most prominent topics in the pediatric neurology literature. However, there are many unsolved aspects, including the conditions associated with migraine. The present study aims to report on the frequency of behavioral comorbidities in the setting of primary headache in childhood. PATIENTS AND METHODS In this study, we enlisted 475 children (290 males and 185 females; ratio 1.6:1), aged 4 to 14 years, who were affected by primary headache. In direct interviews, children and parents gave information on the association of their headache with, attention-deficit/hyperactivity disorder, learning disabilities, tics, anxiety, depression, and obsessive-compulsive disorder. Other 475 children with no history of headache or recognized neurological conditions were matched for age, sex, race, and socioeconomic status and were used as controls. RESULTS A significant association of primary headache was found with anxiety and depression (p-value <0.001); overall, behavioral disorders were more common in children who experienced headache than in controls (p-value <0.001). CONCLUSIONS Primary headache in children is not associated with most of the common behavioral conditions. On the contrary, there was a significant association with anxiety and depression, as reported in adults.
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Affiliation(s)
- C Romano
- Department Clinical and Experimental Medicine, Child and Adolescent Neuropsychiatry, University of Catania, Catania, Italy.
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21
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Kim SM, Cho SY, Kim MW, Roh SR, Shin HS, Suh YH, Geum D, Lee MA. Genome-Wide Analysis Identifies NURR1-Controlled Network of New Synapse Formation and Cell Cycle Arrest in Human Neural Stem Cells. Mol Cells 2020; 43:551-571. [PMID: 32522891 PMCID: PMC7332357 DOI: 10.14348/molcells.2020.0071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 02/07/2023] Open
Abstract
Nuclear receptor-related 1 (Nurr1) protein has been identified as an obligatory transcription factor in midbrain dopaminergic neurogenesis, but the global set of human NURR1 target genes remains unexplored. Here, we identified direct gene targets of NURR1 by analyzing genome-wide differential expression of NURR1 together with NURR1 consensus sites in three human neural stem cell (hNSC) lines. Microarray data were validated by quantitative PCR in hNSCs and mouse embryonic brains and through comparison to published human data, including genome-wide association study hits and the BioGPS gene expression atlas. Our analysis identified ~40 NURR1 direct target genes, many of them involved in essential protein modules such as synapse formation, neuronal cell migration during brain development, and cell cycle progression and DNA replication. Specifically, expression of genes related to synapse formation and neuronal cell migration correlated tightly with NURR1 expression, whereas cell cycle progression correlated negatively with it, precisely recapitulating midbrain dopaminergic development. Overall, this systematic examination of NURR1-controlled regulatory networks provides important insights into this protein's biological functions in dopamine-based neurogenesis.
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Affiliation(s)
- Soo Min Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | | | - Min Woong Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Seung Ryul Roh
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Hee Sun Shin
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Dongho Geum
- Department of Medical Science, Korea University Medical School, Seoul 02841, Korea
| | - Myung Ae Lee
- Department of Brain Science, Ajou University School of Medicine, Suwon 6499, Korea
- Neuroscience Graduate Program, Department of Biomedical Sciences, Graduate School of Ajou University, Suwon 16499, Korea
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22
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Lee EY, Yu JY, Paek AR, Lee SH, Jang H, Cho SY, Kim JH, Kang HG, Yun T, Oh SE, Park SY, You HJ. Targeting TJP1 attenuates cell-cell aggregation and modulates chemosensitivity against doxorubicin in leiomyosarcoma. J Mol Med (Berl) 2020; 98:761-773. [PMID: 32318747 DOI: 10.1007/s00109-020-01909-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/24/2022]
Abstract
Tight junction protein 1 (TJP1) is a membrane-associated cytosolic protein important for cell-cell communication in intercellular barriers in epithelial and non-epithelial cells. Here, we explored the functional involvement of TJP1 in non-epithelial tumors such as soft tissue sarcoma, especially in leiomyosarcoma (LMS). TJP1 expression in soft tissue sarcoma was analyzed in normal and tumor tissues as well as from public datasets such as the TCGA provisional dataset, in which TJP1 expression was compared with other subtypes such as undifferentiated sarcomas, and myxofibrosarcomas. SK-LMS-1 cell lines with reduced TJP1 expression showed attenuated anchorage-independent colony formation as well as reduced intercellular aggregation on non-coated culture plates compared with control as well as parental SK-LMS-1 cells. Transcriptome profiling following TJP1 knockdown in SK-LMS-1 cells suggested the involvement of several signaling pathways, including NF-κB pathway and growth factor receptor signaling. In addition, TJP1 downregulation induced enhanced response against anti-cancer agents, doxorubicin and gefitinib. Taken together, these results suggest that TJP1 contributes to sarcoma genesis and might be useful therapeutic target. KEY MESSAGES: • TJP1 expression at RNA level higher in tumor than in normal tissues of sarcoma. • Targeting TJP1 attenuates cell-cell aggregation and anchorage-independent growth. • Targeting TJP1 is beneficial in anti-cancer therapy in LMS.
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Affiliation(s)
- Eun-Young Lee
- Division of Translational Science, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea.,Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, 38541, South Korea
| | - Jung Yeon Yu
- Division of Translational Science, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea
| | - A Rome Paek
- Division of Translational Science, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea
| | - So Hee Lee
- Division of Translational Science, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea
| | - Hyonchol Jang
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy (NCC-GCSP), National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea.,Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, South Korea
| | - Soo Young Cho
- Clinical Genomic Analysis Branch, Research Institute, National Cancer Center, Goyang, South Korea
| | - June Hyuk Kim
- National Cancer Center Hospital, National Cancer Center, Goyang, South Korea
| | - Hyun Guy Kang
- National Cancer Center Hospital, National Cancer Center, Goyang, South Korea
| | - Tak Yun
- National Cancer Center Hospital, National Cancer Center, Goyang, South Korea
| | - Sung Eun Oh
- National Cancer Center Hospital, National Cancer Center, Goyang, South Korea
| | - Seog Yun Park
- National Cancer Center Hospital, National Cancer Center, Goyang, South Korea
| | - Hye Jin You
- Division of Translational Science, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea. .,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy (NCC-GCSP), National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea.
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23
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Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu CW, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy MF, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SDM, Smedley D, Flicek P, Mallon AM, Parkinson H, Meehan TF. Soft windowing application to improve analysis of high-throughput phenotyping data. Bioinformatics 2020; 36:1492-1500. [PMID: 31591642 PMCID: PMC7115897 DOI: 10.1093/bioinformatics/btz744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/20/2019] [Accepted: 10/04/2019] [Indexed: 11/14/2022] Open
Abstract
Motivation High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. Results Here we introduce ‘soft windowing’, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype–phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. Availability and implementation The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jeremy C Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Violeta Munoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Federico López-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kolawole Babalola
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Elif F Acar
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada.,Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jacqui White
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ritu Bohat
- Baylor College of Medicine, Houston, TX, USA
| | | | | | - Jong Kyoung Kim
- Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
| | | | | | | | - Lore Becker
- Helmholtz Center Munich, Neuherberg, Germany
| | | | - David Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Soo Young Cho
- National Cancer Center (NCC) & Korea Mouse Phenotyping Center (KMPC), Korea
| | | | | | - Kyung Dong Soo
- Seoul National University & Korea Mouse Phenotyping Center (KMPC), Korea
| | - Alexandr Bezginov
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada
| | - Ghina Bou About
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Laurent Vasseur
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | - Patrick T Reilly
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | | | | | | | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France
| | | | - Obata Yuichi
- RIKEN BioResource Research Center, Tsukuba, Japan
| | | | | | - Wurst Wolfgang
- Institute of Developmental Genetics, Helmholtz Centre Munich, Munich, Germany
| | | | | | - Colin McKerlie
- The Centre for Phenogenomics.,The Hospital for Sick Children, Toronto, Canada
| | - Je Kyung Seong
- Seoul National University & Korea Mouse Phenotyping Center (KMPC), Korea
| | - Herault Yann
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404 Illkirch, France
| | | | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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24
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Hyung D, Mallon AM, Kyung DS, Cho SY, Seong JK. TarGo: network based target gene selection system for human disease related mouse models. Lab Anim Res 2019; 35:23. [PMID: 32257911 PMCID: PMC7081697 DOI: 10.1186/s42826-019-0023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022] Open
Abstract
Genetically engineered mouse models are used in high-throughput phenotyping screens to understand genotype-phenotype associations and their relevance to human diseases. However, not all mutant mouse lines with detectable phenotypes are associated with human diseases. Here, we propose the “Target gene selection system for Genetically engineered mouse models” (TarGo). Using a combination of human disease descriptions, network topology, and genotype-phenotype correlations, novel genes that are potentially related to human diseases are suggested. We constructed a gene interaction network using protein-protein interactions, molecular pathways, and co-expression data. Several repositories for human disease signatures were used to obtain information on human disease-related genes. We calculated disease- or phenotype-specific gene ranks using network topology and disease signatures. In conclusion, TarGo provides many novel features for gene function prediction.
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Affiliation(s)
- Daejin Hyung
- 1National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408 Republic of Korea
| | - Ann-Marie Mallon
- 2MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire, OX11 0RD UK
| | - Dong Soo Kyung
- 3Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea.,5Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Soo Young Cho
- 1National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea
| | - Je Kyung Seong
- 3Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea.,5Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, 08826 Republic of Korea
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25
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Hyung D, Kim J, Cho SY, Park C. ASpedia: a comprehensive encyclopedia of human alternative splicing. Nucleic Acids Res 2019; 46:D58-D63. [PMID: 29106599 PMCID: PMC5753336 DOI: 10.1093/nar/gkx1014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/12/2017] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing confers the human genome complexity by increasing the diversity of expressed mRNAs. Hundreds or thousands of splicing regions have been identified through differential alternative splicing analysis of high-throughput datasets. However, it is hard to explain the functional impact of each splicing event. Protein domain formation and nonsense-mediated decay are considered the main functional features of splicing. However, other functional features such as miRNA target sites, phosphorylation sites and single-nucleotide variations are directly affected by alternative splicing and affect downstream function. Hence, we established ASpedia: a comprehensive database for human alternative splicing annotation, which encompasses a range of functions, from genomic annotation to isoform-specific function (ASpedia, http://combio.snu.ac.kr/aspedia). The database provides three features: (i) genomic annotation extracted from DNA, RNA and proteins; (ii) transcription and regulation elements analyzed from next-generation sequencing datasets; and (iii) isoform-specific functions collected from known and published datasets. The ASpedia web application includes three components: an annotation database, a retrieval system and a browser specialized in the identification of human alternative splicing events. The retrieval system supports multiple AS event searches resulting from high-throughput analysis and the AS browser comprises genome tracks. Thus, ASpedia facilitates the systemic annotation of the functional impacts of multiple AS events.
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Affiliation(s)
- Daejin Hyung
- Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea.,Department of Computer Engineering, Dong-A University, 37 Nakdong-daero 550 Beon-gil, Saha-gu, Busan 49315, Republic of Korea
| | - Jihyun Kim
- Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea
| | - Soo Young Cho
- Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea
| | - Charny Park
- Research Institute, National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408, Republic of Korea
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26
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Park C, Yoon K, Kim J, Park IH, Park SJ, Kim MK, Jang W, Cho SY, Park B, Kong S, Lee ES. Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women. Cancer Sci 2019; 110:1760-1770. [PMID: 30811755 PMCID: PMC6500962 DOI: 10.1111/cas.13982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 11/28/2022] Open
Abstract
Very young breast cancer patients are more common in Asian countries than Western countries and are thought to have worse prognosis than older patients. The aim of the current study was to identify molecular characteristics of young patients with estrogen receptor (ER)-positive breast cancer by analyzing mutations and copy number variants (CNV), and by applying expression profiling. The whole exome and transcriptome of 47 Korean young breast cancer (KYBR) patients (age <35) were analyzed. Genomic profiles were constructed using mutations, CNV and differential gene expression from sequencing data. Pathway analyses were also performed using gene sets to identify biological processes. Our data were compared with young ER+ breast cancer patients in The Cancer Genome Atlas (TCGA) dataset. TP53, PIK3CA and GATA3 were highly recurrent somatic mutation genes. APOBEC-associated mutation signature was more frequent in KYBR compared with young TCGA patients. Integrative profiling was used to classify our patients into 3 subgroups based on molecular characteristics. Group A showed luminal A-like subtype and IGF1R signal dysregulation. Luminal B patients were classified into groups B and C, which showed chromosomal instability and enrichment for APOBEC3A/B deletions, respectively. Group B was characterized by 11q13 (CCND1) amplification and activation of the ubiquitin-mediated proteolysis pathway. Group C showed 17q12 (ERBB2) amplification and lower ER and progesterone receptor expression. Group C was also distinguished by immune activation and lower epithelial-mesenchyme transition (EMT) degree compared with group B. This study showed that integrative genomic profiling could classify very young patients with breast cancer into molecular subgroups that are potentially linked to different clinical characteristics.
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Affiliation(s)
- Charny Park
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Kyong‐Ah Yoon
- Laboratory of BiochemistryCollege of Veterinary MedicineKonkuk UniversitySeoulKorea
| | - Jihyun Kim
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - In Hae Park
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
| | - Soo Jin Park
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
| | - Min Kyeong Kim
- Translational Cancer Research BranchDivision of Translational ScienceNational Cancer CenterGoyangKorea
| | - Wooyeong Jang
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Soo Young Cho
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Boyoung Park
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
| | - Sun‐Young Kong
- Translational Cancer Research BranchDivision of Translational ScienceNational Cancer CenterGoyangKorea
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
| | - Eun Sook Lee
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
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27
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Abstract
Intratumor heterogeneity within a single tumor mass is one of the hallmarks of malignancy and has been reported in various tumor types. The molecular characterization of intratumor heterogeneity in breast cancer is a significant challenge for effective treatment. Using single-cell RNA sequencing (RNA-seq) data from a public resource, an ERBB pathway activated triple-negative cell population was identified. The differential expression of three subtyping marker genes (ERBB2, ESR1, and PGR) was not changed in the bulk RNA-seq data, but the single-cell transcriptomes showed intratumor heterogeneity. This result shows that ERBB signaling is activated using an indirect route and that the molecular subtype is changed on a single-cell level. Our data propose a different view on breast cancer subtypes, clarifying much confusion in this field and contributing to precision medicine.
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Affiliation(s)
- Soo Young Cho
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Korea
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Cho BW, Kim HK, Kim MS, Hwang JH, Yoon U, Cho SY, Choo CO. Radon concentrations in the community groundwater system of South Korea. Environ Monit Assess 2019; 191:189. [PMID: 30806813 DOI: 10.1007/s10661-019-7301-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
Groundwater samples were collected from 3818 wells used for the community groundwater system (CGS) in the remote rural areas of South Korea and analyzed to determine radon concentrations. Radon concentrations varied with rock type, ranging from 0.1 to 2393.5 Bq/L with an average of 86.6 Bq/L and a median of 46.4 Bq/L. Among 10 geological units, the median CGS radon concentration was highest (59.6-103.0 Bq/L) in granite, and lower in sedimentary rocks (16.9-21.1 Bq/L) and porous volcanic rocks (17.6 Bq/L), respectively. Of the 3818 samples, 26.1% exceeded the World Health Organization (WHO) radon level limit of 100 Bq/L. The application of the natural radon reduction rate (26.5%) recently suggested by Yun et al. Applied Radiation and Isotopes, 126(1), 23-25 (2017) to the CGS water tank appeared to decrease exceedance of the WHO radon level limit to 20.2%. Because of the high radon concentrations in CGS groundwater in South Korea, the establishment of a radon level limit for drinking water is strongly recommended to ensure the health and safety of the people using CGS water.
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Affiliation(s)
- Byong Wook Cho
- Korea Institute of Geosciences and Mineral Resources (KIGAM), 124, Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Hyeon Koo Kim
- National Institute of Environmental Research (NIER), Hwangyong-ro 42, Seogu, Incheon, South Korea
| | - Moon Su Kim
- National Institute of Environmental Research (NIER), Hwangyong-ro 42, Seogu, Incheon, South Korea
| | - Jae Hong Hwang
- Korea Institute of Geosciences and Mineral Resources (KIGAM), 124, Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Uk Yoon
- Korea Institute of Geosciences and Mineral Resources (KIGAM), 124, Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Soo Young Cho
- Korea Institute of Geosciences and Mineral Resources (KIGAM), 124, Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Chang Oh Choo
- Department of Geology, Kyungpook National University, 80, Daehak-ro, Bukgu, Daegu, South Korea.
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Kan Z, Lal S, Ding Y, Lee JE, Lee SH, Lee SK, Yu JH, Choi YL, Kim SW, Nam SJ, Kim JY, Ram S, Powell E, Ching K, Cho SY, Bonato V, Deng S, Park WY, Rejto P, Bienkowska J, Park YH. Abstract PD5-08: Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-pd5-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Understanding how standard-of-care drug treatments affect tumor intrinsic biology and microenvironment is critical for elucidating drug resistance mechanisms and developing better combination therapies as well as new therapies. To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome, transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole exome and whole transcriptome sequencing of a large longitudinal breast cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%) patients achieved pathologic complete response (pCR) while 85 patients (62%) had residual disease with standard chemotherapy regimen. Tumor biopsies were collected for each patient at three time points – pre-treatment, three weeks after the first cycle of anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype. We detected 5,955 protein-altering somatic mutations affecting 4,414 genes in pretreatment samples and 502 acquired mutations in surgery samples affecting 477 genes including 19recurrently mutated genes such as TP53 and NOTCH1. Across all subtypes, 4,346 genes were differentially expressed (DE) following NAC treatment and significantly enriched in pathways such as cell cycle, ER signaling, PI3K/mTOR, immune and metabolism. Expression-based virtual microdissection analysis indicated that NAC treatment induced an increase in the fractions of stromal and adjacent normal tissue compartment, consistent with observed reduction in tumor cellularity. To assess the NAC induced changes in the molecular landscape of these tumors, we compared molecular features including gene expression signatures, mutation prevalence and copy number alteration between three time points while adjusting for confounding effects of molecular subtype and tumor cellularity. We found that NAC induced dynamic changes in gene expression signatures associated with proliferation and immunomodulatory treatment response. We further validated the observed pattern of change in TILs through histopathology and digital imaging analyses. In pretreatment tumors, 116 genes were DE between patients with pCR vs. those with residual disease with significant enrichment in immune/inflammatory pathways. Further, pre-treatment TIL levels were found to be significantly associated with pCR, echoing previous reports in breast cancers that implicated anti-tumor immunity in mediating the efficacy of chemotherapies. Our analyses also revealed associations between NAC response and baseline genomic attributes such as genomic alterations that affect DNA damage repair pathways. Taken together, these results suggest that NAC induced a multitude of changes on the genomic landscape and immune microenvironment of breast cancers, some of which point to combination strategies with immunomodulatory therapies and therapies that target DNA damage repair.
Citation Format: Kan Z, Lal S, Ding Y, Lee JE, Lee S-H, Lee SK, Yu JH, Choi Y-l, Kim SW, Nam SJ, Kim J-Y, Ram S, Powell E, Ching K, Cho SY, Bonato V, Deng S, Park W-Y, Rejto P, Bienkowska J, Park Y-H. Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD5-08.
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Affiliation(s)
- Z Kan
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - S Lal
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - Y Ding
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - JE Lee
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - S-H Lee
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - SK Lee
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - JH Yu
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - Y-l Choi
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - SW Kim
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - SJ Nam
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - J-Y Kim
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - S Ram
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - E Powell
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - K Ching
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - SY Cho
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - V Bonato
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - S Deng
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - W-Y Park
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - P Rejto
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - J Bienkowska
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
| | - Y-H Park
- Pfizer, San Diego, CA; Samsung Medical Center, Seoul, Korea
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Kim J, Kim JH, Kang HG, Park SY, Yu JY, Lee EY, Oh SE, Kim YH, Yun T, Park C, Cho SY, You HJ. Integrated molecular characterization of adult soft tissue sarcoma for therapeutic targets. BMC Med Genet 2018; 19:216. [PMID: 30598078 PMCID: PMC6311917 DOI: 10.1186/s12881-018-0722-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Several studies have investigated the molecular drivers and therapeutic targets in adult soft tissue sarcomas. However, such studies are limited by the genomic heterogeneity and rarity of sarcomas, particularly in those with complex and unbalanced karyotypes. Additional biomarkers are needed across sarcoma types to improve therapeutic strategies. To investigate the molecular characteristics of complex karyotype sarcomas (CKSs) for therapeutic targets, we performed genomic profiling. Results The mutational landscape showed that TP53, ATRX, and PTEN genes were highly mutated. CKS samples were categorized into three groups based on copy number variations that were associated with CDK4 and RB1 signatures. Integrated analysis of genomic and transcriptomic data revealed several pathways related to PDGFR, which could be a strategic target for anti-sarcoma therapy. Conclusions This study provides a detailed molecular classification of CKSs and proposes several therapeutic targets. Targeted or combinational therapies for treating CKS should be considered before chemotherapy. Electronic supplementary material The online version of this article (10.1186/s12881-018-0722-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jihyun Kim
- Clinical Genomic Analysis Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea
| | - June Hyuk Kim
- Orthopaedic Oncology Clinic, Hospital, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Hyun Guy Kang
- Orthopaedic Oncology Clinic, Hospital, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea.,Department of Cancer Biomedical Science, NCC-GCSP, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Seog Yun Park
- Division of Pathology, Hospital, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Jung Yeon Yu
- Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Eun Young Lee
- Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Sung Eun Oh
- Orthopaedic Oncology Clinic, Hospital, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Young Ho Kim
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Tak Yun
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea
| | - Charny Park
- Clinical Genomic Analysis Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea
| | - Soo Young Cho
- Clinical Genomic Analysis Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Gyeonggi, 10408, South Korea.
| | - Hye Jin You
- Department of Cancer Biomedical Science, NCC-GCSP, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea. .,Translational Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, 10408, South Korea.
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Ko JH, Kang CI, Cornejo-Juárez P, Yeh KM, Wang CH, Cho SY, Gözel MG, Kim SH, Hsueh PR, Sekiya N, Matsumura Y, Lee DG, Cho SY, Shiratori S, Kim YJ, Chung DR, Peck KR. Fluoroquinolones versus trimethoprim-sulfamethoxazole for the treatment of Stenotrophomonas maltophilia infections: a systematic review and meta-analysis. Clin Microbiol Infect 2018; 25:546-554. [PMID: 30448331 DOI: 10.1016/j.cmi.2018.11.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/05/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND Fluoroquinolones are a popular alternative to trimethoprim-sulfamethoxazole for Stenotrophomonas maltophilia infections. OBJECTIVES To compare the effects of fluoroquinolones and trimethoprim-sulfamethoxazole on mortality of S. maltophilia infections. DATA SOURCES PubMed and EMBASE. STUDY ELIGIBILITY CRITERIA Clinical studies reporting mortality outcomes of S. maltophilia infections. PARTICIPANTS Patients with clinical infections caused by S. maltophilia. INTERVENTIONS Fluoroquinolone monotherapy in comparison with trimethoprim-sulfamethoxazole monotherapy. METHODS Systematic review with meta-analysis technique. RESULTS Seven retrospective cohort and seven case-control studies were included. Three cohort studies were designed to compare the two drugs, whereas others had other purposes. A total of 663 patients were identified, 332 of which were treated with trimethoprim-sulfamethoxazole (50.1%) and 331 with fluoroquinolones (49.9%). Three cohort studies were designed to compare the effect of the two drugs, whereas the others had other purposes. Levofloxacin was most frequently used among fluoroquinolones (187/331, 56.5%), followed by ciprofloxacin (114/331, 34.4%). The overall mortality rate was 29.6%. Using pooled ORs for the mortality of each study, fluoroquinolone treatment (OR 0.62, 95% CI 0.39-0.99) was associated with survival benefit over trimethoprim-sulfamethoxazole treatment, with low heterogeneity (I2 = 18%). Specific fluoroquinolones such as ciprofloxacin (OR 0.44, 95% CI 0.17-1.12) and levofloxacin (OR 0.78, 95% CI 0.48-1.26) did not show a significant difference in comparison with trimethoprim-sulfamethoxazole. In the sub-group analyses of adult and bacteraemic patients, significant differences in mortality were not observed between fluoroquinolones and trimethoprim-sulfamethoxazole. CONCLUSIONS Based on a meta-analysis of non-randomized studies, fluoroquinolones demonstrated comparable effects on mortality of S. maltophilia infection to trimethoprim-sulfamethoxazole, supporting the use of fluoroquinolones in clinical S. maltophilia infections. Although the pooled analysis of overall studies favoured fluoroquinolones over trimethoprim-sulfamethoxazole, the studies included were observational, and sub-group analyses of certain fluoroquinolone agents did not show statistical differences with trimethoprim-sulfamethoxazole. Randomized clinical studies are needed to address these issues.
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Affiliation(s)
- J-H Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Armed Forces Capital Hospital, Seongnam, Republic of Korea
| | - C-I Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - P Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - K-M Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Centre, Taipei, Taiwan
| | - C-H Wang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Centre, Taipei, Taiwan
| | - S Y Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - M G Gözel
- Department of Microbiology Reference Laboratories, Ministry of Health, Public Health, Turkey
| | - S-H Kim
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - P-R Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - N Sekiya
- Department of Infection Prevention and Control, Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Centre Komagome Hospital, Tokyo, Japan
| | - Y Matsumura
- Kyoto University Graduate School of Medicine, Department of Clinical Laboratory Medicine, Kyoto, Japan
| | - D-G Lee
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, St Mary's Hospital, Seoul, Republic of Korea
| | - S-Y Cho
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, St Mary's Hospital, Seoul, Republic of Korea
| | - S Shiratori
- Department of Haematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Y-J Kim
- Division of Infectious Diseases, Department of Paediatrics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - D R Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - K R Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Hyung D, Kim J, Cho SY, Park C. Abstract 3294: Functional annotation for alternative splicing to investigate disrupted splicing in cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Alternative splicing (AS) plays a key role to confer human genome complexity. The advent of mRNA high-throughput sequencing facilitates to identify precise differential alternative splicing analysis. Massive result estimated from RNA-Seq should be sorted out whether AS has functional impact or not. Previous studies investigated protein domain or nonsense-mediated decay of AS event region. However other functional sites on exon inclusion region also exist. For example, miRNA binding site, and post-translational modification of AS site already are reported to assign functional impact. Therefore we developed ASpedia (http://combio.snu.ac.kr/aspedia/) to annotation functional impact of AS event. AS events of our database were generated from human genome hg19 ENSEMBL and Refseq. ASpedia provides a database, explore system, and AS browser to annotate functional impact evidence encompassing DNA, RNA, and protein. The user could query multiple AS events from differential AS analysis result. Currently our system supports a jar execution file to convert input query file from MISO or rMATS result.
The variant of splicing factor (SF) disrupts normal splicing. It could be assumed that target genes of mutated SF could be transcribed to aberrant isoforms by changed splicing machinery. Therefore we investigated the comprehensive SF variant status from TCGA somatic mutation and copy number. SF3B1 (2% in BRCA) and U2AF1 (4% in AML, and 2% in LUAD) were shown to recurrent mutation including hotspot. ELAVL2 known dispensable splicing factor to brain tissue were highly recurrent in deletion (18% in GBM). In order to examine aberrant AS events caused SF variants, we estimated exon-inclusion proportion Percent-Spliced-In (PSI) values for identifiable AS events using TCGA RNA-Seq dataset. Using differentially AS event analysis, we identified AS events that were significantly differentially spliced in the presence of a U2AF S34F/Y mutation (119 in AML). And we purposed to finding In order to investigate functional site, the differentially spliced AS events were additionally annotated using ASpedia. Finally we identified the landscape of that AS events were altered by SF variants, and we proved that a part of the events was involved in cancer-associated functions.
Citation Format: Daejin Hyung, Jihyun Kim, Soo Young Cho, Charny Park. Functional annotation for alternative splicing to investigate disrupted splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3294.
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Affiliation(s)
- Daejin Hyung
- National Cancer Center, Goyaungsi Gyeonggi-do, Republic of Korea
| | - Jihyun Kim
- National Cancer Center, Goyaungsi Gyeonggi-do, Republic of Korea
| | - Soo Young Cho
- National Cancer Center, Goyaungsi Gyeonggi-do, Republic of Korea
| | - Charny Park
- National Cancer Center, Goyaungsi Gyeonggi-do, Republic of Korea
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Chung M, Cho SY, Lee YS. Construction of a Transcriptome-Driven Network at the Early Stage of Infection with Influenza A H1N1 in Human Lung Alveolar Epithelial Cells. Biomol Ther (Seoul) 2018; 26:290-297. [PMID: 29401570 PMCID: PMC5933896 DOI: 10.4062/biomolther.2017.240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022] Open
Abstract
We aimed to understand the molecular changes in host cells that accompany infection by the seasonal influenza A H1N1 virus because the initial response rapidly changes owing to the fact that the virus has a robust initial propagation phase. Human epithelial alveolar A549 cells were infected and total RNA was extracted at 30 min, 1 h, 2 h, 4 h, 8 h, 24 h, and 48 h post infection (h.p.i.). The differentially expressed host genes were clustered into two distinct sets of genes as the infection progressed over time. The patterns of expression were significantly different at the early stages of infection. One of the responses showed roles similar to those associated with the enrichment gene sets to known 'gp120 pathway in HIV.' This gene set contains genes known to play roles in preventing the progress of apoptosis, which infected cells undergo as a response to viral infection. The other gene set showed enrichment of 'Drug Metabolism Enzymes (DMEs).' The identification of two distinct gene sets indicates that the virus regulates the cell's mechanisms to create a favorable environment for its stable replication and protection of gene metabolites within 8 h.
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Affiliation(s)
- Myungguen Chung
- Division of Molecular and Life Sciences, Hanyang University, Ansan 15588, Republic of Korea
| | - Soo Young Cho
- National Cancer Center, Goyang 10408, Republic of Korea
| | - Young Seek Lee
- Division of Molecular and Life Sciences, Hanyang University, Ansan 15588, Republic of Korea
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Kim J, Suh BK, Ko CW, Lee KH, Shin CH, Hwang JS, Kim HS, Chung WY, Kim CJ, Han HS, Kwon NY, Cho SY, Yoo HW, Jin DK. Recombinant growth hormone therapy for prepubertal children with idiopathic short stature in Korea: a phase III randomized trial. J Endocrinol Invest 2018; 41:475-483. [PMID: 29103133 PMCID: PMC5852196 DOI: 10.1007/s40618-017-0786-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/25/2017] [Indexed: 11/24/2022]
Abstract
PURPOSE Several studies have evaluated the effects of growth hormone (GH) on auxological and biochemical parameters in children with non-GH-deficient, idiopathic short stature (ISS). This study evaluated the efficacy and safety of Growtropin®-II (recombinant human GH) in Korean patients with ISS. METHODS This was a 1-year, open-label, multicenter, phase III randomized trial of Growtropin®-II in Korean patients with ISS. In total, 70 prepubertal subjects (39 males, 31 females) between 4 and 12 years of age were included in the study. All patients were naive to GH treatment. RESULTS Annual height velocity was significantly higher in the treatment group (10.68 ± 1.95 cm/year) than the control group (5.72 ± 1.72, p < 0.001). Increases in height and weight standard deviation scores (SDSs) at 26 weeks were 0.63 ± 0.16 and 0.64 ± 0.46, respectively, for the treatment group, and 0.06 ± 0.15 and 0.06 ± 0.28, respectively, for the control group (p < 0.001). Serum insulin-like growth factor (IGF-1) and insulin-like growth factor binding protein-3 (IGFBP-3) increased significantly in the treatment group at week 26 compared to baseline. However, the SDS for body mass index (BMI) at 26 weeks did not change significantly in either group. Growtropin®-II was well tolerated and safe over 1 year of treatment. CONCLUSIONS One-year GH treatment for prepubertal children with ISS demonstrated increased annualized velocity, height and weight SDSs, and IGF-1 and IGFBP-3 levels, with a favorable safety profile. Further evaluations are needed to determine the optimal dose, final adult height, and long-term effects of ISS treatment.
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Affiliation(s)
- J Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - B-K Suh
- Department of Pediatrics, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - C W Ko
- Department of Pediatrics, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - K-H Lee
- Department of Pediatrics, Korea University Anam Hospital, Seoul, Republic of Korea
| | - C H Shin
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - J S Hwang
- Department of Pediatrics, Ajou University Hospital, Suwon, Republic of Korea
| | - H S Kim
- Department of Pediatrics, Severance Hospital, Onsei University Health System, Seoul, Republic of Korea
| | - W Y Chung
- Department of Pediatrics, Inje University Busan Paik Hospital, Busan, Republic of Korea
| | - C J Kim
- Department of Pediatrics, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - H-S Han
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - N Y Kwon
- Data Management and Clinical Statistics Team, Dong-A ST Co., LTD, Seoul, Republic of Korea
| | - S Y Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
| | - H-W Yoo
- Department of Pediatrics, Medical Genetics Clinic and Laboratory, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
| | - D-K Jin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
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Kan Z, Powell E, Ram S, Ching K, Ding Y, Vizcarra P, Nichols T, Hardwick J, Lee SH, Cho SY, Choi YL, Yu JH, Park YH. Abstract P2-07-01: Integrative analyses of immunophenotypes and multi-omics profiles in breast cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-07-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The advent of immuno-oncology (IO) therapies has made it an imperative to characterize intratumoral immune microenvironment in addition to oncogenic alterations through molecular profiling of the tumor. To elucidate the baseline profiles of tumor infiltrating leukocytes (TILs) in breast cancer (BC) in the context of molecular subtypes and oncogenic alterations, we performed whole-exome sequencing (WES) and RNA-Seq of an Asian BC cohort (SMC) consisting of 178 treatment naïve primary tumors. A subset of 120 tumors was further analyzed by H&E and IHC using a panel of 8 TIL markers (CD45, CD4, CD8, CD163, PD1, PD-L1, IDO1 and FOXP3). Using expression signatures representing distinct immune cell types, we classified an expression compendium of 2,781 tumor samples, including SMC and multiple cancers from TCGA, into three immune subtypes with high, medium and low levels of TILs. Basal and HER2 subtypes show higher levels of TILs than Luminal subtypes, consistent with observed clinical responses to checkpoint blockade in clinical trials. Moreover, Asian BCs were significantly enriched in TIL-high subtype (35.3%) compared to the primarily Caucasian TCGA BC cohort (20.2%) while 50.6% of the highly immunogenic Lung adenocarcinoma was TIL-high. We then applied machine learning methods to detect and quantify TILs from H&E images of 120 SMC and 349 TCGA BC tumors. The expression signature analysis results were concordant with independently derived histology based TIL data. Taken together, our findings suggest that IO therapies may be more effective in HR negative BC subtypes and Asian BCs.
Leukocyte exclusion (LE), an immunophenotype where TILs concentrate at the tumor periphery, has been linked to worse prognosis and resistance to IO therapies. Visual assessment of whole tumor IHC images identified LE patterns in 25% of SMC cases. We observed differential distribution of LE by molecular subtype and evidence for selective exclusion of immune cell subsets. Covariate analyses with clinical and molecular data while controlling for subtype as a confounder identified significant associations with tumor proliferation index, percent tumor purity and TP53 mutations. LE is also significantly associated with expression signatures of chemokine signaling, macrophages, angiogenesis and hypoxia, indicating that marked distinctions exist in both tumor intrinsic and microenvironment characteristics between TIL excluded and TIL infiltrated tumors. To validate these findings, we independently identified LE for 200 cases of TCGA BCs based on patterns of TILs extracted from H&E images and saw significant concordance of covariate relationships identified between TCGA and SMC. Our study provided a rare comprehensive resource for studying tumor associated immunity in breast cancers by generating the integrated multi-omics and IO profiles for a large cohort of primary tumors. Comparative analyses revealed that TIL activities are highly variable across different intrinsic subtypes and geographic origins of BC, with potential implications for IO therapeutic application. Correlative analyses of immunophenotypes with molecular data further yielded insights into LE's role in immune escape and identified hallmark signatures for LE indicative of causal molecular mechanisms.
Citation Format: Kan Z, Powell E, Ram S, Ching K, Ding Y, Vizcarra P, Nichols T, Hardwick J, Lee S-H, Cho SY, Choi Y-L, Yu J-H, Park YH. Integrative analyses of immunophenotypes and multi-omics profiles in breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-01.
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Affiliation(s)
- Z Kan
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - E Powell
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - S Ram
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - K Ching
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - Y Ding
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - P Vizcarra
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - T Nichols
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - J Hardwick
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - S-H Lee
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - SY Cho
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - Y-L Choi
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - J-H Yu
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
| | - YH Park
- Pfizer Oncology Research, San Diego, CA; Pfizer Korea, Seoul, Korea; Samsung Medical Center, Seoul, Korea
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Kyung DS, Sung HR, Kim YJ, Kim KD, Cho SY, Choi JH, Lee YH, Kim IY, Seong JK. Global transcriptome analysis identifies weight regain-induced activation of adaptive immune responses in white adipose tissue of mice. Int J Obes (Lond) 2017; 42:755-764. [PMID: 29762555 PMCID: PMC5984075 DOI: 10.1038/ijo.2017.297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/30/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022]
Abstract
Objective: Studies have indicated that weight regain following weight loss predisposes obese individuals to metabolic disorders; however, the molecular mechanism of this potential adverse effect of weight regain is not fully understood. Here we investigated global transcriptome changes and the immune response in mouse white adipose tissue caused by weight regain. Design: We established a diet switch protocol to compare the effects of weight regain with those of weight gain without precedent weight loss, weight loss maintenance and chow diet. We conducted a time course analysis of global transcriptome changes in gonadal white adipose tissue (gWAT) during the weight fluctuation. Co-expression network analysis was used to identify functional modules associated with the weigh regain phenotype. Immune cell populations in gWAT were characterized by flow-cytometric immunophenotyping. Metabolic phenotypes were monitored by histological analysis of adipose tissue and liver, and blood-chemistry and body weight/composition analyses. Results: In total, 952 genes were differentially expressed in the gWAT in the weight regain vs the weight gain group. Upregulated genes were associated with immune response and leukocyte activation. Co-expression network analysis showed that genes involved in major histocompatibility complex I and II-mediated antigen presentation and T-cell activation function were upregulated. Consistent with the transcriptome analysis results, flow cytometry demonstrated significant increases in subsets of T cells and proinflammatory M1 macrophages in the gWAT in the weight regain as compared to the weight gain group. In addition, upregulation of adaptive immune responses was associated with high incidence of adipocyte death and upregulation of high mobility group box 1, a well-known component of damage-associated molecular patterns. Conclusions: Our global transcriptome analysis identified weight regain-induced activation of adaptive immune responses in mouse white adipose tissue. Results suggest that activation of adipocyte death-associated adaptive immunity in adipose tissue may contribute to unfavorable metabolic effects of weight regain following weight loss.
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Affiliation(s)
- D S Kyung
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, Republic of Korea
| | - H R Sung
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
| | - Y J Kim
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
| | - K D Kim
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - S Y Cho
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea.,National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - J H Choi
- Department of Life Science, College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Y-H Lee
- College of Pharmacy, Yonsei University, Incheon, South Korea
| | - I Y Kim
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
| | - J K Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, Republic of Korea
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37
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Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SD, Smedley D. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet 2017; 49:1231-1238. [PMID: 28650483 PMCID: PMC5546242 DOI: 10.1038/ng.3901] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.
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Affiliation(s)
- Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathalie Conte
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David B. West
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Julius O. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Warren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chao-Kung Chen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilinca Tudose
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Relac
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Matthews
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Luis Santos
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Tanja Fiegel
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Natalie Ring
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Simon Greenaway
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Duncan Sneddon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Hugh Morgan
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Gemma F Codner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Michelle E Stewart
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - James Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Neil Horner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | | | - Melissa Haendel
- Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nicole Washington
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J. Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corey L Reynolds
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Valerie Gailus-Durner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Guillaume Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Lynette R Bower
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Mark Moore
- IMPC, San Anselmo, California 94960, USA
| | - Iva Morse
- Charles River Laboratories, Wilmington, Massachusetts 01887, USA
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo I-00015, Italy
| | - Yuichi Obata
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Soo Young Cho
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- Research Institute for Veterinary Science, Seoul National University, Republic of Korea
| | - John Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mary E. Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Wolfgang Wurst
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Martin Hrabe de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - K.C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | | | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | - Monica J. Justice
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | | | | | | | - Jacqueline K. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Steve D.M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
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38
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Cho SY, Park JW, Liu Y, Park YS, Kim JH, Yang H, Um H, Ko WR, Lee BI, Kwon SY, Ryu SW, Kwon CH, Park DY, Lee JH, Lee SI, Song KS, Hur H, Han SU, Chang H, Kim SJ, Kim BS, Yook JH, Yoo MW, Kim BS, Lee IS, Kook MC, Thiessen N, He A, Stewart C, Dunford A, Kim J, Shih J, Saksena G, Cherniack AD, Schumacher S, Weiner AT, Rosenberg M, Getz G, Yang EG, Ryu MH, Bass AJ, Kim HK. Sporadic Early-Onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations, but Low Frequency of Somatic RHOA Mutations Compared With Late-Onset Cancers. Gastroenterology 2017; 153:536-549.e26. [PMID: 28522256 PMCID: PMC6863080 DOI: 10.1053/j.gastro.2017.05.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/08/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Early-onset gastric cancer, which develops in patients younger than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea. Patients with pathogenic germline mutations in CDH1, TP53, and ATM were excluded from the onset of this analysis, given our focus on somatic alterations. We used MutSig2CV to evaluate the significance of mutated genes. We recruited 29 additional early-onset Korean DGC samples and performed SNP6.0 array and targeted sequencing analyses of these 109 early-onset DGC samples (54.1% female, median age, 38 years). We compared the SNP6.0 array and targeted sequencing data of the 109 early-onset DGC samples with those from diffuse-type stomach tumor samples collected from 115 patients in Korea who were 46 years or older (late onset) at the time of diagnosis (controls; 29.6% female, median age, 67 years). We compared patient survival times among tumors from different subgroups and with different somatic mutations. We performed gene silencing of RHOA or CDH1 in DGC cells with small interfering RNAs for cell-based assays. RESULTS We identified somatic mutations in the following genes in a significant number of early-onset DGCs: the cadherin 1 gene (CDH1), TP53, ARID1A, KRAS, PIK3CA, ERBB3, TGFBR1, FBXW7, RHOA, and MAP2K1. None of 109 early-onset DGC cases had pathogenic germline CDH1 mutations. A higher proportion of early-onset DGCs had mutations in CDH1 (42.2%) or TGFBR1 (7.3%) compared with control DGCs (17.4% and 0.9%, respectively) (P < .001 and P = .014 for CDH1 and TGFBR1, respectively). In contrast, a smaller proportion of early-onset DGCs contained mutations in RHOA (9.2%) than control DGCs (19.1%) (P = .033). Late-onset DGCs in The Cancer Genome Atlas also contained less frequent mutations in CDH1 and TGFBR1 and more frequent RHOA mutations, compared with early-onset DGCs. Early-onset DGCs from women contained significantly more mutations in CDH1 or TGFBR1 than early-onset DGCs from men. CDH1 alterations, but not RHOA mutations, were associated with shorter survival times in patients with early-onset DGCs (hazard ratio, 3.4; 95% confidence interval, 1.5-7.7). RHOA activity was reduced by an R5W substitution-the RHOA mutation most frequently detected in early-onset DGCs. Silencing of CDH1, but not RHOA, increased migratory activity of DGC cells. CONCLUSIONS In an integrative genomic analysis, we found higher proportions of early-onset DGCs to contain somatic mutations in CDH1 or TGFBR1 compared with late-onset DGCs. However, a smaller proportion of early-onset DGCs contained somatic mutations in RHOA than late-onset DGCs. CDH1 alterations, but not RHOA mutations, were associated with shorter survival times of patients, which might account for the aggressive clinical course of early-onset gastric cancer. Female predominance in early-onset gastric cancer may be related to relatively high rates of somatic CDH1 and TGFBR1 mutations in this population.
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Affiliation(s)
- Soo Young Cho
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Jun Won Park
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Yang Liu
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Young Soo Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ju Hee Kim
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Hanna Yang
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Hyejin Um
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Woo Ri Ko
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Byung Il Lee
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Seung Wan Ryu
- Department of Surgery, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Chae Hwa Kwon
- Department of Pathology and BioMedical Research Institute, Pusan National University Hospital and Pusan National University School of Medicine, Busan, Republic of Korea
| | - Do Youn Park
- Department of Pathology and BioMedical Research Institute, Pusan National University Hospital and Pusan National University School of Medicine, Busan, Republic of Korea
| | - Jae-Hyuk Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sang Il Lee
- Department of Surgery, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyu Sang Song
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hoon Hur
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Heekyung Chang
- Department of Pathology, Kosin University College of Medicine, Busan, Republic of Korea
| | - Su-Jin Kim
- Department of Pathology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Byung-Sik Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong-Hwan Yook
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Moon-Won Yoo
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom-Su Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - In-Seob Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Nina Thiessen
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - An He
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Chip Stewart
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew Dunford
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jaegil Kim
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Juliann Shih
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gordon Saksena
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew D. Cherniack
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven Schumacher
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Amaro-Taylor Weiner
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mara Rosenberg
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Gad Getz
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eun Gyeong Yang
- Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Adam J. Bass
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts;,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hark Kyun Kim
- National Cancer Center, Goyang, Gyeonggi, Republic of Korea; National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Gyeonggi, Republic of Korea.
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Ko JH, Müller MA, Seok H, Park GE, Lee JY, Cho SY, Ha YE, Baek JY, Kim SH, Kang JM, Kim YJ, Jo IJ, Chung CR, Hahn MJ, Drosten C, Kang CI, Chung DR, Song JH, Kang ES, Peck KR. Suggested new breakpoints of anti-MERS-CoV antibody ELISA titers: performance analysis of serologic tests. Eur J Clin Microbiol Infect Dis 2017; 36:2179-2186. [PMID: 28695355 PMCID: PMC7087918 DOI: 10.1007/s10096-017-3043-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/04/2017] [Indexed: 01/03/2023]
Abstract
To provide optimal cut-off values of anti-Middle East respiratory syndrome coronavirus (MERS-CoV) serologic tests, we evaluated performance of ELISA IgG, ELISA IgA, IFA IgM, and IFA IgG using 138 serum samples of 49 MERS-CoV-infected patients and 219 serum samples of 219 rRT-PCR-negative MERS-CoV-exposed healthcare personnel and patients. The performance analysis was conducted for two different purposes: (1) prediction of neutralization activity in MERS-CoV-infected patients, and (2) epidemiologic surveillance of MERS-CoV infections among MERS-CoV-exposed individuals. To evaluate performance according to serum collection time, we used ‘days post onset of illness (dpoi)’ and ‘days post exposure (dpex)’ assessing neutralization activity and infection diagnosis, respectively. Performance of serologic tests improved with delayed sampling time, being maximized after a seroconversion period. In predicting neutralization activity, ELISA IgG tests showed optimal performance using sera collected after 21 dpoi at cut-off values of OD ratio 0.4 (sensitivity 100% and specificity 100%), and ELISA IgA showed optimal performance using sera collected after 14 dpoi at cut-off value of OD ratio 0.2 (sensitivity 85.2% and specificity 100%). In diagnosis of MERS-CoV infection, ELISA IgG exhibited optimal performance using sera collected after 28 dpex, at a cut-off value of OD ratio 0.2 (sensitivity 97.3% and specificity 92.9%). These new breakpoints are markedly lower than previously suggested values (ELISA IgG OD ratio 1.1, sensitivity 34.8% and specificity 100% in the present data set), and the performance data help serologic tests to be practically used in the field of MERS management.
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Affiliation(s)
- J-H Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea.,Division of Infectious Diseases, Department of Internal Medicine, Armed Forces Capital Hospital, Seongnam, South Korea
| | - M A Müller
- Institute of Virology, Charité - Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research, Braunschweig, Germany
| | - H Seok
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - G E Park
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - J Y Lee
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - S Y Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - Y E Ha
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - J Y Baek
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - S H Kim
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - J-M Kang
- Division of Infectious Diseases, Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Y-J Kim
- Division of Infectious Diseases, Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - I J Jo
- Department of Emergency Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - C R Chung
- Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - M-J Hahn
- Department of Molecular Cell Biology, Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746, South Korea
| | - C Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research, Braunschweig, Germany
| | - C-I Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - D R Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea.,Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - J-H Song
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea.,Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - E-S Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - K R Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea.
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Park S, Sim H, Kim HI, Jeong D, Wu G, Cho SY, Lee YS, Kwon HJ, Lee K. CD11b regulates antibody class switching via induction of AID. Mol Immunol 2017; 87:47-59. [DOI: 10.1016/j.molimm.2017.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 04/05/2017] [Indexed: 12/01/2022]
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Park GE, Ko JH, Cho SY, Ha YE, Lee NY, Kang CI, Chung DR, Song JH, Peck KR. Empirical combination of a β-lactam to vancomycin may not improve outcomes of methicillin-susceptible Staphylococcus aureus bacteremia, compared to vancomycin monotherapy. Eur J Clin Microbiol Infect Dis 2017; 36:1091-1096. [PMID: 28078559 DOI: 10.1007/s10096-016-2893-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022]
Abstract
To evaluate effect of empirical combination of a β-lactam to vancomycin and vancomycin monotherapy in Staphylococcus aureus bacteremia (MSSA-B), we conducted a retrospective cohort study. Electronic medical records of individuals who were diagnosed with MSSA-B between January 2005 and February 2015 at a tertiary care center were reviewed. Patients were classified into three groups according to empirical antibiotic regimen (BL group, β-lactam; VAN group, vancomycin; BV group, combination of β-lactam and vancomycin), and 30-day all-cause mortality of each group was compared. During the study period, 561 patients with MSSA-B were identified. After exclusion of 198 patients (36 with poly-microbial infection, 114 expired within 2 days, and 48 already received parenteral antibiotics) and a matching process, 46 patients for each group were included. Baseline characteristics were similar except for severity and comorbidity scores. The 30-day mortality for all three groups were not significantly different (BL 4.3%, VAN 6.5%, BV 8.7%; P = 0.909). In a multivariate analysis, type of empirical antibiotic regimen was not statistically associated with 30-day all-cause mortality. In comparison with the VAN group, the BV group yielded a HR of 0.579 (95% CI = 0.086-3.890, P = 0.574). Pitt bacteremia score was the only significant factor for mortality. The empirical combination of a β-lactam to vancomycin was not associated with lower mortality in treating MSSA-B, compared to vancomycin monotherapy.
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Affiliation(s)
- G E Park
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - J-H Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - S Y Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - Y E Ha
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - N Y Lee
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - C-I Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - D R Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - J-H Song
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea
| | - K R Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Republic of Korea.
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Lee KY, Kim YC, Cho SY, Kim SY, Yoon YY, Koh DC, Ha K, Ko KS. Determination of recharge fraction of injection water in combined abstraction-injection wells using continuous radon monitoring. J Environ Radioact 2016; 165:140-143. [PMID: 27718382 DOI: 10.1016/j.jenvrad.2016.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 07/30/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
The recharge fractions of injection water in combined abstraction-injection wells (AIW) were determined using continuous radon monitoring and radon mass balance model. The recharge system consists of three combined abstraction-injection wells, an observation well, a collection tank, an injection tank, and tubing for heating and transferring used groundwater. Groundwater was abstracted from an AIW and sprayed on the water-curtain heating facility and then the used groundwater was injected into the same AIW well by the recharge system. Radon concentrations of fresh groundwater in the AIWs and of used groundwater in the injection tank were measured continuously using a continuous radon monitoring system. Radon concentrations of fresh groundwater in the AIWs and used groundwater in the injection tank were in the ranges of 10,830-13,530 Bq/m3 and 1500-5600 Bq/m3, respectively. A simple radon mass balance model was developed to estimate the recharge fraction of used groundwater in the AIWs. The recharge fraction in the 3 AIWs was in the range of 0.595-0.798. The time series recharge fraction could be obtained using the continuous radon monitoring system with a simple radon mass balance model. The results revealed that the radon mass balance model using continuous radon monitoring was effective for determining the time series recharge fractions in AIWs as well as for characterizing the recharge system.
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Affiliation(s)
- Kil Yong Lee
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea.
| | - Yong-Chul Kim
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Soo Young Cho
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Seong Yun Kim
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Yoon Yeol Yoon
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Dong Chan Koh
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Kyucheol Ha
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
| | - Kyung-Seok Ko
- Groundwater Department, Korea Institute of Geoscience and Mineral Resources, 124 Gwahang-no, Yuseong-gu, Daejeon 305-350, South Korea
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Park SM, Byeon SK, Sung H, Cho SY, Seong JK, Moon MH. Lipidomic Perturbations in Lung, Kidney, and Liver Tissues of p53 Knockout Mice Analyzed by Nanoflow UPLC-ESI-MS/MS. J Proteome Res 2016; 15:3763-3772. [PMID: 27581229 DOI: 10.1021/acs.jproteome.6b00566] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipids are important signaling molecules regulating biological processes under normal and diseased conditions. Although p53 mutation is well-known for causing cancer, the relationship between p53-related tumorigenesis and altered lipid profile is unclear. We profiled differences in lipid expressions in liver, lung, and kidney in p53 knockout (KO) mice by high-speed quantitative analysis of 320 lipids (399 species identified) using nanoflow ultrahigh performance liquid chromatography-tandem mass spectrometry (nUPLC-MS/MS). Lung tissues were most severely affected by the lack of p53 gene, as shown by significant reduction (24-44%, P < 0.05) in total phosphatidylcholine (PC), phosphatidylethanolamine (PE), sphingomyelin (SM), diacylglycerol (DG), and triacylglycerol (TG), and significant increases (30-50%) in phosphatidylserine (PS), phosphatidylinositol (PI), and monohexosylceramide (MHC). MHC levels increased in all tissues. Dihexosylceramide (DHC) level decreased only in kidney tissue. Most PI, PS, and phosphatidic acid (PA) species showing significant increases contained a saturated acyl chain (18:0) in lung and liver tissues. Neutral glycerolipids (16:0/22:0-DG and most TGs with saturated and monounsaturated acyl chains) decreased 2-4-fold in the liver tissue. Our results suggest that the lack of p53 and altered lipid profiles are closely related, but as their changes vary from one tissue to another, the lipid alterations are tissue-specific.
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Affiliation(s)
- Se Mi Park
- Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Seul Kee Byeon
- Department of Chemistry, Yonsei University , Seoul 03722, Korea
| | - Hyerim Sung
- College of Veterinary Medicine, BK21 Program for Veterinary Science and Research Institute of Veterinary Science, Seoul National University , Seoul 08826, Korea.,Korea Mouse Phenotyping Center (KMPC) , Seoul 08826, Korea
| | - Soo Young Cho
- College of Veterinary Medicine, BK21 Program for Veterinary Science and Research Institute of Veterinary Science, Seoul National University , Seoul 08826, Korea.,Korea Mouse Phenotyping Center (KMPC) , Seoul 08826, Korea
| | - Je Kyung Seong
- College of Veterinary Medicine, BK21 Program for Veterinary Science and Research Institute of Veterinary Science, Seoul National University , Seoul 08826, Korea.,Korea Mouse Phenotyping Center (KMPC) , Seoul 08826, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University , Seoul 03722, Korea
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Abstract
Securing the airway in patients undergoing surgical intervention to control a deep neck infection (DNI) is challenging for anesthesiologists due to the distorted airway anatomy, limited mouth opening, tissue edema, and immobility. It is critical to assess the risk of a potential difficult airway and prepare the most appropriate airway management method.We reviewed our anesthetic experiences managing patients with DNIs, focusing on the need for video-laryngoscope or awake fiberoptic intubation beyond a standard intubation from the anesthesiologist's perspective.When patients had infections in the masticatory space, mouth of floor, oropharyngeal mucosal space, or laryngopharynx, their airways tended to be managed using methods requiring more effort by the anesthesiologists, and more extensive equipment preparation, compared with use of a standard laryngoscope. The degree to which the main lesion influenced the airway anatomy, especially at the level of epiglottis and aryepiglottic fold was related to the airway management method selected.When managing the airways of patients undergoing surgery for DNIs under general anesthesia, anesthesiologists should use imaging with computed tomography to evaluate the preoperative airway status and a comprehensive understanding of radiological findings, comorbidities, and patients' symptoms is needed.
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Affiliation(s)
| | - Jae Hee Woo
- Department of Anesthesiology and Pain Medicine, School of Medicine, Ewha Womans University, Seoul, Korea
- Correspondence: Jae Hee Woo, Department of Anesthesiology and Pain Medicine, School of Medicine, Ewha Womans University, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 158-710, Korea (e-mail: )
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Rowe SP, Gorin MA, Allaf ME, Pienta KJ, Tran PT, Pomper MG, Ross AE, Cho SY. PET imaging of prostate-specific membrane antigen in prostate cancer: current state of the art and future challenges. Prostate Cancer Prostatic Dis 2016; 19:223-30. [PMID: 27136743 DOI: 10.1038/pcan.2016.13] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/10/2016] [Accepted: 03/08/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Prostate-specific membrane antigen (PSMA) is a cell surface enzyme that is highly expressed in prostate cancer (PCa) and is currently being extensively explored as a promising target for molecular imaging in a variety of clinical contexts. Novel antibody and small-molecule PSMA radiotracers labeled with a variety of radionuclides for positron emission tomography (PET) imaging applications have been developed and explored in recent studies. METHODS A great deal of progress has been made in defining the clinical utility of this class of PET agents through predominantly small and retrospective clinical studies. The most compelling data to date has been in the setting of biochemically recurrent PCa, where PSMA-targeted radiotracers have been found to be superior to conventional imaging and other molecular imaging agents for the detection of locally recurrent and metastatic PCa. RESULTS Early data, however, suggest that initial lymph node staging before definitive therapy in high-risk primary PCa patients may be limited, although intraoperative guidance may still hold promise. Other examples of potential promising applications for PSMA PET imaging include non-invasive characterization of primary PCa, staging and treatment planning for PSMA-targeted radiotherapeutics, and guidance of focal therapy for oligometastatic disease. CONCLUSIONS However, all of these indications and applications for PCa PSMA PET imaging are still lacking and require large, prospective, systematic clinical trials for validation. Such validation trials are needed and hopefully will be forthcoming as the fields of molecular imaging, urology, radiation oncology and medical oncology continue to define and refine the utility of PSMA-targeted PET imaging to improve the management of PCa patients.
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Affiliation(s)
- S P Rowe
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M A Gorin
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M E Allaf
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K J Pienta
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P T Tran
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M G Pomper
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A E Ross
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Y Cho
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Radiology, University of Wisconsin School of Medicine and Public Health and University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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Shin JH, Kim IY, Kim YN, Shin SM, Roh KJ, Lee SH, Sohn M, Cho SY, Lee SH, Ko CY, Kim HS, Choi CS, Bae YS, Seong JK. Correction: Obesity Resistance and Enhanced Insulin Sensitivity in Ahnak-/- Mice Fed a High Fat Diet Are Related to Impaired Adipogenesis and Increased Energy Expenditure. PLoS One 2015; 10:e0144478. [PMID: 26629899 PMCID: PMC4668090 DOI: 10.1371/journal.pone.0144478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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47
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Lee SH, Cho SY, Yoo KY, Jeong S. Population pharmacokinetics of ramosetron. J Pharmacokinet Pharmacodyn 2015; 43:73-83. [DOI: 10.1007/s10928-015-9455-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 10/31/2015] [Indexed: 01/27/2023]
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48
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Jang EA, Lee SE, Choi JI, Cho SY. Changes in the hemodynamic parameters between the prone and supine positions measured by an arterial pulse contour cardiac output monitoring system. Anesth Pain Med (Seoul) 2015. [DOI: 10.17085/apm.2015.10.4.291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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49
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Shin JH, Kim IY, Kim YN, Shin SM, Roh KJ, Lee SH, Sohn M, Cho SY, Lee SH, Ko CY, Kim HS, Choi CS, Bae YS, Seong JK. Obesity Resistance and Enhanced Insulin Sensitivity in Ahnak-/- Mice Fed a High Fat Diet Are Related to Impaired Adipogenesis and Increased Energy Expenditure. PLoS One 2015; 10:e0139720. [PMID: 26466345 PMCID: PMC4605776 DOI: 10.1371/journal.pone.0139720] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/16/2015] [Indexed: 11/18/2022] Open
Abstract
Objective Recent evidence has suggested that AHNAK expression is altered in obesity, although its role in adipose tissue development remains unclear. The objective of this study was to determine the molecular mechanism by which Ahnak influences adipogenesis and glucose homeostasis. Design We investigated the in vitro role of AHNAK in adipogenesis using adipose-derived mesenchymal stem cells (ADSCs) and C3H10T1/2 cells. AHNAK-KO male mice were fed a high-fat diet (HFD; 60% calories from fat) and examined for glucose and insulin tolerances, for body fat compositions, and by hyperinsulinemic-euglycemic clamping. Energy expenditures were assessed using metabolic cages and by measuring the expression levels of genes involved in thermogenesis in white or brown adipose tissues. Results Adipogenesis in ADSCs was impaired in AHNAK-KO mice. The loss of AHNAK led to decreased BMP4/SMAD1 signaling, resulting in the downregulation of key regulators of adipocyte differentiation (P<0.05). AHNAK directly interacted with SMAD1 on the Pparγ2 promoter. Concomitantly, HFD-fed AHNAK-KO mice displayed reduced hepatosteatosis and improved metabolic profiles, including improved glucose tolerance (P<0.001), enhanced insulin sensitivity (P<0.001), and increased energy expenditure (P<0.05), without undergoing alterations in food intake and physical activity. Conclusion AHNAK plays a crucial role in body fat accumulation by regulating adipose tissue development via interaction with the SMAD1 protein and can be involved in metabolic homeostasis.
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Affiliation(s)
- Jae Hoon Shin
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Yo Na Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Sun Mee Shin
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
| | - Kyung Jin Roh
- Lee Gil Ya Cancer and Diabetes Institute and Division of Endocrinology Gil Medical Center, Gachon University of Medicine and Science, Incheon, South Korea
| | - Seo Hyun Lee
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Mira Sohn
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
| | - Soo Young Cho
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Sang Hyuk Lee
- Ewha Research Center for Systems Biology, Ewha Womans University, Seoul, South Korea
| | - Chang-Yong Ko
- Department of Biomedical Engineering, College of Health Science, Institute of Medical Engineering, Yonsei University, Wonju, South Korea
| | - Han-Sung Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Cheol Soo Choi
- Lee Gil Ya Cancer and Diabetes Institute and Division of Endocrinology Gil Medical Center, Gachon University of Medicine and Science, Incheon, South Korea
| | - Yun Soo Bae
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
- * E-mail: (JKS); (YSB)
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX Institute, Seoul National University, Seoul, South Korea
- * E-mail: (JKS); (YSB)
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50
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Kiess AP, Banerjee SR, Mease RC, Rowe SP, Rao A, Foss CA, Chen Y, Yang X, Cho SY, Nimmagadda S, Pomper MG. Prostate-specific membrane antigen as a target for cancer imaging and therapy. Q J Nucl Med Mol Imaging 2015; 59:241-68. [PMID: 26213140 PMCID: PMC4859214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The prostate-specific membrane antigen (PSMA) is a molecular target whose use has resulted in some of the most productive work toward imaging and treating prostate cancer over the past two decades. A wide variety of imaging agents extending from intact antibodies to low-molecular-weight compounds permeate the literature. In parallel there is a rapidly expanding pool of antibody-drug conjugates, radiopharmaceutical therapeutics, small-molecule drug conjugates, theranostics and nanomedicines targeting PSMA. Such productivity is motivated by the abundant expression of PSMA on the surface of prostate cancer cells and within the neovasculature of other solid tumors, with limited expression in most normal tissues. Animating the field is a variety of small-molecule scaffolds upon which the radionuclides, drugs, MR-detectable species and nanoparticles can be placed with relative ease. Among those, the urea-based agents have been most extensively leveraged, with expanding clinical use for detection and more recently for radiopharmaceutical therapy of prostate cancer, with surprisingly little toxicity. PSMA imaging of other cancers is also appearing in the clinical literature, and may overtake FDG for certain indications. Targeting PSMA may provide a viable alternative or first-line approach to managing prostate and other cancers.
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Affiliation(s)
- A P Kiess
- Department of Radiation Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA -
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