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Jin Y, Lu R, Liu F, Jiang G, Wang R, Zheng M. DNA methylation analysis in plasma for early diagnosis in lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e38867. [PMID: 38996143 DOI: 10.1097/md.0000000000038867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) represents the most prevalent type of lung cancer. SHOX2 and RASSF1A methylation have been identified as important biomarkers for diagnosis and prognosis of lung cancer. Bronchoalveolar lavage fluid (BALF) exhibits good specificity and sensitivity in diagnosing pulmonary diseases, but its acquisition is challenging and may cause discomfort to patients. In clinical, plasma samples are more convenient to obtain than BALF; however, there is little research on the concurrent detection of SHOX2 and RASSF1A methylation in plasma. This study aims to assess the diagnostic value of a combined promoter methylation assay for SHOX2 and RASSF1A in early-stage LUAD using plasma samples. METHODS BALF and blood samples were obtained from 36 early-stage LUAD patients, with a control group of nineteen non-tumor individuals. The promoter methylation levels of SHOX2 and RASSF1A in all subjects were assessed using the human SHOX2 and RASSF1A gene methylation kit. RESULTS The methylation detection rate of SHOX2 and RASSF1A in plasma was 61.11%, slightly lower than that in BALF (66.7%). The Chi-square test revealed no significant difference in the methylation rate between BALF and plasma (P > 0.05). The area under the receiver operating characteristic (ROC) curve analysis for blood was 0.806 (95% CI, 0.677 to 0.900), while for BALF it was 0.781 (95% CI, 0.649 to 0.881). Additionally, we conducted an analysis on the correlation between SHOX2 and RASSF1A methylation levels in plasma with gender, age, tumor differentiation, pathologic classification, and other clinicopathological variables; however, no significant correlations were observed. CONCLUSIONS Measurement of SHOX2 and RASSF1A methylation for early diagnosis of LUAD can be achieved with high sensitivity and specificity by using plasma as a substitute for BALF samples.
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Affiliation(s)
- Yulin Jin
- Department of Thoracic Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
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Sun JR, Kong CF, Ye YX, Wang Q, Qu XK, Jia LQ, Wu S. Integrated analysis of single-cell and bulk RNA-sequencing reveals a novel signature based on NK cell marker genes to predict prognosis and immunotherapy response in gastric cancer. Sci Rep 2024; 14:7648. [PMID: 38561388 PMCID: PMC10985121 DOI: 10.1038/s41598-024-57714-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK) cells play essential roles in the tumor development, diagnosis, and prognosis of tumors. In this study, we aimed to establish a reliable signature based on marker genes in NK cells, thus providing a new perspective for assessing immunotherapy and the prognosis of patients with gastric cancer (GC). We analyzed a total of 1560 samples retrieved from the public database. We performed a comprehensive analysis of single-cell RNA-sequencing (scRNA-seq) data of gastric cancer and identified 377 marker genes for NK cells. By performing Cox regression analysis, we established a 12-gene NK cell-associated signature (NKCAS) for the Cancer Genome Atlas (TCGA) cohort, that assigned GC patients into a low-risk group (LRG) or a high-risk group (HRG). In the TCGA cohort, the areas under curve (AUC) value were 0.73, 0.81, and 0.80 at 1, 3, and 5 years. External validation of the predictive ability for the signature was then validated in the Gene Expression Omnibus (GEO) cohorts (GSE84437). The expression levels of signature genes were measured and validated in GC cell lines by real-time PCR. Moreover, NKCAS was identified as an independent prognostic factor by multivariate analysis. We combined this with a variety of clinicopathological characteristics (age, M stage, and tumor grade) to construct a nomogram to predict the survival outcomes of patients. Moreover, the LRG showed higher immune cell infiltration, especially CD8+ T cells and NK cells. The risk score was negatively associated with inflammatory activities. Importantly, analysis of the independent immunotherapy cohort showed that the LRG had a better prognosis and immunotherapy response when compared with the HRG. The identification of NK cell marker genes in this study suggests potential therapeutic targets. Additionally, the developed predictive signatures and nomograms may aid in the clinical management of GC.
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Affiliation(s)
- Jian-Rong Sun
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Chen-Fan Kong
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China
| | - Yi-Xiang Ye
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Qin Wang
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Xiang-Ke Qu
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Li-Qun Jia
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China.
| | - Song Wu
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China.
- Department of Urology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China.
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Grossi I, Assoni C, Lorini L, Smussi D, Gurizzan C, Grisanti S, Paderno A, Mattavelli D, Piazza C, Pelisenco IA, De Petro G, Salvi A, Bossi P. Evaluation of DNA methylation levels of SEPT9 and SHOX2 in plasma of patients with head and neck squamous cell carcinoma using droplet digital PCR. Oncol Rep 2024; 51:52. [PMID: 38299234 PMCID: PMC10865173 DOI: 10.3892/or.2024.8711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the seventh most commonly diagnosed cancer globally. HNSCC develops from the mucosa of the oral cavity, pharynx and larynx. Methylation levels of septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) genes in circulating cell‑free DNA (ccfDNA) are considered epigenetic biomarkers and have shown predictive value in preliminary reports in HNSCC. Liquid biopsy is a non‑invasive procedure that collects tumor‑derived molecules, including ccfDNA. In the present study, a droplet digital PCR (ddPCR)‑based assay was developed to detect DNA methylation levels of circulating SEPT9 and SHOX2 in the plasma of patients with HNSCC. The assay was first set up using commercial methylated and unmethylated DNA. The dynamic changes in the methylation levels of SEPT9 and SHOX2 were then quantified in 20 patients with HNSCC during follow‑up. The results highlighted: i) The ability of the ddPCR‑based assay to detect very low copies of methylated molecules; ii) the significant decrease in SEPT9 and SHOX2 methylation levels in the plasma of patients with HNSCC at the first time points of follow‑up with respect to T0; iii) a different trend of longitudinally DNA methylation variations in small groups of stratified patients. The absolute and precise quantification of SEPT9 and SHOX2 methylation levels in HNSCC may be useful for studies with translational potential.
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Affiliation(s)
- Ilaria Grossi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Claudia Assoni
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Luigi Lorini
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Smussi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cristina Gurizzan
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Salvatore Grisanti
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Alberto Paderno
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Mattavelli
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cesare Piazza
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Iulia Andreea Pelisenco
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Paolo Bossi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
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Büttner T, Dietrich D, Zarbl R, Klümper N, Ellinger J, Krausewitz P, Ritter M. Feasibility of Monitoring Response to Metastatic Prostate Cancer Treatment with a Methylation-Based Circulating Tumor DNA Approach. Cancers (Basel) 2024; 16:482. [PMID: 38339235 PMCID: PMC10854643 DOI: 10.3390/cancers16030482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Metastatic prostate cancer (mPCA) poses challenges in treatment response assessment, particularly in cases where prostate-specific antigen (PSA) levels do not reliably indicate a response. Liquid biopsy, focusing on circulating cell-free DNA (ccfDNA) methylation analysis as a proxy for circulating tumor DNA, offers a non-invasive and cost-effective approach. This study explores the potential of two methylation markers, short stature homeobox 2 (SHOX2) and Septin 9 (SEPT9), as on-mPCA-treatment biomarkers. METHODS Plasma samples were collected from 11 mPCA patients undergoing various treatments. Quantitative assessment of hypermethylated SHOX2 (mSHOX2) and SEPT9 (mSEPT9) levels in ccfDNA was conducted through methylation-specific real-time PCR. Early and overall dynamics of PSA, mSHOX2, and mSEPT9 were analyzed. Statistical evaluation employed Wilcoxon tests. RESULTS mSHOX2 demonstrated a significant decline post-treatment in patients with a radiographic treatment response as well as in an early treatment setting. mSEPT9 and PSA exhibited non-significant declines. In individual cases, biomarker dynamics revealed unique patterns compared to PSA. DISCUSSION mSHOX2 and mSEPT9 exhibit dynamics on mPCA treatment. This proof-of-concept study lays the groundwork for further investigation into these markers as valuable additions to treatment response monitoring in mPCA. Further validation in larger cohorts is essential for establishing clinical utility.
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Affiliation(s)
- Thomas Büttner
- Department of Urology and Pediatric Urology, Venusberg-Campus 1, University Hospital Bonn, 53127 Bonn, Germany; (N.K.); (J.E.); (P.K.); (M.R.)
| | - Dimo Dietrich
- Department of Otorhinolaryngology, University Hospital Bonn, 53127 Bonn, Germany; (D.D.); (R.Z.)
| | - Romina Zarbl
- Department of Otorhinolaryngology, University Hospital Bonn, 53127 Bonn, Germany; (D.D.); (R.Z.)
| | - Niklas Klümper
- Department of Urology and Pediatric Urology, Venusberg-Campus 1, University Hospital Bonn, 53127 Bonn, Germany; (N.K.); (J.E.); (P.K.); (M.R.)
| | - Jörg Ellinger
- Department of Urology and Pediatric Urology, Venusberg-Campus 1, University Hospital Bonn, 53127 Bonn, Germany; (N.K.); (J.E.); (P.K.); (M.R.)
| | - Philipp Krausewitz
- Department of Urology and Pediatric Urology, Venusberg-Campus 1, University Hospital Bonn, 53127 Bonn, Germany; (N.K.); (J.E.); (P.K.); (M.R.)
| | - Manuel Ritter
- Department of Urology and Pediatric Urology, Venusberg-Campus 1, University Hospital Bonn, 53127 Bonn, Germany; (N.K.); (J.E.); (P.K.); (M.R.)
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Yang W, Chen H, Ma L, Dong J, Wei M, Xue X, Li Y, Jin Z, Xu W, Ji Z. SHOX2 promotes prostate cancer proliferation and metastasis through disruption of the Hippo-YAP pathway. iScience 2023; 26:107617. [PMID: 37664594 PMCID: PMC10470409 DOI: 10.1016/j.isci.2023.107617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
The transcription factor SHOX2 gene is critical in regulating gene expression and the development of tumors, but its biological role in prostate cancer (PCa) remains unclear. In this study, we found that SHOX2 expression was significantly raised in PCa tissues and was associated with clinicopathological features as well as disease-free survival (DFS) of PCa patients. Phenotypic tests showed that the absence of SHOX2 inhibited PCa growth and invasion, while SHOX2 overexpression promoted these effects. Mechanistically, SHOX2 was found to activate the transcription of nephronophthisis type 4 (NPHP4), a gene located downstream of SHOX2. Further analysis revealed that SHOX2 could potentially interfere with the Hippo-YAP signaling pathway through NPHP4 activation, facilitating the oncogenic behavior of PCa cells. These findings highlight SHOX2 as an oncogene in PCa and provide a basis for developing potential therapeutic approaches against this disease.
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Affiliation(s)
- Wenjie Yang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Hualin Chen
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Lin Ma
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Jie Dong
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Mengchao Wei
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Xiaoqiang Xue
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Yingjie Li
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Zhaoheng Jin
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Weifeng Xu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing 100000, China
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