1.p27 Cell Cycle Inhibitor and Survival in Luminal-Type Breast Cancer:Gene Ontology, Machine Learning, and Drug Screening Analysis
In Ah PARK ; Yung-Kyun NOH ; Kyueng-Whan MIN ; Dong-Hoon KIM ; Jeong-Yeon LEE ; Byoung Kwan SON ; Mi Jung KWON ; Myung-Hoon HAN ; Joon Young HUR ; Jung Soo PYO
Journal of Breast Cancer 2024;27(5):305-322
Purpose:
A widely distributed cell cycle inhibitor, p27, regulates cyclin-dependent kinase-cyclin complexes. Although the prognostic value of p27 has been established for various types of carcinomas, its role in luminal breast cancer remains poorly understood. This study aimed to explore the functional enrichment of p27 and identify potential drug targets in patients with luminal-type breast cancer.
Methods:
Clinicopathological data were collected from 868 patients with luminal-type breast cancer. Additionally, publicly available data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset (1,500 patients) and the Gene Expression Omnibus database (855 patients) were included in the analysis. Immunohistochemical staining for p27, differential gene expression analysis, disease ontology analysis, survival prediction modeling using machine learning (ML), and in vitro drug screening were also performed.
Results:
Low p27 expression correlated with younger age, advanced tumor stage, estrogen receptor/progesterone receptor negativity, decreased cluster of differentiation 8+ T cell count, and poorer survival outcomes in luminal-type breast cancer. The METABRIC data revealed that reduced cyclin-dependent kinase inhibitor 1B (CDKN1B) expression (encoding p27) was associated with cell proliferation-related pathways and epigenetic polycomb repressive complex 2. Using ML, p27 emerged as the second most significant survival factor after N stage, thereby enhancing survival model performance. Additionally, luminal-type breast cancer cell lines with low CDKN1B expression demonstrated increased sensitivity to specific anticancer drugs such as voxtalisib and serdemetan, implying a potential therapeutic synergy between CDKN1B-targeted approaches and these drugs.
Conclusion
The integration of ML and bioinformatic analyses of p27 has the potential to enhance risk stratification and facilitate personalized treatment strategies for patients with breast cancer.
2.p27 Cell Cycle Inhibitor and Survival in Luminal-Type Breast Cancer:Gene Ontology, Machine Learning, and Drug Screening Analysis
In Ah PARK ; Yung-Kyun NOH ; Kyueng-Whan MIN ; Dong-Hoon KIM ; Jeong-Yeon LEE ; Byoung Kwan SON ; Mi Jung KWON ; Myung-Hoon HAN ; Joon Young HUR ; Jung Soo PYO
Journal of Breast Cancer 2024;27(5):305-322
Purpose:
A widely distributed cell cycle inhibitor, p27, regulates cyclin-dependent kinase-cyclin complexes. Although the prognostic value of p27 has been established for various types of carcinomas, its role in luminal breast cancer remains poorly understood. This study aimed to explore the functional enrichment of p27 and identify potential drug targets in patients with luminal-type breast cancer.
Methods:
Clinicopathological data were collected from 868 patients with luminal-type breast cancer. Additionally, publicly available data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset (1,500 patients) and the Gene Expression Omnibus database (855 patients) were included in the analysis. Immunohistochemical staining for p27, differential gene expression analysis, disease ontology analysis, survival prediction modeling using machine learning (ML), and in vitro drug screening were also performed.
Results:
Low p27 expression correlated with younger age, advanced tumor stage, estrogen receptor/progesterone receptor negativity, decreased cluster of differentiation 8+ T cell count, and poorer survival outcomes in luminal-type breast cancer. The METABRIC data revealed that reduced cyclin-dependent kinase inhibitor 1B (CDKN1B) expression (encoding p27) was associated with cell proliferation-related pathways and epigenetic polycomb repressive complex 2. Using ML, p27 emerged as the second most significant survival factor after N stage, thereby enhancing survival model performance. Additionally, luminal-type breast cancer cell lines with low CDKN1B expression demonstrated increased sensitivity to specific anticancer drugs such as voxtalisib and serdemetan, implying a potential therapeutic synergy between CDKN1B-targeted approaches and these drugs.
Conclusion
The integration of ML and bioinformatic analyses of p27 has the potential to enhance risk stratification and facilitate personalized treatment strategies for patients with breast cancer.
3.p27 Cell Cycle Inhibitor and Survival in Luminal-Type Breast Cancer:Gene Ontology, Machine Learning, and Drug Screening Analysis
In Ah PARK ; Yung-Kyun NOH ; Kyueng-Whan MIN ; Dong-Hoon KIM ; Jeong-Yeon LEE ; Byoung Kwan SON ; Mi Jung KWON ; Myung-Hoon HAN ; Joon Young HUR ; Jung Soo PYO
Journal of Breast Cancer 2024;27(5):305-322
Purpose:
A widely distributed cell cycle inhibitor, p27, regulates cyclin-dependent kinase-cyclin complexes. Although the prognostic value of p27 has been established for various types of carcinomas, its role in luminal breast cancer remains poorly understood. This study aimed to explore the functional enrichment of p27 and identify potential drug targets in patients with luminal-type breast cancer.
Methods:
Clinicopathological data were collected from 868 patients with luminal-type breast cancer. Additionally, publicly available data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset (1,500 patients) and the Gene Expression Omnibus database (855 patients) were included in the analysis. Immunohistochemical staining for p27, differential gene expression analysis, disease ontology analysis, survival prediction modeling using machine learning (ML), and in vitro drug screening were also performed.
Results:
Low p27 expression correlated with younger age, advanced tumor stage, estrogen receptor/progesterone receptor negativity, decreased cluster of differentiation 8+ T cell count, and poorer survival outcomes in luminal-type breast cancer. The METABRIC data revealed that reduced cyclin-dependent kinase inhibitor 1B (CDKN1B) expression (encoding p27) was associated with cell proliferation-related pathways and epigenetic polycomb repressive complex 2. Using ML, p27 emerged as the second most significant survival factor after N stage, thereby enhancing survival model performance. Additionally, luminal-type breast cancer cell lines with low CDKN1B expression demonstrated increased sensitivity to specific anticancer drugs such as voxtalisib and serdemetan, implying a potential therapeutic synergy between CDKN1B-targeted approaches and these drugs.
Conclusion
The integration of ML and bioinformatic analyses of p27 has the potential to enhance risk stratification and facilitate personalized treatment strategies for patients with breast cancer.
4.JAK2 Loss Arising From Tumor-SpreadThrough-Air-Spaces (STAS) Promotes Tumor Progression by Suppressing CD8+ T Cells in Lung Adenocarcinoma:A Machine Learning Approach
Soohwan CHOI ; Hyung Suk KIM ; Kyueng-Whan MIN ; Yung-Kyun NOH ; Jeong-Yeon LEE ; Ji-Yong MOON ; Un Suk JUNG ; Mi Jung KWON ; Dong-Hoon KIM ; Byoung Kwan SON ; Jung Soo PYO ; Sun Kyun RO
Journal of Korean Medical Science 2024;39(2):e16-
Background:
Tumor spread through air spaces (STAS) is a recently discovered risk factor for lung adenocarcinoma (LUAD). The aim of this study was to investigate specific genetic alterations and anticancer immune responses related to STAS. By using a machine learning algorithm and drug screening in lung cancer cell lines, we analyzed the effect of Janus kinase 2 (JAK2) on the survival of patients with LUAD and possible drug candidates.
Methods:
This study included 566 patients with LUAD corresponding to clinicopathological and genetic data. For analyses of LUAD, we applied gene set enrichment analysis (GSEA), in silico cytometry, pathway network analysis, in vitro drug screening, and gradient boosting machine (GBM) analysis.
Results:
The patients with STAS had a shorter survival time than those without STAS (P < 0.001). We detected gene set-related downregulation of JAK2 associated with STAS using GSEA. Low JAK2 expression was related to poor prognosis and a low CD8+ T-cell fraction. In GBM, JAK2 showed improved survival prediction performance when it was added to other parameters (T stage, N stage, lymphovascular invasion, pleural invasion, tumor size). In drug screening, mirin, CCT007093, dihydroretenone, and ABT737 suppressed the growth of lung cancer cell lines with low JAK2 expression.
Conclusion
In LUAD, low JAK2 expression linked to the presence of STAS might serve as an unfavorable prognostic factor. A relationship between JAK2 and CD8+ T cells suggests that STAS is indirectly related to the anticancer immune response. These results may contribute to the design of future experimental research and drug development programs for LUAD with STAS.
5.Erratum: Korean Practice Guidelines for Gastric Cancer 2022: An Evidencebased, Multidisciplinary Approach
Tae-Han KIM ; In-Ho KIM ; Seung Joo KANG ; Miyoung CHOI ; Baek-Hui KIM ; Bang Wool EOM ; Bum Jun KIM ; Byung-Hoon MIN ; Chang In CHOI ; Cheol Min SHIN ; Chung Hyun TAE ; Chung sik GONG ; Dong Jin KIM ; Arthur Eung-Hyuck CHO ; Eun Jeong GONG ; Geum Jong SONG ; Hyeon-Su IM ; Hye Seong AHN ; Hyun LIM ; Hyung-Don KIM ; Jae-Joon KIM ; Jeong Il YU ; Jeong Won LEE ; Ji Yeon PARK ; Jwa Hoon KIM ; Kyoung Doo SONG ; Minkyu JUNG ; Mi Ran JUNG ; Sang-Yong SON ; Shin-Hoo PARK ; Soo Jin KIM ; Sung Hak LEE ; Tae-Yong KIM ; Woo Kyun BAE ; Woong Sub KOOM ; Yeseob JEE ; Yoo Min KIM ; Yoonjin KWAK ; Young Suk PARK ; Hye Sook HAN ; Su Youn NAM ; Seong-Ho KONG
Journal of Gastric Cancer 2023;23(2):365-373
6.Korean Practice Guidelines for Gastric Cancer 2022: An Evidence-based, Multidisciplinary Approach
Tae-Han KIM ; In-Ho KIM ; Seung Joo KANG ; Miyoung CHOI ; Baek-Hui KIM ; Bang Wool EOM ; Bum Jun KIM ; Byung-Hoon MIN ; Chang In CHOI ; Cheol Min SHIN ; Chung Hyun TAE ; Chung sik GONG ; Dong Jin KIM ; Arthur Eung-Hyuck CHO ; Eun Jeong GONG ; Geum Jong SONG ; Hyeon-Su IM ; Hye Seong AHN ; Hyun LIM ; Hyung-Don KIM ; Jae-Joon KIM ; Jeong Il YU ; Jeong Won LEE ; Ji Yeon PARK ; Jwa Hoon KIM ; Kyoung Doo SONG ; Minkyu JUNG ; Mi Ran JUNG ; Sang-Yong SON ; Shin-Hoo PARK ; Soo Jin KIM ; Sung Hak LEE ; Tae-Yong KIM ; Woo Kyun BAE ; Woong Sub KOOM ; Yeseob JEE ; Yoo Min KIM ; Yoonjin KWAK ; Young Suk PARK ; Hye Sook HAN ; Su Youn NAM ; Seong-Ho KONG ;
Journal of Gastric Cancer 2023;23(1):3-106
Gastric cancer is one of the most common cancers in Korea and the world. Since 2004, this is the 4th gastric cancer guideline published in Korea which is the revised version of previous evidence-based approach in 2018. Current guideline is a collaborative work of the interdisciplinary working group including experts in the field of gastric surgery, gastroenterology, endoscopy, medical oncology, abdominal radiology, pathology, nuclear medicine, radiation oncology and guideline development methodology. Total of 33 key questions were updated or proposed after a collaborative review by the working group and 40 statements were developed according to the systematic review using the MEDLINE, Embase, Cochrane Library and KoreaMed database. The level of evidence and the grading of recommendations were categorized according to the Grading of Recommendations, Assessment, Development and Evaluation proposition. Evidence level, benefit, harm, and clinical applicability was considered as the significant factors for recommendation. The working group reviewed recommendations and discussed for consensus. In the earlier part, general consideration discusses screening, diagnosis and staging of endoscopy, pathology, radiology, and nuclear medicine. Flowchart is depicted with statements which is supported by meta-analysis and references. Since clinical trial and systematic review was not suitable for postoperative oncologic and nutritional follow-up, working group agreed to conduct a nationwide survey investigating the clinical practice of all tertiary or general hospitals in Korea. The purpose of this survey was to provide baseline information on follow up. Herein we present a multidisciplinary-evidence based gastric cancer guideline.
7.Safety and efficacy of nilotinib in adult patients with chronic myeloid leukemia: a post-marketing surveillance study in Korea
Seo-Yeon AHN ; Sang Kyun SON ; Gyu Hyung LEE ; Inho KIM ; June-Won CHEONG ; Won Sik LEE ; Byung Soo KIM ; Deog-Yeon JO ; Chul Won JUNG ; Chu Myoung SEONG ; Jae Hoon LEE ; Young Jin YUH ; Min Kyoung KIM ; Hun-Mo RYOO ; Moo-Rim PARK ; Su-Hee CHO ; Hoon-Gu KIM ; Dae Young ZANG ; Jinny PARK ; Hawk KIM ; Seryeon LEE ; Sung-Hyun KIM ; Myung Hee CHANG ; Ho Sup LEE ; Chul Won CHOI ; Jihyun KWON ; Sung-Nam LIM ; Suk-Joong OH ; Inkyung JOO ; Dong-Wook KIM
Blood Research 2022;57(2):144-151
Background:
Nilotinib is a tyrosine kinase inhibitor approved by the Ministry of Food and Drug Safety for frontline and 2nd line treatment of Philadelphia chromosome-positive chronic myeloid leukemia (Ph+ CML). This study aimed to confirm the safety and efficacy of nilotinib in routine clinical practice within South Korea.
Methods:
An open-label, multicenter, single-arm, 12-week observational post-marketing surveillance (PMS) study was conducted on 669 Korean adult patients with Ph + CML from December 24, 2010, to December 23, 2016. The patients received nilotinib treatment in routine clinical practice settings. Safety was evaluated by all types of adverse events (AEs) during the study period, and efficacy was evaluated by the complete hematological response (CHR) and cytogenetic response.
Results:
During the study period, AEs occurred in 61.3% (410 patients, 973 events), adverse drug reactions (ADRs) in 40.5% (271/669 patients, 559 events), serious AEs in 4.5% (30 patients, 37 events), and serious ADRs in 0.7% (5 patients, 8 events). Furthermore, unexpected AEs occurred at a rate of 6.9% (46 patients, 55 events) and unexpected ADRs at 1.2% (8 patients, 8 events). As for the efficacy results, CHR was achieved in 89.5% (442/494 patients), and minor cytogenetic response or major cytogenetic response was achieved in 85.8% (139/162 patients).
Conclusion
This PMS study shows consistent results in terms of safety and efficacy compared with previous studies. Nilotinib was well tolerated and efficacious in adult Korean patients with Ph + CML in routine clinical practice settings.
8.Serum levels of carbohydrate antigen 125 in combination with N-terminal pro-brain natriuretic peptide in patients with acute decompensated heart failure
Jae Yong YOON ; Dong Heon YANG ; Hyun Jun CHO ; Nam Kyun KIM ; Chang Yeon KIM ; Jihyun SON ; Jae Hyung ROH ; Se Yong JANG ; Myung Hwan BAE ; Jang Hoon LEE ; Hun Sik PARK ; Yongkeun CHO ; Shung Chull CHAE
The Korean Journal of Internal Medicine 2019;34(4):811-818
BACKGROUND/AIMS:
Carbohydrate antigen 125 (CA-125) is an emerging prognostic biomarker for heart failure. We aimed to test the long-term prognostic value of CA-125 in combination with N-terminal pro-brain natriuretic peptide (NT-proBNP) in patients with acute decompensated heart failure (ADHF).
METHODS:
This observational study included a total of 413 patients (64.1 ± 15.6 year-old, 214 men) with ADHF. All-cause mortality during the 2-year follow-up was investigated for the prognosis.
RESULTS:
During the follow-up (mean follow-up, 591 ± 233 days), 109 deaths (26.0%) were recorded. In the multivariable analysis model, CA-125 was an independent factor associated with all-cause mortality (log CA-125: hazard ratio, 1.23; 95% confidence interval, 1.02 to 1.48; p = 0.030) together with age, sex, New York Heart Association class, β-blocker, and NT-proBNP. The Kaplan-Meier survival analysis demonstrated that the group with both low marker levels showed the best 2-year survival (87.9%) followed by the group with low NT-proBNP and high CA-125 (76.1%), high NT-proBNP and low CA-125 (64.7%) and high NT-proBNP and high CA-125 levels (54.3%) (p < 0.001). Addition of CA-125 in combination with NT-proBNP and established risk factors further increased the predictive power for mortality in patients with ADHF.
CONCLUSIONS
CA-125 was an independent factor associated with all-cause mortality in patients with ADHF. Combination of CA-125 with NT-proBNP significantly improved the prediction of mortality in patients with ADHF.
9.Esophageal Endoscopic Vacuum Therapy with Enteral Feeding Using a Sengstaken-Blakemore Tube
So Young LEE ; Kun Woo KIM ; Jae Ik LEE ; Dong Kyun PARK ; Kook Yang PARK ; Chul Hyun PARK ; Kuk Hui SON
The Korean Journal of Thoracic and Cardiovascular Surgery 2018;51(1):76-80
Early diagnosis followed by primary repair is the best treatment for spontaneous esophageal perforation. However, the appropriate management of esophageal leakage after surgical repair is still controversial. Recently, the successful adaptation of vacuum-assisted closure therapy, which is well established for the treatment of chronic surface wounds, has been demonstrated for esophageal perforation or leakage. Conservative treatment methods require long-term fasting with total parenteral nutrition or enteral feeding through invasive procedures, such as percutaneous endoscopic gastrostomy or a feeding jejunostomy. We report 2 cases of esophageal leakage after primary repair treated by endoscopic vacuum therapy with continuous enteral feeding using a Sengstaken-Blakemore tube.
10.Esophageal Endoscopic Vacuum Therapy with Enteral Feeding Using a Sengstaken-Blakemore Tube
So Young LEE ; Kun Woo KIM ; Jae Ik LEE ; Dong Kyun PARK ; Kook Yang PARK ; Chul Hyun PARK ; Kuk Hui SON
The Korean Journal of Thoracic and Cardiovascular Surgery 2018;51(1):76-80
Early diagnosis followed by primary repair is the best treatment for spontaneous esophageal perforation. However, the appropriate management of esophageal leakage after surgical repair is still controversial. Recently, the successful adaptation of vacuum-assisted closure therapy, which is well established for the treatment of chronic surface wounds, has been demonstrated for esophageal perforation or leakage. Conservative treatment methods require long-term fasting with total parenteral nutrition or enteral feeding through invasive procedures, such as percutaneous endoscopic gastrostomy or a feeding jejunostomy. We report 2 cases of esophageal leakage after primary repair treated by endoscopic vacuum therapy with continuous enteral feeding using a Sengstaken-Blakemore tube.
Early Diagnosis
;
Endoscopy
;
Enteral Nutrition
;
Esophageal Perforation
;
Fasting
;
Gastrostomy
;
Jejunostomy
;
Negative-Pressure Wound Therapy
;
Parenteral Nutrition, Total
;
Vacuum
;
Wounds and Injuries

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