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Allan Z, Witts S, Tie J, Tebbutt N, Clemons NJ, Liu DS. The prognostic impact of peritoneal tumour DNA in gastrointestinal and gynaecological malignancies: a systematic review. Br J Cancer 2023; 129:1717-1726. [PMID: 37700064 PMCID: PMC10667497 DOI: 10.1038/s41416-023-02424-6] [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: 05/29/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Peritoneal metastases from various abdominal cancer types are common and carry poor prognosis. The presence of peritoneal disease upstages cancer diagnosis and alters disease trajectory and treatment pathway in many cancer types. Therefore, accurate and timely detection of peritoneal disease is crucial. The current practice of diagnostic laparoscopy and peritoneal lavage cytology (PLC) in detecting peritoneal disease has variable sensitivity. The significant proportion of peritoneal recurrence seen during follow-up in patients where initial PLC was negative indicates the ongoing need for a better diagnostic tool for detecting clinically occult peritoneal disease, especially peritoneal micro-metastases. Advancement in liquid biopsy has allowed the development and use of peritoneal tumour DNA (ptDNA) as a cancer-specific biomarker within the peritoneum, and the presence of ptDNA may be a surrogate marker for early peritoneal metastases. A growing body of literature on ptDNA in different cancer types portends promising results. Here, we conduct a systematic review to evaluate the prognostic impact of ptDNA in various cancer types and discuss its potential future clinical applications, with a focus on gastrointestinal and gynaecological malignancies.
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Affiliation(s)
- Zexi Allan
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia.
| | - Sasha Witts
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
| | - Jeanne Tie
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Niall Tebbutt
- Department of Surgery, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Department of Medical Oncology, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
| | - David S Liu
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Upper Gastrointestinal Surgery Unit, Division of Surgery, Anaesthesia, and Procedural Medicine, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
- General and Gastrointestinal Surgery Research and Trials Group, The University of Melbourne Department of Surgery, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
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Wątor G, Seweryn M, Kapusta P, Świrta J, Wałęga P, Barczyński M, Wołkow PP. Intratumor heterogeneity in colorectal cancer: Distribution of tumor suppressor gene variants with regard to patient lymph node status. Clin Genet 2023; 104:406-417. [PMID: 37339860 DOI: 10.1111/cge.14388] [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: 04/19/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/22/2023]
Abstract
Intratumor heterogeneity (ITH) results from accumulation of somatic mutations in the fractions of successive cancer cell generations. We aimed to use deep sequencing to investigate ITH in colorectal tumors with particular emphasis on variants in oncogenes (ONC) and tumor suppressor genes (TSG). Samples were collected from 16 patients with colorectal cancer and negative or positive lymph node status (n = 8 each). We deep-sequenced a panel of 56 cancer-related genes in the central and peripheral locations of T3 size primary tumors and healthy mucosa. The central region of T3 tumors has a different frequency profile and composition of genetic variants. This mutation profile is capable of independently discriminating patients with different lymph node status (p = 0.028) in the central region. We noted an increasing number of mutations outside of the central region of the tumor and a higher number of mutations in tumors from node-positive patients. Unexpectedly, in the healthy mucosa, we identified somatic mutations with variant allele frequencies, characteristic not only of heterozygotes and homozygotes but also of other discrete peaks (e.g., around 10%, 20%), suggestive of clonal expansion of certain mutant alleles. We found differences in the distribution of variant allele frequencies in TSGs when comparing node-negative and node-positive tumors (p = 0.029), as well as central and peripheral regions (p = 0.00399). TSGs may play an important role in the escape of the tumor toward metastatic colonization.
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Affiliation(s)
- Gracjan Wątor
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Seweryn
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
| | - Przemysław Kapusta
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
| | - Jarosław Świrta
- Department of Endocrine Surgery, Third Chair of General Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Piotr Wałęga
- Department of Endocrine Surgery, Third Chair of General Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Marcin Barczyński
- Department of Endocrine Surgery, Third Chair of General Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł P Wołkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
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Chang CM, Lin KC, Hsiao NE, Hong WA, Lin CY, Liu TC, Chang YS, Chang JG. Clinical application of liquid biopsy in cancer patients. BMC Cancer 2022; 22:413. [PMID: 35428225 PMCID: PMC9011972 DOI: 10.1186/s12885-022-09525-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/04/2022] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
This study was to determine the prevalence and clinical significance of clonal hematopoiesis (CH)-related variants, and somatic and germline mutations in cancer patients and healthy individuals.
Methods
We performed next-generation sequencing of 275 cancer-related genes be-tween plasma and white blood cells in 92 cancer patients and 47 controls without cancer. Blood samples were recruited from May 2017 to July 2021, and blood cancer patients were excluded. For all statistical analysis in this study, p < 0.05 was considered statistically significant.
Results
Overall, 38.04% of patients and 46.81% of controls harbored at least one CH-related mutation in plasma cell-free DNA. Based on our results, older cancer patients exhibited a CH phenomenon more frequently than younger patients (p = 0.0024). A total of 39 somatic pathogenic (P)/likely pathogenic (LP) mutations were identified in 17 genes in 21 of 92 patients. We found that the presence of P/LP variants in cancer-related gene predicted shorter overall survival (OS) (p = 0.001). Multivariate analysis adjusted for CH-related mutations, germline mutations, and tumor stage, also indicated that somatic mutations correlated significantly with OS (p = 0.022). Moreover, the frequency of a germline P/LP variant was that of seven of 92 individuals in the cancer group and one of 42 individuals in the control group.
Conclusions
We characterized the CH-related variants, and somatic and germline mutations in cancer patients and healthy individuals, and the results have important clinical significance.
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Abstract
Repeat surgical resection (redo) for pulmonary metastases is a questionable, albeit intriguing topic. We performed an extensive review of the literature, to specifically analyze results of redo pulmonary metastasectomies. We reviewed a total of 3,523 papers. Among these, 2,019 were excluded for redundancy and 1,105 because they were not completely retrievable. Out of 399 eligible papers, 183 had missing information or missing abstract, while 96 lacked data on survival. A total of 120 papers dated from 1991 onwards were finally included. Data regarding mortality, major morbidity, prognostic factors and long-term survivals of the first redo pulmonary metastasectomies were retrieved and analyzed. Homogeneity of data was affected by the lack of guidelines for redo pulmonary metastasectomy and the risks of bias when comparing different studies has to be considered. According to the histology sub-types, redo metastasectomies papers were grouped as: colorectal (n=42), sarcomas (n=36), others (n=20) and all histologies (n=22); the total number of patients was 3,015. Data about chemotherapy were reported in half of the papers, whereas targeted or immunotherapy in 9. None of these associated therapies, except chemotherapy in two records, did significantly modify outcomes. Disease-free interval before the redo procedure was the prevailing prognostic factor and nearly all papers showed a significant correlation between patients’ comorbidities and prognosis. No perioperative mortality was reported, while perioperative major morbidity was overall quite low. Where available, overall survival after the first redo metastasectomy ranged from 10 to 72 months, with a 5-years survival of approximately 50%. The site of first recurrence after the redo procedure was mainly lung. Despite the data retrievable from literature are heterogeneous and confounding, we can state that redo lung metastasectomy is worthwhile when the lesions are resectable and the perioperative risk is low. At present, there are no “non-surgical” therapeutic options to replace redo pulmonary metastasectomies.
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Affiliation(s)
- Vincenzo Ambrogi
- Thoracic Surgery Unit, Tor Vergata University Polyclinic, Rome, Italy
| | | | - Riccardo Tajé
- Tor Vergata University School of Medicine, Rome, Italy
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Kang J, Lee JH, Lee HS, Cho ES, Park EJ, Baik SH, Lee KY, Park C, Yeu Y, Clemenceau JR, Park S, Xu H, Hong C, Hwang TH. Radiomics Features of 18F-Fluorodeoxyglucose Positron-Emission Tomography as a Novel Prognostic Signature in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13030392. [PMID: 33494345 PMCID: PMC7866240 DOI: 10.3390/cancers13030392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 01/08/2023] Open
Abstract
The aim of this study was to investigate the prognostic value of radiomics signatures derived from 18F-fluorodeoxyglucose (18F-FDG) positron-emission tomography (PET) in patients with colorectal cancer (CRC). From April 2008 to Jan 2014, we identified CRC patients who underwent 18F-FDG-PET before starting any neoadjuvant treatments and surgery. Radiomics features were extracted from the primary lesions identified on 18F-FDG-PET. Patients were divided into a training and validation set by random sampling. A least absolute shrinkage and selection operator Cox regression model was applied for prognostic signature building with progression-free survival (PFS) using the training set. Using the calculated radiomics score, a nomogram was developed, and its clinical utility was assessed in the validation set. A total of 381 patients with surgically resected CRC patients (training set: 228 vs. validation set: 153) were included. In the training set, a radiomics signature labeled as a rad_score was generated using two PET-derived features, such as gray-level run length matrix long-run emphasis (GLRLM_LRE) and gray-level zone length matrix short-zone low-gray-level emphasis (GLZLM_SZLGE). Patients with a high rad_score in the training and validation set had a shorter PFS. Multivariable analysis revealed that the rad_score was an independent prognostic factor in both training and validation sets. A radiomics nomogram, developed using rad_score, nodal stage, and lymphovascular invasion, showed good performance in the calibration curve and comparable predictive power with the staging system in the validation set. Textural features derived from 18F-FDG-PET images may enable detailed stratification of prognosis in patients with CRC.
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Affiliation(s)
- Jeonghyun Kang
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (E.J.P.); (S.H.B.)
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
- Correspondence: (J.K.); (T.H.H.); Tel.: +82-2-2019-3372 (J.K.); +1-216-442-5565 (T.H.H.)
| | - Jae-Hoon Lee
- Department of Nuclear Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Hye Sun Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Eun-Suk Cho
- Department of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Eun Jung Park
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (E.J.P.); (S.H.B.)
| | - Seung Hyuk Baik
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea; (E.J.P.); (S.H.B.)
| | - Kang Young Lee
- Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Chihyun Park
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
- Department of Computer Science and Engineering, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
- Interdisciplinary Graduate Program in Medical Bigdata Convergence, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Yunku Yeu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
| | - Jean R. Clemenceau
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
| | - Sunho Park
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
| | - Hongming Xu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
| | - Changjin Hong
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
| | - Tae Hyun Hwang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.P.); (Y.Y.); (J.R.C.); (S.P.); (H.X.); (C.H.)
- Correspondence: (J.K.); (T.H.H.); Tel.: +82-2-2019-3372 (J.K.); +1-216-442-5565 (T.H.H.)
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Zheng Z, Yu T, Zhao X, Gao X, Zhao Y, Liu G. Intratumor heterogeneity: A new perspective on colorectal cancer research. Cancer Med 2020; 9:7637-7645. [PMID: 32853464 PMCID: PMC7571807 DOI: 10.1002/cam4.3323] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancers generally consist of multiple subclones. These subclones have their own unique characteristics, resulting in intratumor heterogeneity (ITH). As the discussion of ITH has advanced, a model describing the relationship of ITH to the tumor has gradually emerged. ITH can be divided into two types of intraprimary tumor heterogeneity and intraindividual tumor heterogeneity, the former for further understanding of tumor composition, and the latter for providing more information about evolutionary patterns. With the rapid development of new methods, such as next‐generation, polyguanine region sequencing, and Image detection, researchers may unravel the secrets underlying ITH. The higher the ITH of the tumor, the richer the interaction between the subclones maybe, or the greater the chance of the tumor getting more powerful subclones may be, thus increasing the malignant potential of the tumor. Existing evidence suggests that ITH may increase the ability of tumors to resist treatment and can be used as an independent influence on the prognosis of colorectal cancer. We reviewed 80 recent studies to give researchers a new perspective on colorectal cancer. There is still a limited amount of research in this area. Further study of the relationship between ITH and clinical endpoints may lead to the development of new treatment strategies.
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Affiliation(s)
- Zicheng Zheng
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Tao Yu
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xinyu Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Xin Gao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Yao Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Gang Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
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Chan HT, Nagayama S, Chin YM, Otaki M, Hayashi R, Kiyotani K, Fukunaga Y, Ueno M, Nakamura Y, Low S. Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy. Mol Oncol 2020; 14:1719-1730. [PMID: 32449983 PMCID: PMC7400786 DOI: 10.1002/1878-0261.12727] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
As the use of next-generation sequencing (NGS) for plasma cell-free DNA (cfDNA) continues to expand in clinical settings, accurate identification of circulating tumor DNA mutations is important to validate its use in the clinical management for cancer patients. Here, we aimed to characterize mutations including clonal hematopoiesis (CH)-related mutations in plasma cfDNA and tumor tissues using the same ultradeep NGS assay and evaluate the clinical significance of CH-related mutations on the interpretation of liquid biopsy results. Ultradeep targeted NGS using Oncomine Pan-Cancer Panel was performed on matched surgically resected tumor tissues, peripheral blood cells (PBCs), and 120 plasma cfDNA samples from 38 colorectal cancer patients. The clinical significance of the CH-related mutations in plasma cfDNA was evaluated by longitudinal monitoring of the postoperative plasma samples. Among the 38 patients, 74 nonsynonymous mutations were identified from tumor tissues and 64 mutations from the preoperative plasma samples. Eleven (17%) of the 64 mutations identified in plasma cfDNA were also detected in PBC DNA and were identified to be CH-related mutations. Overall, 11 of 38 (29%) patients in this cohort harbored at least one CH-related mutation in plasma cfDNA. These CH-related mutations were continuously detected in subsequent postoperative plasma samples from three patients which could be misinterpreted as the presence of residual disease or as lack of treatment response. Our results indicated that it is essential to integrate the mutational information of PBCs to differentiate tumor-derived from CH-related mutations in liquid biopsy analysis. This would prevent the misinterpretation of results to avoid misinformed clinical management for cancer patients.
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Affiliation(s)
- Hiu Ting Chan
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Satoshi Nagayama
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yoon Ming Chin
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Masumi Otaki
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Rie Hayashi
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Kazuma Kiyotani
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yosuke Fukunaga
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Masashi Ueno
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yusuke Nakamura
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Siew‐Kee Low
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
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Xu Y, Xu Q, Ma Y, Duan J, Zhang H, Liu T, Li L, Sun H, Shi K, Xie S, Wang W. Characterizing MRI features of rectal cancers with different KRAS status. BMC Cancer 2019; 19:1111. [PMID: 31727020 PMCID: PMC6857233 DOI: 10.1186/s12885-019-6341-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND To investigate whether MRI findings, including texture analysis, can differentiate KRAS mutation status in rectal cancer. METHODS Totally, 158 patients with pathologically proved rectal cancers and preoperative pelvic MRI examinations were enrolled. Patients were stratified into two groups: KRAS wild-type group (KRASwt group) and KRAS mutation group (KRASmt group) according to genomic DNA extraction analysis. MRI findings of rectal cancers (including texture features) and relevant clinical characteristics were statistically evaluated to identify the differences between the two groups. The independent samples t test or Mann-Whitney U test were used for continuous variables. The differences of the remaining categorical polytomous variables were analyzed using the Chi-square test or Fisher exact test. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the discriminatory power of MRI features. The area under the ROC curve (AUC) and the optimal cut-off values were calculated using histopathology diagnosis as a reference; meanwhile, sensitivity and specificity were determined. RESULTS Mean values of six texture parameters (Mean, Variance, Skewness, Entropy, gray-level nonuniformity, run-length nonuniformity) were significantly higher in KRASmt group compared to KRASwt group (p < 0.0001, respectively). The AUC values of texture features ranged from 0.703~0.813. In addition, higher T stage and lower ADC values were observed in the KRASmt group compared to KRASwt group (t = 7.086, p = 0.029; t = - 2.708, p = 0.008). CONCLUSION The MRI findings of rectal cancer, especially texture features, showed an encouraging value for identifying KRAS status.
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Affiliation(s)
- Yanyan Xu
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Qiaoyu Xu
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yanhui Ma
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Jianghui Duan
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Haibo Zhang
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Tongxi Liu
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Lu Li
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Hongliang Sun
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Kaining Shi
- Philips Healthcare, Beijing, 100001, People's Republic of China
| | - Sheng Xie
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Wu Wang
- Department of Radiology, China-Japan Friendship Hospital, No.2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
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Targeted mutational analysis of inflammatory bowel disease-associated colorectal cancers. Hum Pathol 2019; 89:44-50. [PMID: 31054900 DOI: 10.1016/j.humpath.2019.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/28/2022]
Abstract
Inflammatory bowel disease-associated colorectal carcinomas (IBD-CRCs) develop in a background of chronic inflammation, and thus, the molecular landscape of these tumors likely differs from that of sporadic colorectal cancer. To add to emerging data on molecular alterations present in these tumors, we analyzed our institution's cohort of IBD-CRCs. CRCs resected from patients with IBD underwent molecular analysis via a 50-gene hot-spot solid tumor panel (OncoScreen ST2.0). In-house sporadic CRCs and The Cancer Genome Atlas project data were used for comparison. Fifty-five IBD-CRCs from 48 patients were successfully analyzed. Mutations in TP53 were most common and were present in 69% of IBD-CRCs; a similar percentage of TP53 mutations was detected in sporadic colorectal carcinomas (70%). APC and KRAS mutations were significantly less common in IBD-CRCs than in sporadic CRCs (15% versus 53%, P < .001 and 20% versus 38%, P = .02, respectively). Additionally, the potentially targetable IDH1 R132 mutation was present in 7% of IBD-CRCs but only 1% of sporadic CRCs and The Cancer Genome Atlas CRCs; alterations in other genes with potential targeted therapies were very rare. In conclusion, IBD-CRCs exhibit molecular differences when compared to sporadic CRCs, suggesting different pathways of carcinogenesis, although certain alterations are common to both types of tumors. IDH1 mutations are present in a subset of IBD-CRCs, which may expand therapeutic options in the future.
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10
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Targeted next-generation sequencing of endometrial cancer and matched circulating tumor DNA: identification of plasma-based, tumor-associated mutations in early stage patients. Mod Pathol 2019; 32:405-414. [PMID: 30315273 PMCID: PMC6395490 DOI: 10.1038/s41379-018-0158-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/01/2018] [Accepted: 09/01/2018] [Indexed: 01/03/2023]
Abstract
There is currently no blood-based marker in routine use for endometrial cancer patients. Such a marker could potentially be used for early detection, but it could also help to track tumor recurrence following hysterectomy. This is important, as extra-vaginal recurrence of endometrial endometrioid adenocarcinoma is usually incurable. This proof-of-principle study was designed to determine if tumor-associated mutations could be detected in cell-free DNA from the peripheral blood of early and late stage endometrial endometrioid carcinoma patients. Approximately 90% of endometrioid carcinomas have at least one mutation in the genes CTNNB1, KRAS, PTEN, or PIK3CA. Using a custom panel targeting 30 hotspot amplicons in these four genes, next-generation sequencing was performed on cell-free DNA extracted from plasma obtained from a peripheral blood draw at the time of hysterectomy and the matching tumor DNA from 48 patients with endometrioid endometrial carcinomas. At least one mutation in the tumor was detected in 45/48 (94%) of patients. Fifteen of 45 patients (33%) had a mutation in the plasma that matched a mutation in the tumor. These same mutations were not detected in the matched negative control buffy coat. Presence of a plasma mutation was significantly associated with advanced stage at hysterectomy, deep myometrial invasion, lymphatic/vascular invasion, and primary tumor size. Detecting a plasma-based mutation was independent of the amount of cell-free DNA isolated from the plasma. Overall, 18% of early stage patients had a mutation detected in the plasma. These results demonstrate that mutations in genes relevant to endometrial cancer can be identified in the peripheral blood of patients at the time of surgery. Future studies can help to determine the post-operative time course of mutation clearance from the peripheral blood and if mutation re-emergence is predictive of recurrence.
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Molinari C, Marisi G, Passardi A, Matteucci L, De Maio G, Ulivi P. Heterogeneity in Colorectal Cancer: A Challenge for Personalized Medicine? Int J Mol Sci 2018; 19:E3733. [PMID: 30477151 PMCID: PMC6321493 DOI: 10.3390/ijms19123733] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
High inter-patient variability and high spatial heterogeneity are features of colorectal cancer (CRC). This may influence the molecular characterization of tumor tissue, now mandatory for patients with metastatic CRC who are candidates for treatment with an anti-EGFR mAb, as false-negative results can occur, leading to non optimal therapy. Moreover, temporal molecular heterogeneity during treatment is known to influence the response to therapy and prognosis. We present a literature overview of advances made in characterizing molecular heterogeneity in CRC, underlining that the analysis of liquid biopsy could represent an efficient non-invasive tool to overcome the problem. We believe that understanding CRC heterogeneity is fundamental for a more accurate diagnosis, for selecting the best targets to ensure prolonged antitumor response, and for monitoring minimal residual disease and the onset of resistance to therapy, all essential components of successful personalized treatment.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Alessandro Passardi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Laura Matteucci
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Giulia De Maio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
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Henzler C, Schomaker M, Yang R, Lambert AP, LaRue R, Kincaid R, Beckman K, Kemmer T, Wilson J, Yohe S, Thyagarajan B, Nelson AC. Optimization of a microfluidics-based next generation sequencing assay for clinical oncology diagnostics. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:162. [PMID: 29911110 DOI: 10.21037/atm.2018.05.07] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Massively parallel, or next-generation, sequencing is a powerful technique for the assessment of somatic genomic alterations in cancer samples. Numerous gene targets can be interrogated simultaneously with a high degree of sensitivity. The clinical standard of care for many advanced solid and hematologic malignancies currently requires mutation analysis of several genes in the front-line setting, making focused next generation sequencing (NGS) assays an effective tool for clinical molecular diagnostic laboratories. Methods We have utilized an integrated microfluidics circuit (IFC) technology for multiplex PCR-based library preparation coupled with a bioinformatic method designed to enhance indel detection. A parallel low input PCR-based library preparation method was developed for challenging specimens with low DNA yield. Computational data filters were written to optimize analytic sensitivity and specificity for clinically relevant variants. Results Minimum sequencing coverage and precision of variant calls were the two primary criteria used to establish minimum DNA mass input onto the IFC. Wet-bench and bioinformatics protocols were modified based on data from the optimization and familiarization process to improve assay performance. The NGS platform was then clinically validated for single nucleotide and indel (up to 93 base pair) variant detection with overall analytic accuracy of 98% (97% sensitivity; 100% specificity) using as little as 3 ng of formalin-fixed, paraffin-embedded DNA or 0.3 ng of unfixed DNA. Conclusions We created a targeted clinical NGS assay for common solid and hematologic cancers with high sensitivity, high specificity, and the flexibility to test very limited tissue samples often encountered in routine clinical practice.
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Affiliation(s)
- Christine Henzler
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.,Research Informatics Solutions, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Matthew Schomaker
- M Health University of Minnesota Medical Center-Fairview, Minneapolis, MN, USA
| | - Rendong Yang
- Research Informatics Solutions, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.,The Hormel Institute, Austin, MN, USA
| | - Aaron P Lambert
- M Health University of Minnesota Medical Center-Fairview, Minneapolis, MN, USA
| | - Rebecca LaRue
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.,Research Informatics Solutions, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Robyn Kincaid
- M Health University of Minnesota Medical Center-Fairview, Minneapolis, MN, USA
| | - Kenneth Beckman
- University of Minnesota Genomics Center, Minneapolis, MN, USA
| | - Teresa Kemmer
- M Health University of Minnesota Medical Center-Fairview, Minneapolis, MN, USA
| | - Jon Wilson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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