Publications by authors named "Jee-Young Park"

67 Publications

The complete chloroplast genome sequence of Mill (Anacardiaceae).

Mitochondrial DNA B Resour 2016 Sep 1;1(1):696-697. Epub 2016 Sep 1.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

In this study, complete chloroplast genome sequences of was characterized by assembly using whole genome sequence data. The chloroplast genome of were 149,011bp long, which was comprised of a large single copy region of 96,882 bp, a small single copy region of 18,647bp, and a pair of inverted repeats of 16,741 bp. The genome contained 77 protein-coding genes, four rRNA genes and 30 tRNA genes. Phylogenetic tree revealed that was closely grouped with species, and belonging to the Anacardiaceae family.
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http://dx.doi.org/10.1080/23802359.2016.1222250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871870PMC
September 2016

Standardized Pathology Report for Breast Cancer.

J Breast Cancer 2021 Feb;24(1):1-21

Department of Pathology, Busan Paik Hospital, Inje University, Busan, Korea.

Given the recent advances in management and understanding of breast cancer, a standardized pathology report reflecting these changes is critical. To meet this need, the Breast Pathology Study Group of the Korean Society of Pathologists has developed a standardized pathology reporting format for breast cancer, consisting of 'standard data elements,' 'conditional data elements,' and a biomarker report form. The 'standard data elements' consist of the basic pathologic features used for prognostication, while other factors related to prognosis or diagnosis are described in the 'conditional data elements.' In addition to standard data elements, all recommended issues are also presented. We expect that this standardized pathology report for breast cancer will improve diagnostic concordance and communication between pathologists and clinicians, as well as between pathologists inter-institutionally.
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http://dx.doi.org/10.4048/jbc.2021.24.e5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920867PMC
February 2021

Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F hybrid combinations.

Sci Rep 2021 Jan 28;11(1):2506. Epub 2021 Jan 28.

Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.

Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F hybrid seeds in cucumber breeding.
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http://dx.doi.org/10.1038/s41598-021-81988-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843999PMC
January 2021

Standardized pathology report for breast cancer.

J Pathol Transl Med 2021 Jan 11;55(1):1-15. Epub 2021 Jan 11.

Department of Pathology, Busan Paik Hospital, Inje University, Busan, Korea.

Given the recent advances in management and understanding of breast cancer, a standardized pathology report reflecting these changes is critical. To meet this need, the Breast Pathology Study Group of the Korean Society of Pathologists has developed a standardized pathology reporting format for breast cancer, consisting of 'standard data elements,' 'conditional data elements,' and a biomarker report form. The 'standard data elements' consist of the basic pathologic features used for prognostication, while other factors related to prognosis or diagnosis are described in the 'conditional data elements.' In addition to standard data elements, all recommended issues are also presented. We expect that this standardized pathology report for breast cancer will improve diagnostic concordance and communication between pathologists and clinicians, as well as between pathologists inter-institutionally.
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http://dx.doi.org/10.4132/jptm.2020.11.20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829577PMC
January 2021

The complete chloroplast genome sequence of a medicinal herb (Asparagaceae).

Mitochondrial DNA B Resour 2019 Dec 12;5(1):85-86. Epub 2019 Dec 12.

Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

is herbaceous perennial plant belonging to the Asparagaceae family and widely used both as ornamental plant and herbal medicine. The complete chloroplast genome of was 156,754 bp in length, which was composed of four distinct parts; a large single copy (LSC) of 85,118 bp, a small single copy (SSC) of 18,680 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,478 bp. A total of 130 genes including 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes were identified. The phylogenetic tree showed that has a close relationship with other Nolinoideae plants, especially with and
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http://dx.doi.org/10.1080/23802359.2019.1698327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720963PMC
December 2019

Assessing the genetic and chemical diversity of Taraxacum species in the Korean Peninsula.

Phytochemistry 2021 Jan 6;181:112576. Epub 2020 Nov 6.

College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea. Electronic address:

The genetic relationship between Taraxacum species, also known as the dandelion, is complicated because of asexual and mixed sexual apomictic reproduction. The usage of Taraxacum species in traditional medicines make their specialized metabolism important, but interspecific chemical difference has rarely been reported for the genus. In this study, we assembled the chloroplast genome and 45S rDNA of six Taraxacum species that occur in Korea (T. campylodes, T. coreanum, T. erythrospermum, T. mongolicum, T. platycarpum, and T. ussuriense), and performed a comparative analysis, which revealed their phylogenetic relationships and possible natural hybridity. We also performed a liquid chromatography-mass spectrometry-based phytochemical analysis to reveal interspecific chemical diversity. The comparative metabolomics analysis revealed that Taraxacum species could be separated into three chemotypes according to their major defensive specialized metabolites, which were the sesquiterpene lactones, the phenolic inositols, and chlorogenic acid derivatives. The CP DNA- and 45S rDNA-based phylogenetic trees showed a tangled relationship, which supports the notion of ongoing hybridization of wild Taraxacum species. The untargeted LC-MS analysis revealed that each Taraxacum plant exhibits species-specific defensive specialized metabolism. Moreover, 45S rDNA-based phylogenetic tree correlated with the hierarchical cluster relied on metabolite compositions. Given the coincidence between these analyses, we represented that 45S rDNA could well reflect overall nuclear genome variation in Taraxacum species.
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http://dx.doi.org/10.1016/j.phytochem.2020.112576DOI Listing
January 2021

The Therapeutic Effect of Cyclin-Dependent Kinase 4/6 Inhibitor on Relapsed Ectopic Male Breast Cancer.

J Breast Cancer 2020 Oct 30;23(5):560-566. Epub 2020 Jun 30.

Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, Kyungpook National University Cancer Research Institute, Kyungpook National University School of Medicine, Daegu, Korea.

Ectopic male breast cancer is very rare. Consequently, there is a lack of prospective clinical trials, and most recommendations for treatment are based on the experiences of clinicians and data from female breast cancer patients. The United States Food and Drug Administration has recently approved palbociclib combined with endocrine therapy for advanced male breast cancer because of the positive results of its use in metastatic female breast cancer. Therefore, it is worth considering cyclin-dependent kinase 4/6 inhibitors as alternatives to conventional chemotherapies for advanced male breast cancer patients with hormone receptor-positive and human epidermal growth factor receptor 2-negative cancers. The present case report introduces the use of palbociclib plus letrozole as first-line therapy for an elderly male patient with relapsed ectopic breast cancer, notwithstanding the limitations of the current national health insurance policy.
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http://dx.doi.org/10.4048/jbc.2020.23.e39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7604375PMC
October 2020

CytoPAN-Portable cellular analyses for rapid point-of-care cancer diagnosis.

Sci Transl Med 2020 08;12(555)

Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

Rapid, automated, point-of-care cellular diagnosis of cancer remains difficult in remote settings due to lack of specialists and medical infrastructure. To address the need for same-day diagnosis, we developed an automated image cytometry system (CytoPAN) that allows rapid breast cancer diagnosis of scant cellular specimens obtained by fine needle aspiration (FNA) of palpable mass lesions. The system is devoid of moving parts for stable operations, harnesses optimized antibody kits for multiplexed analysis, and offers a user-friendly interface with automated analysis for rapid diagnoses. Through extensive optimization and validation using cell lines and mouse models, we established breast cancer diagnosis and receptor subtyping in 1 hour using as few as 50 harvested cells. In a prospective patient cohort study ( = 68), we showed that the diagnostic accuracy was 100% for cancer detection and the receptor subtyping accuracy was 96% for human epidermal growth factor receptor 2 and 93% for hormonal receptors (ER/PR), two key biomarkers associated with breast cancer. A combination of FNA and CytoPAN offers faster, less invasive cancer diagnoses than the current standard (core biopsy and histopathology). This approach should enable the ability to more rapidly diagnose breast cancer in global and remote settings.
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http://dx.doi.org/10.1126/scitranslmed.aaz9746DOI Listing
August 2020

Tumor budding in cervical cancer as a prognostic factor and its possible role as an additional intermediate-risk factor.

Gynecol Oncol 2020 Oct 31;159(1):157-163. Epub 2020 Jul 31.

Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea.

Objective: To evaluate the prognostic value and its possible role as an additional intermediate-risk factor of tumor budding (TB) in cervical cancer following radical hysterectomy.

Methods: In total, 136 patients with cervical cancer who underwent radical hysterectomy with pelvic and/or paraaortic lymphadenectomy were included. We assessed the status of TB in available hematoxylin and eosin-stained specimens. Univariate and multivariate analyses for predicting tumor recurrence and death were performed using TB and other clinicopathologic parameters. To evaluate additional intermediate-risk factors of TB, patients who had at least one high-risk factor were excluded, and a total of 81 patients were included. We added TB to three conventional intermediate-risk models and compared their performance with new and conventional models using the log-rank test and receiver operating characteristic analysis.

Results: High TB was defined as ≥5 per high-power field for disease-free survival and ≥ 8 per high-power field for overall survival. Multivariate analysis revealed that high TB was an independent prognostic factor for predicting overall survival (hazard ratio, 4.96; 95% confidence intervals, 1.06-23.29; p = .0423). The addition of TB to the conventional intermediate-risk models improved the accuracy of recurrence prediction. Among the risk models, the new model using at least two risk factors, including tumor size (≥ 4 cm), deep stromal invasion (outer one-third of entire cervical thickness), lymphovascular invasion, and high TB, was the most accurate for predicting tumor recurrence (area under the curve, 0.708, hazard ratio, 4.25; p = .0231).

Conclusion: High TB may be a prognostic biomarker of cervical cancer. Moreover, the addition of TB to the conventional intermediate-risk models improves the stratification of tumor recurrence.
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http://dx.doi.org/10.1016/j.ygyno.2020.07.030DOI Listing
October 2020

Mitochondrial plastid DNA can cause DNA barcoding paradox in plants.

Sci Rep 2020 04 9;10(1):6112. Epub 2020 Apr 9.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively. In both species, it is estimated that 35% of the ancestral plastid genomes were transferred to mitochondrial genomes over the past 10 million years and remain conserved in these genomes. Some plastid barcoding markers co-amplified the conserved MTPTs and caused a barcoding paradox, resulting in mis-authentication of botanical ingredients and/or taxonomic mis-positioning. We identified dynamic and lineage-specific MTPTs that have contributed to mitochondrial genome complexity and might cause a putative barcoding paradox across 81 plant species. We suggest that a DNA barcoding guidelines should be developed involving the use of multiple markers to help regulate economically motivated adulteration.
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http://dx.doi.org/10.1038/s41598-020-63233-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145815PMC
April 2020

FGFR1 is associated with c-MYC and proangiogenic molecules in metastatic renal cell carcinoma under anti-angiogenic therapy.

Histopathology 2020 May 28;76(6):838-851. Epub 2020 Apr 28.

Department of Pathology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea.

Aims: This study aimed to investigate the clinicopathological significance of FGFR1 and c-MYC expression, particularly in relation to angiogenesis in clear cell renal cell carcinoma (CCRCC).

Methods And Results: Immunohistochemistry and fluorescence in-situ hybridisation were conducted with tissue microarrays from 91 metastatic CCRCC patients who received VEGF receptor tyrosine kinase inhibitors (VEGFR-TKIs). The expression of angiogenic molecules, FGFR1 and c-MYC, and tumoral vascular density (TVD) and mRNA expression and TVD of 533 CCRCCs in The Cancer Genome Atlas (TCGA) were analysed. FGFR1, pFGFR1 and c-MYC expression was observed in 29.1, 74.4 and 30.8% of tumours, respectively. FGFR1 was an independent worse prognostic factor for overall (HR = 1.871, P = 0.032) and progression-free (HR = 1.976, P = 0.016) survival. FGFR1 was significantly related to VEGFR-TKI responsiveness (P = 0.011). The presence of FGFR1 /c-MYC showed a positive correlation with proangiogenic markers, including VEGF (P = 0.018) and HIF-1α (P < 0.0001). FGFR1 /c-MYC tumours showed higher TVDs together with higher VEGFR2 and PDGFR-β expression (both P < 0.0001). FGFR1 and c-MYC expression was also positively correlated with the expression of hypoxia-related and proangiogenic-related genes in the TCGA data.

Conclusions: FGFR1 and c-MYC may be involved in tumour angiogenesis and FGFR1 may represent a promising therapeutic target in metastatic CCRCC.
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http://dx.doi.org/10.1111/his.14076DOI Listing
May 2020

Comparison of clinical features and oncologic outcomes between familial non-hereditary and hereditary breast cancer in Korean female patients.

Asian J Surg 2020 Oct 7;43(10):996-1001. Epub 2020 Jan 7.

Department of Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. Electronic address:

Background: The authors compared the clinical features between familial (non-hereditary) and hereditary breast cancer. And we also analyzed their oncologic outcomes to establish appropriate surveillance protocol for familial (non-hereditary) and hereditary breast cancer.

Methods: Among 232 patients with breast cancer who were performed BRCA gene evaluation, twenty-eight patients were diagnosed as hereditary breast cancer with BRCA gene mutation and one-hundred and seventy-six patients were familial (non-hereditary) breast cancer. The clinical characteristics and oncologic outcomes were compared between two groups.

Results: While the incidence of multifocality was higher in familial (non-hereditary) breast cancer group (p < 0.001), the bilaterality was higher in hereditary breast cancer group (p < 0.001). And the rate of pathologic complete remission was also significantly higher in hereditary breast cancer group (p = 0.030). The characteristics of tumor were different between familial (non-hereditary) breast cancer and hereditary breast cancer. The oncologic outcome was better in familial (non-hereditary) breast cancer group than hereditary breast cancer group except death.

Conclusion: The clinical characteristics of familial (non-hereditary) breast cancer were different from those of hereditary breast cancer but similar to those of sporadic breast cancer. The prognosis of the familial (non-hereditary) breast cancer was significantly better than hereditary breast cancer.
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http://dx.doi.org/10.1016/j.asjsur.2019.12.001DOI Listing
October 2020

A rare pericytic tumor of the kidney: The first case in Korea.

Int J Surg Case Rep 2020 9;66:178-181. Epub 2019 Nov 9.

Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Joint Institute for Regenerative Medicine, Kyungpook National University, Daegu, Republic of Korea. Electronic address:

Introduction: A pericytic tumor is a group of mesenchymal neoplasm found in superficial tissues and only rarely described in viscera. The family of pericytic tumors includes glomus tumors and variants, myopericytoma including myofibroma, and angioleiomyoma etc. The renal pericytic tumor is extremely rare, and only few comprehensive discussions about this entity have been done.

Presentation Of Case: A 58-year-old man was transferred to our institute with suspicions of renal cell carcinoma. The kidney dynamic computed tomography scan showed a 3 cm sized solid mass in the upper pole of the right kidney. Laparoscopic radical nephrectomy was performed due to the deep-seated mass. Pathological result confirmed that the kidney mass was renal pericytic tumor.

Discussion: Although general biological behavior of published renal pericytic tumors is likely to be benign, the clinicopathologic experiences are very limited. Therefore, we should evaluate the malignant potential of the entity according to the parameters proposed for soft tissue tumors, including tumor location, tumor size, growth pattern, cellularity, cytological atypia, and mitotic figures with atypical forms. The current case shows several worrisome features, including an extremely rare tumor location, partially infiltrative growth, and a mildly increased proliferating index, which resulted in it being classified as an uncertain malignant potential.

Conclusion: We described the first case of renal pericytic tumor, addressing uncertain malignant potential, in a Korean male, which would be a distinct mesenchymal neoplasm differentiating from other groups of perivascular tumor families based on histological and immunohistochemical features.
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http://dx.doi.org/10.1016/j.ijscr.2019.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6926292PMC
November 2019

Clinical Validation of BCT Scores With Prognostic Factors in Hormone Receptor-positive, HER2-negative Early Breast Cancer.

In Vivo 2019 Nov-Dec;33(6):2133-2139

Department of Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea

Background/aim: Multigene profiling assays provide strong evidence for predicting the prognosis of breast cancer. In this study, we aimed to evaluate the clinical validation of the BCT score with various prognostic factors.

Materials And Methods: A total of 133 cases of hormone receptor-positive, cT1N0 breast cancers were analyzed. Risk stratification using the BCT score (Low, n=105; High, n=28) was analyzed with Ki67 index, p53 mutation, Immunohistochemistry 4 (IHC4) score, Nottingham Prognostic Index (NPI) and online PREDICT.

Results: Ki67 index and NPI showed strong correlations with risk stratification based on BCT scores. Although the IHC4 score and online PREDICT were not associated with BCT score, there was a significant tendency of association with the online PREDICT results as the time of overall survival was increasing.

Conclusion: Risk classification based on BCT scores might have a clinical significance as a prognostic marker in hormone receptor-positive, HER2-negative, early breast cancer.
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http://dx.doi.org/10.21873/invivo.11714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6899082PMC
March 2020

Overcoming Tamoxifen Resistance by Regulation of Del-1 in Breast Cancer.

Oncology 2019 22;97(3):180-188. Epub 2019 Jul 22.

Department of Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.

Background: Hormone receptor-positive breast cancer accounts for nearly two-thirds of breast cancer cases; it ultimately acquires resistance during endocrine treatment and becomes more aggressive. This study evaluated the role of developmental endothelial locus (Del)-1 in tamoxifen-resistant (TAM-R) breast cancer.

Methods: Del-1 expression in recurrent TAM-R breast cancer tissue was evaluated and compared to that in the original tumor tissue from the same patients. Del-1 expression was also evaluated in TAM-R cells by quantitative real-time PCR, western blotting, and enzyme-linked immunosorbent assay. The effects of Del-1 knockdown on the proliferation, migration, and invasion of TAM-R cells was assessed with wound-healing and Matrigel transwell assays.

Results: Del-1 was more highly expressed in recurrent breast cancer as compared to the original tumor tissues before initiation of endocrine treatment. Del-1 mRNA was upregulated in TAM-R and small interfering RNA-mediated knockdown of Del-1 suppressed the migration and proliferation of TAM-R cells while partly restoring TAM sensitivity. And the TAM resistance was recovered by knockdown of Del-1.

Conclusions: TAM-R breast cancer is characterized by Del-1 overexpression and tumor progression can be inhibited by Del-1 depletion, which restores TAM sensitivity. Thus, therapeutic strategies that target Del-1 may be effective for the treatment of hormone-resistant breast cancer.
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http://dx.doi.org/10.1159/000501340DOI Listing
September 2019

Absence of estrogen receptor is associated with worse oncologic outcome in patients who were received neoadjuvant chemotherapy for breast cancer.

Asian J Surg 2020 Mar 14;43(3):467-475. Epub 2019 Jun 14.

Department of Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea. Electronic address:

Background/objective: Neoadjuvant chemotherapy (NAC) is a standard treatment for locally advanced breast cancer, especially for HER2-positive or triple negative breast cancer which shows good response to chemotherapy. However, because a result of biomarkers is, occasionally, changed after NAC, the treatment strategy should be differently applied for patients with locally advanced breast cancer. We compared the results of biomarkers before and after NAC to evaluate the association with disease prognosis and oncologic results.

Methods: Fifty-seven patients with locally advanced breast cancer underwent NAC and the immunohistochemical (IHC) staining results were compared between before and after NAC. And the association between oncologic outcomes and biomarkers was analyzed.

Results: Negative status of estrogen receptor (ER) was associated with locoregional recurrence and distant metastasis both before and after NAC (p = 0.021, 0.019; p = 0.018, 0.036). And the negative status of progesterone receptor (PR) and triple negative status before neoadjuvant chemotherapy were also associated with death and distant metastasis, respectively. However, the changes of biomarkers after NAC in breast cancer were not directly associated with any oncologic outcomes.

Conclusion: The absence of ER in breast cancer before and after NAC would be a significant prognostic factor for local recurrence and distant metastasis. Therefore, the absence of ER should be considered as important factor in determining the treatment strategy.
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http://dx.doi.org/10.1016/j.asjsur.2019.05.010DOI Listing
March 2020

ARID3A Positivity Correlated With Favorable Prognosis in Patients With Residual Rectal Cancer After Neoadjuvant Chemoradiotherapy.

Anticancer Res 2019 Jun;39(6):2845-2853

Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea

Background/aim: Recent studies have shown a marked increase of AT-rich interactive domain 3A (ARID3A) in colon cancer tissue compared to normal colon mucosa. However, the role of ARID3A has not yet been determined in rectal cancer. We, therefore, investigated the clinical relevance of ARID3A expression in patients with residual rectal cancer after neoadjuvant chemoradiotherapy (NACRT).

Materials And Methods: One hundred thirty-four patients who underwent surgical resection for residual rectal cancer after NACRT were analyzed. ARID3A expression was evaluated using immunohistochemistry on whole-tissue sections. KRAS exon 2 (codons 12 and 13) and BRAF V600E mutation status were determined using polymerase chain reaction.

Results: ARID3A positivity was found in 91 cases (64.5%), and it correlated with absence of perineural invasion (p=0.031), longer disease-free survival (DFS) (p=0.048) and cancer-specific survival (CSS) (p=0.006). However, ARID3A positivity was not correlated with KRAS (p=0.231) or BRAF mutation status (p=0.577). In multivariate analysis, ARID3A positivity was independently associated with a favorable CSS (p=0.035), but not DFS (p=0.051).

Conclusion: ARID3A positivity can predict favorable prognosis in patients with residual rectal cancer after NACRT.
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http://dx.doi.org/10.21873/anticanres.13413DOI Listing
June 2019

Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb "Bang-Poong".

Int J Mol Sci 2019 May 4;20(9). Epub 2019 May 4.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Three Apiaceae species , , and are used as Asian herbal medicines, with the confusingly similar common name "Bang-poong". We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of , , and were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the cp genome, phylogenetic analysis revealed that diverged 5-6 million years ago (Mya), while diverged from only 2-3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for and . We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between , , and ; provides a method of species identification; and sheds light on the evolutionary history of these three species.
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http://dx.doi.org/10.3390/ijms20092196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539805PMC
May 2019

Efficacy of an RNA-based multigene assay with core needle biopsy samples for risk evaluation in hormone-positive early breast cancer.

BMC Cancer 2019 Apr 25;19(1):388. Epub 2019 Apr 25.

Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea.

Background: Gene expression profiling provides key information for prognosis of breast cancer to establish treatment strategy. However, the genetic assessment should be available before induction of treatment to be useful for clinical practice. To evaluate the reliability of using needle biopsy samples for gene assays, we compared gene-expression profiling results between core needle biopsy (CNB) samples and surgical specimens in breast cancer.

Methods: Thirty-one paired, formalin-fixed, paraffin-embedded CNB and surgical specimen samples were selected from patients with hormone receptor-positive breast cancer. Total RNA was extracted from the samples and the risk classifications based on GenesWell BCT scores were compared.

Results: The BCT scores correlated between CNB samples and surgical specimens of hormone receptor-positive breast cancer (Pearson r = 0.66). The overall concordance rate of risk classification (high/low risk) was 83.9%. However, when the breast cancer does not contain intratumoral microcalcification, the concordance rate increased as 92.0%. And, when the breast cancer formed a solitary nodule (non-multifocal), the concordance rate increased up to 95.8%.

Conclusion: Risk classification using the GenesWell BCT multigene kit with CNB samples could be considered reliable, when the breast cancer is a solitary nodule without intratumoral microcalcification. Such genetic profiling results should be helpful for establishing a treatment plan for hormone receptor-positive breast cancer before treatment induction.
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http://dx.doi.org/10.1186/s12885-019-5608-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485070PMC
April 2019

The complete chloroplast genome sequence of Magic Lily ().

Mitochondrial DNA B Resour 2018 Oct 26;3(2):1210-1211. Epub 2018 Oct 26.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.

Magic Lily (), belonging to the Amaryllidaceae family, is cultivated for ornamental and medicinal purposes. To characterize its genomic information, we obtained the complete chloroplast genome sequence of by assembling Illumina whole genome sequence data. The complete chloroplast genome is 158,482 bp in length which is composed of four unique regions, a large single copy region (LSC) of 86,454 bp, a small single copy region (SSC) of 18,500 bp, and a pair of inverted repeats (IR) of 26,764 bp. The genome annotation predicted 159 genes including 105 protein-coding genes, 46 genes, and 8 genes. Phylogenetic tree analysis revealed that clustered with species belonging to the Amaryllidaceae family.
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http://dx.doi.org/10.1080/23802359.2018.1527193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799502PMC
October 2018

The complete chloroplast genome sequence of (Koidz.) Nakai (Asparagaceae).

Mitochondrial DNA B Resour 2018 Oct 8;3(2):1052-1053. Epub 2018 Oct 8.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.

(Koidz.) Nakai is an herbaceous perennial plant belonging to the Asparagaceae family and has become a popular ornamental plant. In this study, the chloroplast genome sequence of was completed by assembly with whole genome sequence data. The chloroplast genome of is 156,416 bp in length, which is composed of a large single-copy (LSC) of 84,788 bp, a small single-copy (SSC) of 18,206 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,711 bp, as four distinct parts. In total, 114 genes were identified including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis revealed that has a close relationship with other species, and , but is farther than the distance between them.
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http://dx.doi.org/10.1080/23802359.2018.1511858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799732PMC
October 2018

The complete chloroplast genome sequence of Korean and intra-species diversity.

Mitochondrial DNA B Resour 2018 Aug 23;3(2):941-942. Epub 2018 Aug 23.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

is a traditional medicinal plant well known for its anti-inflammatory effect. The complete chloroplast genome sequence of collected from Korea was obtained by assembly using whole genome sequence data. The chloroplast genome is 155,060 bp in length, containing 88,853 bp in a large single copy (LSC), 18,653 bp in a small single copy (SSC) and 23,777 bp in a pair of inverted repeats (IRs). A total of 112 genes including 78 protein-coding genes and 34 structural RNA genes were identified. The sequence comparison of two collected from Korea and China revealed 48 single nucleotide polymorphisms (SNPs) and 45 insertions/deletions (InDels). In addition, phylogenetic analysis represented intraspecific diversity within species collected in Korea and China.
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http://dx.doi.org/10.1080/23802359.2018.1502637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800441PMC
August 2018

Chemical and genomic diversity of six Lonicera species occurring in Korea.

Phytochemistry 2018 Nov 16;155:126-135. Epub 2018 Aug 16.

College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Lonicera spp. (Caprifoliaceae) are important not only as a common medicinal herb in East Asia but also as one of the most problematic invasive species in North America. In the present study, we performed a systemic analysis of genomic and chemical diversity among six Lonicera species occurring in Korea, L. japonica, L. maackii, L. insularis, L. sachalinensis, L. praeflorens, and L. vesicaria, using chloroplast DNA whole genome shotgun (WGS) sequencing and LC-MS analyses. The phylogenetic and phylochemical relationships did not coincide with each other, but partial consistency could be found among them. InDel-based cDNA marker for authentication was developed based on the genome sequences. Flavonoids, iridoids, and organic acids were identified in the LC-MS analyses, and their inter-species distribution and localization were also revealed.
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http://dx.doi.org/10.1016/j.phytochem.2018.07.012DOI Listing
November 2018

Rapid and Efficient FISH using Pre-Labeled Oligomer Probes.

Sci Rep 2018 05 29;8(1):8224. Epub 2018 May 29.

Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.

Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.
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http://dx.doi.org/10.1038/s41598-018-26667-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974128PMC
May 2018

Tumorigenic role of YAP in hepatocellular carcinogenesis is involved in SHP2 whose function is different in vitro and in vivo.

Pathol Res Pract 2018 Jul 21;214(7):1031-1039. Epub 2018 Apr 21.

Department of Pathology, School of Medicine and Institute for cancer research, Keimyung University, Daegu, Republic of Korea. Electronic address:

Yes-associated protein (YAP) is a nuclear effector of the cell-density sensing Hippo pathway and interacts with Src homology phosphotyrosine phosphatase 2 (SHP2), which controls cell proliferation and survival. The tumor promoting/suppressing activities of YAP and SHP2 during liver tumorigenesis remain controversial. This study aimed to investigate the tumorigenic roles of YAP and SHP2 in hepatocellular carcinogenesis. Cell density associated subcellular distributions of YAP and SHP2 in normal human hepatocytes (THLE-2) and hepatocellular carcinoma (HCC) cells (SK-Hep1, SNU-182) were investigated by Western blotting and cell block immunohistochemistry. The effects of YAP knockdown on proliferation, migration and invasion were studied using YAP-specific siRNAs. The prognostic significance of YAP and SHP2 expressions was investigated immunohistochemically using a tissue microarray (TMA) from 50 HCC cases. High-cell density decreased the nuclear expression of YAP and SHP2 in normal hepatocytes as compared with low-cell density. However, in HCC cells, nuclear YAP and SHP2 were observed regardless of cell density. Nuclear YAP influenced SHP2 expression and cell proliferation. In particular, YAP knockdown impacted nuclear levels of SHP2 protein in SK-Hep1 cells. In HCC tissues, nuclear YAP expression was elevated and cytoplasmic SHP2 expression was diminished as compared with adjacent non-tumor tissues. Notably, these expressions were found to be significantly associated with poor recurrence-free and overall survival rate in patients with HCC. Consequently, the tumor promoting role of YAP is involved in SHP2 which functions as a tumor promoter in vitro but as a tumor suppressor in vivo. YAP and SHP2 can be unfavorable prognostic markers in HCC.
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http://dx.doi.org/10.1016/j.prp.2018.04.010DOI Listing
July 2018

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

BMC Plant Biol 2018 Apr 12;18(1):62. Epub 2018 Apr 12.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

Background: The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb.

Description: The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page.

Conclusion: This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.
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http://dx.doi.org/10.1186/s12870-018-1282-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898050PMC
April 2018

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Plant Biotechnol J 2018 11 25;16(11):1904-1917. Epub 2018 May 25.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.
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http://dx.doi.org/10.1111/pbi.12926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181221PMC
November 2018

Authentication of Zanthoxylum Species Based on Integrated Analysis of Complete Chloroplast Genome Sequences and Metabolite Profiles.

J Agric Food Chem 2017 Nov 10;65(47):10350-10359. Epub 2017 Nov 10.

Department of Biological Sciences, Kangwon National University , Chuncheon, Gangwon 24341, Republic of Korea.

We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species. Metabolite profile analysis pointed to three metabolic groups, one with Korean Z. piperitum samples, one with Korean Z. schinifolium samples, and the last containing all the tested Chinese Zanthoxylum species samples, which are considered to be Z. bungeanum based on our results. Two markers were capable of distinguishing among these three groups. The chloroplast genome sequences identified in this study represent a valuable genomics resource for exploring diversity in Rutaceae, and the molecular markers will be useful for authenticating dried Zanthoxylum berries in the marketplace.
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http://dx.doi.org/10.1021/acs.jafc.7b04167DOI Listing
November 2017

A refined karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs.

J Ginseng Res 2017 Oct 11;41(4):469-476. Epub 2016 Aug 11.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

Background: Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification.

Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR.

Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the karyotype.

Conclusion: Identification of individual chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of .
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http://dx.doi.org/10.1016/j.jgr.2016.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628329PMC
October 2017

Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species.

Sci Rep 2017 07 7;7(1):4917. Epub 2017 Jul 7.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1-99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values. Four genes, petN, psaJ, psbF, and psbN, related to photosynthesis and one gene, rpl23, related to the ribosomal large subunit remain conserved in all 10 Araliaceae species. Phylogenetic analysis revealed that the ten species could be resolved into two monophyletic lineages, the Panax-Aralia and the Eleutherococcus-Dendropanax groups, which diverged approximately 8.81-10.59 million years ago (MYA). The Panax genus divided into two groups, with diploid species including P. notoginseng, P. vietnamensis, and P. japonicus surviving in Southern Asia and a tetraploid group including P. ginseng and P. quinquefolius Northern Asia and North America 2.89-3.20 MYA.
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http://dx.doi.org/10.1038/s41598-017-05218-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501832PMC
July 2017