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Original Articles
Radiomics-Based Prediction of Lymphedema after Radiotherapy in Breast Cancer: Integrating Clinical and Dosimetric Features
Jae Sik Kim, Seung Hyuck Jeon, Bum-Sup Jang, Jin Ho Kim, Ji Hyun Chang, Dowook Kim, Kyung Hwan Shin
Received September 9, 2025  Accepted January 11, 2026  Published online January 13, 2026  
DOI: https://doi.org/10.4143/crt.2025.985    [Accepted]
AbstractAbstract PDF
Purpose
Arm lymphedema is a common, debilitating complication in patients with breast cancer undergoing postoperative radiotherapy (PORT). Although clinical and dosimetric factors have been used for risk prediction, radiomics offers a novel approach for improving the predictive accuracy.
Materials and Methods
We designed a predictive model for lymphedema using clinical, dosimetric, and radiomic features. We included 532 patients (399 training and 133 testing) who underwent breast cancer surgery followed by PORT. Radiomic features were extracted from axillary levels I, II, III, and supraclavicular regions, which were automatically contoured on PORT-planning computed tomography scans. Least absolute shrinkage and selection operator regression was used for feature selection. Model performance was evaluated using the area under the curve (AUC), accuracy, sensitivity, and specificity.
Results
The Combined model integrating clinical, dosimetric, and radiomic features showed higher predictive performance (AUC: training 0.783, test 0.767, total 0.779) than the Clinical/Dosimetric (AUC: training 0.730, test 0.671, total 0.717) and Radiomics-only (AUC: training 0.721, test 0.668, total 0.708) models. The Combined model also achieved a higher accuracy (training 78.9%, test 78.2%, total 78.8%), sensitivity (training 74.6%, test 62.5%, total 72.0%), and specificity (training 79.7%, test 80.3%, total 79.9%) than the other models. DeLong’s test confirmed that the Combined model significantly outperformed the Clinical/Dosimetric model (p=0.036 in training and p=0.010 in all datasets).
Conclusion
Integrating radiomic features with clinical and dosimetric factors showed potential to enhance lymphedema prediction in patients with breast cancer receiving PORT. This model can potentially guide personalized treatment strategies and improve patient outcomes.
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Hematologic malignancy
Higher Microbial Abundance and Diversity in Bronchus-Associated Lymphoid Tissue Lymphomas Than in Non-cancerous Lung Tissues
Jung Heon Kim, Jae Sik Kim, Noorie Choi, Jiwon Koh, Yoon Kyung Jeon, Ji Hyun Chang, Eung Soo Hwang, Il Han Kim
Cancer Res Treat. 2025;57(2):580-589.   Published online September 30, 2024
DOI: https://doi.org/10.4143/crt.2024.689
AbstractAbstract PDFSupplementary MaterialPubReaderePub
Purpose
It is well known that the majority of the extranodal marginal zone lymphomas of mucosa-associated lymphoid tissues (MALT lymphomas) are associated with microbiota, e.g., gastric MALT lymphoma with Helicobacter pylori. In general, they are very sensitive to low-dose radiotherapy and chemotherapeutic agents. The microbiota profile is not clearly elucidated in bronchus-associated lymphoid tissue (BALT) lymphoma, a rare type of MALT lymphoma in the lung. Thus, this study aimed to clarify the intratumor microbiome in BALT lymphoma using the third-generation next-generation sequencing (NGS) method.
Materials and Methods
DNAs were extracted from 12 formalin-fixed paraffin-embedded (FFPE) tumor tissues obtained from BALT lymphoma patients diagnosed between 1990 and 2016. 16S rRNA gene was amplified by polymerase chain reaction. Amplicons were sequenced using a Nanopore platform. Next-generation sequencing analysis was performed to assess microbial profiles. For comparison, FFPE specimens from nine non-cancerous lung tissues were also analyzed.
Results
Specific bacterial families including Burkholderiaceae, Bacillaceae, and Microbacteriaceae were associated with BALT lymphoma by a linear discriminant analysis effect size approach. Although the number of specimens was limited, BALT lymphomas exhibited significantly higher microbial abundance and diversity with distinct microbial composition patterns and correlation networks than non-cancerous lung tissues.
Conclusion
This study provides the first insight into intratumor microbiome in BALT lymphoma using the third-generation NGS method. A distinct microbial composition suggests the presence of a unique tumor microenvironment of BALT lymphoma.

Citations

Citations to this article as recorded by  
  • Microbial infection and treatment strategies in cancer patients
    Kejing Zhu, Zhibo Yuan, Jingli Li, Ailing Fu
    Frontiers in Microbiology.2025;[Epub]     CrossRef
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General
Identification of Genes Involved in EGF-induced Apoptosis Using CRISPR/Cas9 Knockout Screening: Implications for Novel Therapeutic Targets in EGFR-Overexpressing Cancers
Jae Sik Kim, Joo Ho Lee, Sang-Rok Jeon, Yongsub Kim, Seung Hyuck Jeon, Hong-Gyun Wu
Cancer Res Treat. 2023;55(3):737-745.   Published online January 4, 2023
DOI: https://doi.org/10.4143/crt.2022.1414
AbstractAbstract PDFSupplementary MaterialPubReaderePub
Purpose
Exogenous epidermal growth factor (EGF) causes apoptosis in EGF receptor (EGFR)–overexpressing cell lines. The apoptosis-inducing factors could be a therapeutic target. We aimed to determine the mechanism of EGF-induced apoptosis using a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-based knockout screen.
Materials and Methods
Two-vector system of the human genome-scale CRISPR knockout library v2 was used to target 19,050 genes using 123,411 single guide RNAs (sgRNAs). Recombinant human EGF (100 nM) or distilled water four times was administered to the experimental and control groups, respectively. The read counts of each sgRNA obtained from next-generation sequencing were analyzed using the edgeR algorithm. We used another EGFR-overexpressing cell line (A549) and short hairpin RNAs (shRNAs) targeting five EGF-resistance genes for validation. DUSP1 expression in A431, A549, and HEK293FT cells was calculated using reverse transcription–quantitative polymerase chain reaction.
Results
We found 77 enriched and 189 depleted genes in the experimental group using the CRISPR-based knockout screen and identified the top five EGF-resistance genes: DDX20, LHFP, REPS1, DUSP1, and KRTAP10-12. Transfecting shRNAs targeting these genes into A549 cells significantly increased the surviving fractions after EGF treatment, compared with those observed in the control shRNA-transfected cells. The expression ratio of DUSP1 (inhibits ERK signaling) increased in A431 and A549 cells after EGF treatment. However, DUSP1 expression remained unchanged in HEK293FT cells after EGF treatment.
Conclusion
The CRISPR-based knockout screen revealed 266 genes possibly responsible for EGF-induced apoptosis. DUSP1 might be a critical component of EGF-induced apoptosis and a novel target for EGFR-overexpressing cancers.

Citations

Citations to this article as recorded by  
  • Comprehensive strategies for constructing efficient CRISPR/Cas based cancer therapy: Target gene selection, sgRNA optimization, delivery methods and evaluation
    Sathishbabu Paranthaman, Chinnappa A. Uthaiah, Shadab Md, Huda Mohammed Alkreathy
    Advances in Colloid and Interface Science.2025; 341: 103497.     CrossRef
  • RIPK4-p53 interaction drives aflatoxin B1-induced renal mitochondrial apoptosis via Ser15 phosphorylation: A CRISPR-Cas9 mechanistic study
    Yuhan Ma, Qin Zhao, Jianlin Yuan, Dan Wang, Xizhu Chen, Yang Yu, Jinfeng Li, Miao Yu, Jian Yuan, Jianan Lou, Senyan Du, Yiping Wen, Yiping Wang, Rui Wu, Qi-Gui Yan, Xiaobo Huang, Yi Zheng, Fei Zhao, San-Jie Cao
    International Journal of Biological Macromolecules.2025; 330: 148130.     CrossRef
  • Profiling the Complexity of Resistance Factors in Cancer Cells Towards Berberine and Its Derivatives
    Nadire Özenver, Nadeen T. Ali, Rümeysa Yücer, Xiao Lei, Gerhard Bringmann, Thomas Efferth, Mona Dawood
    Pharmaceuticals.2025; 19(1): 27.     CrossRef
  • Uncovering the bookshelves of CRISPR-based libraries: Advances and applications in cancer studies
    Nathalia Quintero-Ruiz, Wesley de Lima Oliveira, Marcos Vinicius Esteca, Daniela Campos Granato, Fernando Moreira Simabuco
    Critical Reviews in Oncology/Hematology.2024; 196: 104287.     CrossRef
  • CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy
    Mingming Qin, Chunhao Deng, Liewei Wen, Guoqun Luo, Ya Meng
    Journal of Translational Medicine.2024;[Epub]     CrossRef
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  • 288 Download
  • 5 Web of Science
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Gynecologic cancer
Plasma Cell-Free DNA in Uterine Cervical Cancer: Therapeutic Monitoring and Prognostic Values after Radical Radiotherapy
Jae Sik Kim, Sunah Yang, Kyeonghun Jeong, Dong-Yun Kim, Kwangsoo Kim, Hyun-Cheol Kang
Cancer Res Treat. 2023;55(2):659-670.   Published online December 12, 2022
DOI: https://doi.org/10.4143/crt.2022.1440
AbstractAbstract PDFSupplementary MaterialPubReaderePub
Purpose
In the present study, we aimed to establish a liquid biopsy-based monitoring method using peripheral blood cell-free DNA (cfDNA) for patients with cervical cancer who underwent radical radiotherapy (RT).
Materials and Methods
Twenty-five patients with cervical cancer were prospectively recruited and treated with external beam RT and brachytherapy. In all patients, except one, chemotherapy was administered concurrently during RT. Whole peripheral blood samples were obtained at least twice from each patient. We performed next-generation sequencing (NGS) for the target-captured libraries (67 oncogenes and human papillomavirus [HPV] type 16/18) using 64 plasma cfDNA samples from the 25 participants. The ratio of HPV cfDNA and the variant allele frequency (VAF) in cfDNA was calculated, and their dynamic changes were monitored. The median follow-up duration was 25.4 months.
Results
In total, we identified 21,866 cfDNA variants. ARID1A and frameshift variants occupied the largest portion of altered genes and HIGH-grade variant types, respectively. In most cases, tumor shrinkage was followed by a decrease in the HPV ratio; however, an increase in HPV ratio indicated distant metastasis, despite the reduced tumor size. The initial HPV ratio reflecting the tumor burden was likely associated with treatment outcomes (p = 0.16). We did not determine a role for serial changes in the VAF in cfDNA.
Conclusion
Our findings suggest that the HPV cfDNA ratio, calculated after targeted NGS, may be valuable for monitoring and predicting treatment responses. Accordingly, further validation of these findings is warranted.

Citations

Citations to this article as recorded by  
  • Biopsy‐proven residual cervical cancer at the end of combined chemoradiation predicts poor outcome—Retrospective single‐center cohort study
    Christoph Ebner, Ricarda Purtscheller, Barin Feroz, Jana Rieker, Linda Ebner, Mara Mantovan, Sergej Skvortsov, Mario Brüggl, Katharina Leitner, Verena Wieser, Irina Tsibulak, Christian Marth, Alain Gustave Zeimet
    Acta Obstetricia et Gynecologica Scandinavica.2026; 105(2): 368.     CrossRef
  • The role of circulating tumor DNA in gynecological cancer management
    Min Gao, Pei-Yan Yu, Run-Xuan Li, Chen Chen, Xiao-Feng Cong, Zi-Ling Liu
    Frontiers in Oncology.2026;[Epub]     CrossRef
  • Diagnostic and Prognostic Significance of Circulating HPV cfDNA in Cervical Cancer: A Systematic Review and Meta-analysis
    Preetiparna Parida, Ankita Mehta, Elstin Anbu Raj, Shyamala Guruvare, Mahadev Rao, Rama Rao Damerla, Shirley Lewis
    Critical Reviews in Oncology/Hematology.2026; : 105161.     CrossRef
  • Cell-Free HPV-DNA in Screening, Diagnosis, Prognosis, and Treatment Response Monitoring of Cervical Cancer
    Nayara Nascimento Toledo Silva, Ana Carolina Silva Santos, Isadora Oliveira Ansaloni Pereira, Glenda Nicioli da Silva, Angélica Alves Lima
    Molecular Diagnosis & Therapy.2025; 29(4): 483.     CrossRef
  • Circulating cell-free DNA as a diagnostic and prognostic marker for cervical cancer
    Preetiparna Parida, Gayathri Baburaj, Mahadev Rao, Shirley Lewis, Rama Rao Damerla
    International Journal of Gynecological Cancer.2024; 34(2): 307.     CrossRef
  • Prognostic value of circulating short-length DNA fragments in unresected glioblastoma patients
    Arthur Daban, Ludivine Beaussire-Trouvay, Émilie Lévêque, Cristina Alexandru, Isabelle Tennevet, Olivier Langlois, Ovidiu Veresezan, Florent Marguet, Florian Clatot, Frédéric Di Fiore, Nasrin Sarafan-Vasseur, Maxime Fontanilles
    Translational Oncology.2024; 42: 101897.     CrossRef
  • Cervical Cancer Genetic Profile through Circulating Tumor DNA: What Can We Learn from Blood?
    Sevastiani Antonouli, Valentina Di Nisio, Nikoletta Daponte, Athina-Ioanna Daponte, Alexandros Daponte
    Biomolecules.2024; 14(7): 825.     CrossRef
  • High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors.
    Chonghe Xu, Dangui Zhou, Mei Zhu
    Investigación Clínica.2024; 65(4): 476.     CrossRef
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Breast cancer
The Pattern of Care for Brain Metastasis from Breast Cancer over the Past 10 Years in Korea: A Multicenter Retrospective Study (KROG 16-12)
Jae Sik Kim, Kyubo Kim, Wonguen Jung, Kyung Hwan Shin, Seock-Ah Im, Hee-Jun Kim, Yong Bae Kim, Jee Suk Chang, Jee Hyun Kim, Doo Ho Choi, Yeon Hee Park, Dae Yong Kim, Tae Hyun Kim, Byung Ock Choi, Sea-Won Lee, Suzy Kim, Jeanny Kwon, Ki Mun Kang, Woong-Ki Chung, Kyung Su Kim, Ji Ho Nam, Won Sup Yoon, Jin Hee Kim, Jihye Cha, Yoon Kyeong Oh, In Ah Kim
Cancer Res Treat. 2022;54(4):1121-1129.   Published online December 31, 2021
DOI: https://doi.org/10.4143/crt.2021.1083
AbstractAbstract PDFSupplementary MaterialPubReaderePub
Purpose
We aimed to investigate manifestations and patterns of care for patients with brain metastasis (BM) from breast cancer (BC) and compared their overall survival (OS) from 2005 through 2014 in Korea.
Materials and Methods
We retrospectively reviewed 600 BC patients with BM diagnosed between 2005 and 2014. The median follow-up duration was 12.5 months. We categorized the patients into three groups according to the year when BM was initially diagnosed (group I [2005-2008], 98 patients; group II [2009-2011], 200 patients; and group III [2012-2014], 302 patients).
Results
Over time, the median age at BM diagnosis increased by 2.2 years (group I, 49.0 years; group II, 48.3 years; and group III, 51.2 years; p=0.008). The percentage of patients with extracranial metastasis was 73.5%, 83.5%, and 86.4% for group I, II, and III, respectively (p=0.011). The time interval between BC and BM was prolonged in patients with stage III primary BC (median, 2.4 to 3 years; p=0.029). As an initial brain-directed treatment, whole-brain radiotherapy alone decreased from 80.0% in 2005 to 41.1% in 2014. Meanwhile, stereotactic radiosurgery or fractionated stereotactic radiotherapy alone increased from 13.3% to 34.7% during the same period (p=0.005). The median OS for group I, II, and III was 15.6, 17.9, and 15.0 months, respectively, with no statistical significance.
Conclusion
The manifestations of BM from BC and the pattern of care have changed from 2005 to 2014 in Korea. However, the OS has remained relatively unchanged over the 10 years.

Citations

Citations to this article as recorded by  
  • Comparison of initial and sequential salvage brain-directed treatment in patients with 1–4 vs. 5–10 brain metastases from breast cancer (KROG 16–12)
    Jae Sik Kim, Kyubo Kim, Wonguen Jung, Kyung Hwan Shin, Seock-Ah Im, Hee-Jun Kim, Yong Bae Kim, Jee Suk Chang, Jee Hyun Kim, Doo Ho Choi, Yeon Hee Park, Dae Yong Kim, Tae Hyun Kim, Byung Ock Choi, Sea-Won Lee, Suzy Kim, Jeanny Kwon, Ki Mun Kang, Woong-Ki C
    Breast Cancer Research and Treatment.2023; 200(1): 37.     CrossRef
  • 8,517 View
  • 195 Download
  • 1 Web of Science
  • 1 Crossref
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The Prognostic Value of Albumin-to-Alkaline Phosphatase Ratio before Radical Radiotherapy in Patients with Non-metastatic Nasopharyngeal Carcinoma: A Propensity Score Matching Analysis
Jae Sik Kim, Bhumsuk Keam, Dae Seog Heo, Doo Hee Han, Chae-Seo Rhee, Ji-hoon Kim, Kyeong Cheon Jung, Hong-Gyun Wu
Cancer Res Treat. 2019;51(4):1313-1323.   Published online January 29, 2019
DOI: https://doi.org/10.4143/crt.2018.503
AbstractAbstract PDFPubReaderePub
Purpose
We first analyzed the prognostic power of albumin-to-alkaline phosphatase ratio (AAPR) before radical radiotherapy (RT) in non-metastatic nasopharyngeal carcinoma (NPC) patients.
Materials and Methods
The records of 170 patients with biopsy-proven, non-metastatic NPC treated by radical RT between 1998 and 2016 at our institution were retrospectively reviewed. Median follow-up duration was 50.6 months. All patients received intensity-modulated RT and cisplatin based chemotherapy before, during, or after RT. The major treatment of patients was based on concurrent chemoradiotherapy (92.4%). The AAPR was calculated by the last value of both albumin and alkaline phosphatase within 1 month immediately preceding RT. The optimal cut-off level of AAPR was determined by using Cutoff Finder, a web-based system. Propensity score matching (PSM) analysis was performed.
Results
The optimal cut-off level of AAPR was 0.4876. After PSM analysis of whole cohort, an AAPR was not related to survival outcomes. In PSM analysis for patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC), an AAPR ≥ 0.4876 was related to better overall survival (OS), progression-free survival (PFS), and locoregional relapse–free survival (LRRFS) (OS: hazard ratio [HR], 0.341; 95% confidence interval [CI], 0.144 to 0.805; p=0.014; PFS: HR, 0.416; 95% CI, 0.189 to 0.914; p=0.029; and LRRFS: HR, 0.243; 95% CI, 0.077 to 0.769; p=0.016, respectively).
Conclusion
The AAPR, inexpensive and readily derived from a routine blood test, could be an independent prognostic factor for patients with LA-NPC. And it might help physicians determine treatment plans by identifying the patient's current status. Future prospective clinical trials to validate its prognostic value are needed.

Citations

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  • Prognostic Significance of the Combined Albumin-To-Alkaline Phosphatase Ratio (AAPR) and Haemoglobin–Albumin–Lymphocyte–Platelet (HALP) Score in Patients with Metastatic Renal Cell Carcinoma Treated by Targeted Therapy: A New Prognostic Combined Risk Scor
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  • Nonlinear association of alkaline phosphatase-to-albumin ratio with all-cause and cancer mortality: Evidence from NHANES 2005 to 2016
    Jiang Wang, Bo Wang, Shiwang Yuan, Guangyi Cheng, Sijia Deng, Yuyan Wang, Yu Shen, Liantao Li
    Medicine.2024; 103(46): e40430.     CrossRef
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    Frontiers in Oncology.2020;[Epub]     CrossRef
  • Prognostic Value of Pretreatment Albumin-to-Alkaline Phosphatase Ratio in Extensive-Disease Small-Cell Lung Cancer: A Retrospective Cohort Study


    Shaozhang Zhou, Huiling Wang, Wei Jiang, Qitao Yu, Aiping Zeng
    Cancer Management and Research.2020; Volume 12: 2015.     CrossRef
  • Predictive value of pretreatment albumin‐to‐alkaline phosphatase ratio for overall survival for patients with advanced non‐small cell lung cancer
    Shaozhang Zhou, Wei Jiang, Huilin Wang, Ni Wei, Qitao Yu
    Cancer Medicine.2020; 9(17): 6268.     CrossRef
  • Prognostic effect of pretreatment albumin-to-alkaline phosphatase ratio in human cancers: A meta-analysis
    Xiaoli Guo, Qijiu Zou, Jiaxin Yan, Xingxing Zhen, Hongmei Gu, Jason Chia-Hsun Hsieh
    PLOS ONE.2020; 15(8): e0237793.     CrossRef
  • Prognostic Value of Pretreatment Albumin‐to‐Alkaline Phosphatase Ratio in Cancer: A Meta‐Analysis
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    BioMed Research International.2020;[Epub]     CrossRef
  • Prognostic Value of Preoperative Albumin-to-Alkaline Phosphatase Ratio in Patients with Muscle-Invasive Bladder Cancer After Radical Cystectomy
    Ming Zhao, Mingxin Zhang, Yonghua Wang, Xuecheng Yang, Xue Teng, Guangdi Chu, Xinsheng Wang, Haitao Niu
    OncoTargets and Therapy.2020; Volume 13: 13265.     CrossRef
  • Albumin-to-alkaline phosphatase ratio as a novel prognostic indicator for patients undergoing minimally invasive lung cancer surgery: Propensity score matching analysis using a prospective database
    Shuang-Jiang Li, Wen-Yu Lv, Heng Du, Yong-Jiang Li, Wen-Biao Zhang, Guo-Wei Che, Lun-Xu Liu
    International Journal of Surgery.2019; 69: 32.     CrossRef
  • New prognostic indicators in surgery
    Burcin Ekser, Massimiliano Veroux
    International Journal of Surgery.2019; 68: 176.     CrossRef
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  • 33 Web of Science
  • 30 Crossref
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