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Chen RH, Cao JY, Feng S, Huang HT, Lin YM, Jiang JY, Yi XW, Ling Q. Integrated chromosomal instability and tumor microbiome redefined prognosis-related subtypes of pancreatic cancer. Hepatobiliary Pancreat Dis Int 2024:S1499-3872(24)00041-9. [PMID: 38556382 DOI: 10.1016/j.hbpd.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Pancreatic cancer is a common malignancy with poor prognosis and limited treatment. Here we aimed to investigate the role of host chromosomal instability (CIN) and tumor microbiome in the prognosis of pancreatic cancer patients. METHODS One hundred formalin-fixed paraffin-embedded (FFPE) pancreatic cancer samples were collected. DNA extracted from FFPE samples were analyzed by low-coverage whole-genome sequencing (WGS) via a customized bioinformatics workflow named ultrasensitive chromosomal aneuploidy detector. RESULTS Samples are tested according to the procedure of ultrasensitive chromosomal aneuploidy detector (UCAD). We excluded 2 samples with failed quality control, 1 patient lost to follow-up and 6 dead in the perioperative period. The final 91 patients were admitted for the following analyses. Thirteen (14.3%) patients with higher CIN score had worse overall survival (OS) than those with lower CIN score. The top 20 microbes in pancreatic cancer samples included 15 species of bacteria and 5 species of viruses. Patients with high human herpesvirus (HHV)-7 and HHV-5 DNA reads exhibited worse OS. Furthermore, we classified 91 patients into 3 subtypes. Patients with higher CIN score (n =13) had the worst prognosis (median OS 6.9 mon); patients with lower CIN score but with HHV-7/5 DNA load (n = 24) had worse prognosis (median OS 10.6 mon); while patients with lower CIN score and HHV-7/5 DNA negative (n = 54) had the best prognosis (median OS 21.1 mon). CONCLUSIONS High CIN and HHV-7/5 DNA load were associated with worse survival of pancreatic cancer. The novel molecular subtypes of pancreatic cancer based on CIN and microbiome had prognostic value.
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Affiliation(s)
- Rui-Han Chen
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Jia-Ying Cao
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Shi Feng
- Department of Pathology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hai-Tao Huang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China; Department of Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yi-Mou Lin
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Jing-Yu Jiang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Xue-Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China
| | - Qi Ling
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou 310003, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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Xia X, Zhao S, Song X, Zhang M, Zhu X, Li C, Chen W, Zhao D. The potential use and experimental validation of genomic instability-related lncRNA in pancreatic carcinoma. Medicine (Baltimore) 2023; 102:e35300. [PMID: 37713870 PMCID: PMC10508516 DOI: 10.1097/md.0000000000035300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
This study explored the potential role of long noncoding RNA (lncRNAs) associated with genomic instability in the diagnosis and treatment of pancreatic adenocarcinoma (PAAD). Transcriptome and single-nucleotide variation data of PAAD samples were downloaded from the cancer genome atlas database to explore genomic instability-associated lncRNAs. We constructed a genomic instability-associated lncRNA prognostic signature. Then gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses were used to explore the physiological role of lncRNAs involved in genomic instability. Tumor microenvironments, immunotherapy response, immune cell infiltration, immune checkpoint, and drug sensitivity were compared between high-risk and low-risk groups. In vitro experiments were performed for external validation. Six lncRNAs associated with genomic instability were identified, capable of predicting the prognosis of PAAD. Patients were assigned to low-risk or high-risk groups using these biomarkers, with better or worse prognosis, respectively. The tumor immune score, immune cell infiltration, and efficacy of immunotherapy were worse in the high-risk group. A drug sensitivity analysis revealed the high- and low-risk groups had different half-maximal inhibitory concentrations. The expression of cancer susceptibility candidate 8 was significantly higher in tumor tissues than in normal tissues, while the expression of LYPLAL1-AS1 exhibited an opposite pattern. They may be potential diagnostic or prognostic biomarkers for patients with pancreatic cancer. Genomic instability-associated lncRNAs were explored in this study and predicted the prognosis of PAAD and stratified patients risk in PAAD. These lncRNAs also predicted the efficacy of immunotherapy and potential therapeutic targets in PAAD.
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Affiliation(s)
- Xiuli Xia
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Gastroenterology, Handan Central Hospital, Handan, China
| | - Shushan Zhao
- Department of Gastroenterology, Handan Central Hospital, Handan, China
| | - Xiaoming Song
- Department of Gastroenterology, Handan Central Hospital, Handan, China
| | - Mengyue Zhang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xinying Zhu
- Department of Gastroenterology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Changjuan Li
- Department of Gastroenterology, The First Hospital of Handan, Handan, China
| | - Wenting Chen
- Digestive Endoscopy Center, The First Affiliated Hospital of Hebei North. University, Zhangjiakou, China
| | - Dongqiang Zhao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Kim DY, Cho EH, Kim JS, Chie EK, Kang HC. Plasma Circulating Cell-free DNA in Advanced Hepatocellular Carcinoma Patients Treated With Radiation Therapy. In Vivo 2023; 37:2306-2313. [PMID: 37652507 PMCID: PMC10500495 DOI: 10.21873/invivo.13333] [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: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND/AIM Although radiation therapy (RT) is an effective and safe treatment when administered locally for various stages of hepatocellular carcinoma (HCC), adequate biomarkers that are predictive of therapeutic efficacy have not been identified. We evaluated the clinical utility of circulating cell-free DNA (cfDNA) to predict treatment response of patients with HCC treated with RT. PATIENTS AND METHODS We prospectively recruited 37 patients diagnosed with HCC between March 2019 and May 2020. All patients were treated with RT as salvage therapy. Whole peripheral blood was collected twice, one before RT (baseline; V1) and another aliquot one week after the end of RT (V2). We determined whether cfDNA genomic copy number variations (CNVs) could predict treatment outcome. An I-score was calculated from the plasma cfDNA that reflected CNVs of cfDNA, which is evidence of genomic instability. RESULTS The I-score at V1 exhibited a strong correlation with the planning target volume (PTV) (coefficient=0.65) and was a predictive marker for progression-free survival (PFS). In particular, a mean I-score value at V1 of ≥6.3 had a significant positive correlation with PFS (p=0.017). Compared with patients who had a complete response (CR) following RT, non-CR patients had a higher mean I-score value at V2 ≥6.2 (p=0.034). Furthermore, I-score values at V1 and V2 and the delta I-score ratio were significantly associated with a pre-RT alpha-fetoprotein level ≥200 among non-CR patients. CONCLUSION I-score values calculated from plasma cfDNA represent a potential biomarker for predicting treatment outcomes in patients with advanced HCC receiving RT.
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Affiliation(s)
- Dong-Yun Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Radiation Oncology, Chung-Ang University Hospital, Seoul, Republic of Korea
| | - Eun-Hae Cho
- Genome Research Center, GC Genome, Yongin-si, Republic of Korea
| | - Jae Sik Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Radiation Oncology, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyun-Cheol Kang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea;
- Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea
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Zhang X, Lam TW, Ting HF. Genome instability-derived genes as a novel prognostic signature for lung adenocarcinoma. Front Cell Dev Biol 2023; 11:1224069. [PMID: 37655157 PMCID: PMC10467266 DOI: 10.3389/fcell.2023.1224069] [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: 05/17/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Background: An increasing number of patients are being diagnosed with lung adenocarcinoma, but there remains limited progress in enhancing prognostic outcomes and improving survival rates for these patients. Genome instability is considered a contributing factor, as it enables other hallmarks of cancer to acquire functional capabilities, thus allowing cancer cells to survive, proliferate, and disseminate. Despite the importance of genome instability in cancer development, few studies have explored the prognostic signature associated with genome instability for lung adenocarcinoma. Methods: In the study, we randomly divided 397 lung adenocarcinoma patients from The Cancer Genome Atlas database into a training group (n = 199) and a testing group (n = 198). By calculating the cumulative counts of genomic alterations for each patient in the training group, we distinguished the top 25% and bottom 25% of patients. We then compared their gene expressions to identify genome instability-related genes. Next, we used univariate and multivariate Cox regression analyses to identify the prognostic signature. We also performed the Kaplan-Meier survival analysis and the log-rank test to evaluate the performance of the identified prognostic signature. The performance of the signature was further validated in the testing group, in The Cancer Genome Atlas dataset, and in external datasets. We also conducted a time-dependent receiver operating characteristic analysis to compare our signature with established prognostic signatures to demonstrate its potential clinical value. Results: We identified GULPsig, which includes IGF2BP1, IGF2BP3, SMC1B, CLDN6, and LY6K, as a prognostic signature for lung adenocarcinoma patients from 42 genome instability-related genes. Based on the risk score of the risk model with GULPsig, we successfully stratified the patients into high- and low-risk groups according to the results of the Kaplan-Meier survival analysis and the log-rank test. We further validated the performance of GULPsig as an independent prognostic signature and observed that it outperformed established prognostic signatures. Conclusion: We provided new insights to explore the clinical application of genome instability and identified GULPsig as a potential prognostic signature for lung adenocarcinoma patients.
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Affiliation(s)
| | | | - Hing-Fung Ting
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Cheng H, Yang J, Fu X, Mao L, Chu X, Lu C, Li G, Qiu Y, He W. Folate receptor-positive circulating tumor cells predict survival and recurrence patterns in patients undergoing resection for pancreatic cancer. Front Oncol 2022; 12:1012609. [PMID: 36313690 PMCID: PMC9606765 DOI: 10.3389/fonc.2022.1012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To evaluate the prognostic impact of folate receptor (FR)-positive circulating tumor cells (FR+ CTCs) for patients with pancreatic cancer (PC). Background Risk stratification before surgery for PC patients remains challenging as there are no reliable prognostic markers currently. FR+ CTCs, detected by ligand-targeted polymerase chain reaction (LT-PCR), have shown excellent diagnostic value for PC in our previous study and prognostic value in a variety of cancer types. Methods Peripheral blood samples from 44 consecutive patients diagnosed with PC were analyzed for FR+ CTCs. 25 patients underwent tumor resection and were assigned to the surgical group. 19 patients failed to undergo radical resection because of local advance or distant metastasis and were assigned to the non-surgical group. The impact of CTCs on relapse and survival were explored. Results For the prognostic stratification, the optimal cut-off value of CTCs analyzed by receiver operating characteristic (ROC) curve was 14.49 folate units (FU)/3 ml. High CTC levels (> 14.49 FU/3 ml) were detected in 52.0% (13/25) of the patients in the surgical group and 63.2% (12/19) in the non-surgical group. In the surgical group, median disease-free survival (DFS) for patients with high CTC levels versus low CTC levels (< 14.49 FU/3 ml) was 8.0 versus 26.0 months (P = 0.008). In multivariable analysis, CTCs were an independent risk factor for DFS (HR: 4.589, P = 0.012). Concerning the recurrence patterns, patients with high CTC levels showed a significantly frequent rate of distant and early recurrence (P = 0.017 and P = 0.011). CTC levels remained an independent predictor for both distant (OR: 8.375, P = 0.014) and early recurrence (OR: 8.412, P = 0.013) confirmed by multivariable logistic regression. However, CTCs did not predict survival in the non-surgical group (P = 0.220). Conclusion FR+ CTCs in resected PC patients could predict impaired survival and recurrence patterns after surgery. Preoperative CTC levels detected by LT-PCR may help guide treatment strategies and further studies in a larger cohort are warranted.
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Affiliation(s)
- Hao Cheng
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jun Yang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xu Fu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Liang Mao
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xuehui Chu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Chenglin Lu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Gang Li
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yudong Qiu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Yudong Qiu, ; Wei He,
| | - Wei He
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Yudong Qiu, ; Wei He,
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A Genomic Instability-Related Long Noncoding RNA Signature for Predicting Hepatocellular Carcinoma Prognosis. JOURNAL OF ONCOLOGY 2022; 2022:3090523. [PMID: 36072979 PMCID: PMC9444385 DOI: 10.1155/2022/3090523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/02/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Background. Long noncoding RNAs (lncRNAs) are found to be novel biomarkers for hepatocellular carcinoma (HCC) and play an important role in tumor progression. We established a genomic instability-related long noncoding RNA signature (GIlncSig) as an independent prognosis factor and also investigated its impact on prognosis significance. Method. Somatic mutation profiles, clinical characteristics, and RNA sequencing data were obtained from The Cancer Genome Atlas (TCGA) database. Lasso regression was used to construct GIlncSig. KEGG was used to identify the possible biological pathways. ESTIMATE and CIBERSORT algorithms were used to calculate the immune microenvironment scores and proportion of immune cells in HCC patients. The expression of LINC00501 was conducted by qRT-PCR. Cell proliferation was measured by EdU, CCK-8, and colony formation assay, and cell migration and invasion ability were measured by wound healing and transwell assay. Results. 135 genomic instability-related lncRNAs were identified, and GIlncSig was constructed using 13 independent lncRNAs with significant prognosis values. Based on the GIlncSig, high-risk group had worse clinical outcomes than low-risk group, while high-risk group also had higher UBQLN4, KRAS, ARID1A, and PIK3CA expression. Moreover, the efficiency of GIlncSig combining single-gene mutation was higher than single-gene mutation alone such as TP53. The results of CIBERSORT and ESTIMATE showed that GS group and GU group had significantly different immune infiltration. In addition, LINC00501 was identified as a potential biomarker in HCC with strong relationship with clinical characteristics. In vitro assays validated that LINC00501 promoted proliferation and migration of HCC cell lines. Conclusion. Our results showed that GIlncSig serves as a potential independent prognosis factor to predict HCC patients’ prognosis for exploring potential mechanism and therapy strategy. Besides, LINC00501 plays an important role in the progression of HCC, which may be a potential therapy target.
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