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Zhao X, Jin S, Peng M, Wang J. A retrospective study on the efficacy of the ERAS protocol in patients who underwent laparoscopic left and right colectomy surgeries. Front Surg 2024; 11:1395271. [PMID: 38983588 PMCID: PMC11231639 DOI: 10.3389/fsurg.2024.1395271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/25/2024] [Indexed: 07/11/2024] Open
Abstract
Objective Retrospective analysis and comparison of the effects of Enhanced Recovery After Surgery (ERAS) protocol for patients having left and right colectomy surgeries. Method Out of the patients admitted to Chengdu Shang Jin Nan Fu Hospital and West China Hospital from December 2019 to December 2022, a total of 498 who met the inclusion criteria were selected, 255 with right colectomy(RC) and 243 with left colectomy (LC). Under the conditions of strict compliance with ERAS protocol, the relevant physical indexes of RC and LC, including postoperative rehabilitation (especially median post-operative stay) and complications (especially prolonged postoperative ileus, PPOI), were statistically analyzed and compared. Results In terms of intraoperative variables, fluid doses were higher in the LC group than in the RC group (P < 0.05), and there was no significant difference between them in terms of operative time, blood loss, need for open surgery, peritoneal contamination, epidural catheter placement, or opioid use (P > 0.05). Compared with the RC group, the LC group had a higher intake of oral liquid at the second postoperative day (POD), and faster first flatulence (P < 0.05). 30 (11.76%) RC patients required nasogastric tube insertion, while only 3 (1.23%) patients in the LC group required the same (P < 0.05). Prolonged postoperative ileus (PPOI) occurred in 48 (18.82%) and 29 (11.93%) patients in the RC and LC groups, respectively (P < 0.05). No significant differences in terms of postoperative complications or length of hospital stay (LoS). stay were observed. Conclusion As the location of colon cancer changes, the effectiveness of ERAS also varies. More personalized and precise ERAS protocols can reduce the incidence of postoperative complications and promote rapid recovery after surgery.
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Affiliation(s)
- Xuemei Zhao
- Outpatient Department, Chengdu Shang Jin Nan Fu Hospital/Shang Jin Hospital of West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Siyu Jin
- Outpatient Department, Chengdu Shang Jin Nan Fu Hospital/Shang Jin Hospital of West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingxiu Peng
- Outpatient Department, Chengdu Shang Jin Nan Fu Hospital/Shang Jin Hospital of West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingjing Wang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Kun W, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype. Cancer Res 2024; 84:1719-1732. [PMID: 38451249 PMCID: PMC11096054 DOI: 10.1158/0008-5472.can-23-4070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling. SIGNIFICANCE The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.
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Affiliation(s)
- Vahid Bahrambeigi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaewon J. Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Vittorio Branchi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimal I. Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naishu Kui
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T. Henry
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wang Kun
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bret M. Stephens
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Dhebat
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark W. Hurd
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Yang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Statistics Rice University, Houston, TX, USA
| | - Eytan Ruppin
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wenyi Wang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola A. Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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3
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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4
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Xu SM, Cheng Y, Fisher H, Janitz M. Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer. Int J Biochem Cell Biol 2024; 168:106529. [PMID: 38246262 DOI: 10.1016/j.biocel.2024.106529] [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: 09/23/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Gene fusions have had a significant role in the development of various types of cancer, oftentimes involved in oncogenic activities through dysregulation of gene expression or signalling pathways. Some cancer-associated chromosomal translocations can undergo backsplicing, resulting in fusion-circular RNAs, a more stable isoform immune to RNase degradation. This stability makes fusion circular RNAs a promising diagnostic biomarker for cancer. While the detection of linear fusion RNAs and their function in certain cancers have been described in literature, fusion circular RNAs lag behind due to their low abundance in cancer cells. This review highlights current literature on the role of linear and circular fusion transcripts in cancer, tools currently available for detecting of these chimeric RNAs and their function and how they play a role in tumorigenesis.
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Affiliation(s)
- Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Harry Fisher
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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5
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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6
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Baranov E, Nowak JA. Pathologic Evaluation of Therapeutic Biomarkers in Colorectal Adenocarcinoma. Surg Pathol Clin 2023; 16:635-650. [PMID: 37863556 DOI: 10.1016/j.path.2023.05.002] [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] [Indexed: 10/22/2023]
Abstract
Molecular testing is an essential component of the pathologic evaluation of colorectal carcinoma providing diagnostic, prognostic, and predictive therapeutic information. Mismatch repair status evaluation is required for all tumors. Advanced and metastatic tumors also require determination of tumor mutational burden, KRAS, NRAS, and BRAF mutation status, ERBB2 amplification status, and NTRK and RET gene rearrangement status to guide therapy. Multiple assays, including immunohistochemistry, microsatellite instability testing, MLH1 promoter methylation, and next-generation sequencing, are typically needed. Pathologists must be aware of these requirements to optimally triage tissue. Advances in colorectal cancer molecular diagnostics will continue to drive refinements in colorectal cancer personalized therapy.
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Affiliation(s)
- Esther Baranov
- Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Jonathan A Nowak
- Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
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7
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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8
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Nanishi K, Hino H, Hatakeyama K, Shiomi A, Kagawa H, Manabe S, Yamaoka Y, Nagashima T, Ohshima K, Urakami K, Akiyama Y, Yamaguchi K. Incidence and clinical significance of 491 known fusion genes in a large cohort of Japanese patients with colorectal cancer. Int J Clin Oncol 2023; 28:785-793. [PMID: 37022622 DOI: 10.1007/s10147-023-02335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND The clinical significance of fusion genes in colorectal cancer remains unclear. The purpose of this study was to determine the incidence of fusion genes in colorectal cancer and explore their clinical significance by screening for common fusion genes in a large Japanese cohort. METHODS This study involved 1588 patients. The incidence of 491 fusion genes was examined using a designed fusion panel. In addition, the patients were classified into two groups (RSPO fusion-positive or -negative) according to the presence of RSPO fusions, and the clinicopathological and genetic characteristics of both groups were compared. Long-term outcomes were analyzed in patients without distant metastases. RESULTS Fusion genes were detected in 2% (31/1588) of colorectal cancers. The incidence of RSPO fusions (such as PTPRK-RSPO3 and EIF3E-RSPO2) was 1.5% (24/1588), making them the most common fusions, whereas the incidence of other fusion genes was extremely low. The distribution of consensus molecular subtypes and frequency of APC mutations were significantly different between the RSPO fusion-positive and -negative groups. The 3-year cumulative incidence rate of recurrence was higher in the RSPO fusion-positive group than in the RSPO fusion-negative group (positive, 31.2% vs. negative, 13.5%, hazard ratio = 2.357; p = 0.040). CONCLUSION Broad screening for fusion genes showed that RSPO fusions were the most common in colorectal cancer, with an incidence of 1.5%. RSPO fusions may be clinically significant in identifying patients at a high risk of recurrence who would be responsive to specific treatments.
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Affiliation(s)
- Kenji Nanishi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Hitoshi Hino
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan.
| | - Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Shoichi Manabe
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Yusuke Yamaoka
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka Prefecture, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- SRL Inc., Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
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Differential Diagnosis of Hematologic and Solid Tumors Using Targeted Transcriptome and Artificial Intelligence. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:51-59. [PMID: 36243045 DOI: 10.1016/j.ajpath.2022.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/14/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
Diagnosis and classification of tumors is increasingly dependent on biomarkers. RNA expression profiling using next-generation sequencing provides reliable and reproducible information on the biology of cancer. This study investigated targeted transcriptome and artificial intelligence for differential diagnosis of hematologic and solid tumors. RNA samples from hematologic neoplasms (N = 2606), solid tumors (N = 2038), normal bone marrow (N = 782), and lymph node control (N = 24) were sequenced using next-generation sequencing using a targeted 1408-gene panel. Twenty subtypes of hematologic neoplasms and 24 subtypes of solid tumors were identified. Machine learning was used for diagnosis between two classes. Geometric mean naïve Bayesian classifier was used for differential diagnosis across 45 diagnostic entities with assigned rankings. Machine learning showed high accuracy in distinguishing between two diagnoses, with area under the curve varying between 1 and 0.841. Geometric mean naïve Bayesian algorithm was trained using 3045 samples and tested on 1415 samples, and showed correct first-choice diagnosis in 100%, 88%, 85%, 82%, 88%, 72%, and 72% of acute lymphoblastic leukemia, acute myeloid leukemia, diffuse large B-cell lymphoma, colorectal cancer, lung cancer, chronic lymphocytic leukemia, and follicular lymphoma cases, respectively. The data indicate that targeted transcriptome combined with artificial intelligence are highly useful for diagnosis and classification of various cancers. Mutation profiles and clinical information can improve these algorithms and minimize errors in diagnoses.
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10
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Neuroendocrine neoplasms of the lung and gastrointestinal system: convergent biology and a path to better therapies. Nat Rev Clin Oncol 2023; 20:16-32. [PMID: 36307533 DOI: 10.1038/s41571-022-00696-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/08/2022]
Abstract
Neuroendocrine neoplasms (NENs) can develop in almost any organ and span a spectrum from well-differentiated and indolent neuroendocrine tumours (NETs) to poorly differentiated and highly aggressive neuroendocrine carcinomas (NECs), including small-cell lung cancer (SCLC). These neoplasms are thought to primarily derive from neuroendocrine precursor cells located throughout the body and can also arise through neuroendocrine transdifferentiation of organ-specific epithelial cell types. Hence, NENs constitute a group of tumour types that share key genomic and phenotypic characteristics irrespective of their site of origin, albeit with some organ-specific differences. The establishment of representative preclinical models for several of these disease entities together with analyses of human tumour specimens has provided important insights into crucial aspects of their biology with therapeutic implications. In this Review, we provide a comprehensive overview of the current understanding of NENs of the gastrointestinal system and lung from clinical and biological perspectives. Research on NENs has typically been siloed by the tumour site of origin, and a cross-cutting view might enable advances in one area to accelerate research in others. Therefore, we aim to emphasize that a better understanding of the commonalities and differences of NENs arising in different organs might more effectively inform clinical research to define therapeutic targets and ultimately optimize patient care.
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11
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Akhoundova D, Hussung S, Sivakumar S, Töpfer A, Rechsteiner M, Kahraman A, Arnold F, Angst F, Britschgi C, Zoche M, Moch H, Weber A, Sokol E, Fritsch RM. ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer. Int J Cancer 2022; 151:2161-2171. [PMID: 36053834 PMCID: PMC9804412 DOI: 10.1002/ijc.34257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 01/05/2023]
Abstract
c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials.
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Affiliation(s)
- Dilara Akhoundova
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Saskia Hussung
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Smruthy Sivakumar
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Antonia Töpfer
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Fabian Arnold
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Florian Angst
- Institute of Diagnostic and Interventional RadiologyUniversity Hospital of ZurichZurichSwitzerland
| | - Christian Britschgi
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Martin Zoche
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Holger Moch
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Achim Weber
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Ethan Sokol
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Ralph M. Fritsch
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
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12
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Hashimoto T, Takayanagi D, Yonemaru J, Naka T, Nagashima K, Yatabe Y, Shida D, Hamamoto R, Kleeman SO, Leedham SJ, Maughan T, Takashima A, Shiraishi K, Sekine S. Clinicopathological and molecular characteristics of RSPO fusion-positive colorectal cancer. Br J Cancer 2022; 127:1043-1050. [PMID: 35715628 PMCID: PMC9470590 DOI: 10.1038/s41416-022-01880-w] [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: 10/21/2021] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND RSPO fusions that lead to WNT pathway activation are potential therapeutic targets in colorectal cancer (CRC), but their clinicopathological significance remains unclear. METHODS We screened 1019 CRCs for RSPO fusions using multiplex reverse transcription-PCR. The RSPO fusion-positive tumours were subjected to whole-exome sequencing (WES). RESULTS Our analysis identified 29 CRCs with RSPO fusions (2.8%), consisting of five with an EIF3E-RSPO2 fusion and 24 with PTPRK-RSPO3 fusions. The patients were 17 women and 12 men. Thirteen tumours (45%) were right-sided. Histologically, approximately half of the tumours (13/29, 45%) had a focal or extensive mucinous component that was significantly more frequent than the RSPO fusion-negative tumours (13%; P = 8.1 × 10-7). Four tumours (14%) were mismatch repair-deficient. WES identified KRAS, BRAF, and NRAS mutations in a total of 27 tumours (93%). In contrast, pathogenic mutations in major WNT pathway genes, such as APC, CTNNB1 and RNF43, were absent. RSPO fusion status did not have a statistically significant influence on the overall or recurrence-free survival. These clinicopathological and genetic features were also confirmed in a pooled analysis of previous studies. CONCLUSION RSPO fusion-positive CRCs constitute a rare subgroup of CRCs with several characteristic clinicopathological and genetic features.
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Affiliation(s)
- Taiki Hashimoto
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Daisuke Takayanagi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Junpei Yonemaru
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Tomoaki Naka
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kengo Nagashima
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Dai Shida
- Division of Colorectal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Division of Frontier Surgery, The Institute of Medical Science, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Simon J Leedham
- Intestinal Stem Cell Biology Lab, Welcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
| | | | - Atsuo Takashima
- Division of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan. .,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.
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13
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mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase. Int J Mol Sci 2022; 23:ijms231911007. [PMID: 36232302 PMCID: PMC9569610 DOI: 10.3390/ijms231911007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. For six patients, a pathognomonic fusion transcript was readily detected, i.e., PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in four URCS patients. For the 11 remaining patients, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this study shows that mRNA capture sequencing enhances the detection rate of pathognomonic fusions and enables the identification of novel and secondary fusion transcripts in sarcomas.
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14
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Molecular characterization of colorectal cancer related peritoneal metastatic disease. Nat Commun 2022; 13:4443. [PMID: 35927254 PMCID: PMC9352687 DOI: 10.1038/s41467-022-32198-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/21/2022] [Indexed: 12/11/2022] Open
Abstract
A significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course of their disease. PMs are associated with a poor quality of life, significant morbidity and dismal disease outcome. To improve care for this patient group, a better understanding of the molecular characteristics of CRC-PM is required. Here we present a comprehensive molecular characterization of a cohort of 52 patients. This reveals that CRC-PM represent a distinct CRC molecular subtype, CMS4, but can be further divided in three separate categories, each presenting with unique features. We uncover that the CMS4-associated structural protein Moesin plays a key role in peritoneal dissemination. Finally, we define specific evolutionary features of CRC-PM which indicate that polyclonal metastatic seeding underlies these lesions. Together our results suggest that CRC-PM should be perceived as a distinct disease entity. Colorectal cancer can lead to the development of peritoneal metastases, which are associated with worse disease outcome. Here, the authors characterize peritoneal metastases from 52 patients using RNA-seq and mutational sequencing and show a distinct molecular subtype.
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15
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Talebi A, Shahidsales S, Aliakbarian M, Pezeshki Rad M, Kerachian MA. Oncogenic fusion transcript analysis identified ADAP1-NOC4L, potentially associated with metastatic colorectal cancer. Cancer Med 2022; 12:525-540. [PMID: 35702822 PMCID: PMC9844608 DOI: 10.1002/cam4.4943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Fusion transcripts are transcriptome-mediated alterations involved in tumorigenesis and are considered as diagnostic, prognostic, and therapeutic biomarkers. In metastatic colorectal carcinoma (mCRC), fusion transcripts are rarely reported. The main challenge is to identify driver chimeras with a significant role in cancer progression. METHODS In the present study, 86 RNA sequencing data samples were analyzed to discover driver fusion transcripts. Functional assays included clonogenic cell survival, wound-healing, and transwell cell invasion. Quantitative expression analysis of epithelial-mesenchymal transition (EMT), apoptotic regulators, and metastatic markers were examined for the candidate fusion genes. Kaplan-Meier survival analysis was performed using patient overall survival (OS). RESULTS A variety of driver fusions were identified. Fourteen fusion genes (51% of mCRC), each at least found in two mCRC samples, were determined as oncogenic fusion transcripts by in silico analysis of their functions. Among them, two recurrent chimeric transcripts confirmed by Sanger sequencing were selected. Positive expression of ADAP1-NOC4L was significantly associated with an increased risk of poor OS in mCRC patients. In vitro transforming potential for the chimera, resulting from the fusion of ADAP1 and NOC4L was assessed. Overexpression of this fusion gene increased cell proliferation and enhanced migration and invasion of CRC cells. In addition, it significantly upregulated EMT and anti-apoptotic markers. CONCLUSIONS ADAP1-NOC4L transcript chimera, a driver chimera identified in this study, provides new insight into the underlying mechanisms involved in the development and spread of mCRC. It suggests the potential of RNA-based alterations as novel targets for personalized medicine in clinical practice.
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Affiliation(s)
- Amin Talebi
- Medical Genetics Research CenterMashhad University of Medical SciencesMashhadIran,Faculty of Medicine, Department of Medical GeneticsMashhad University of Medical SciencesMashhadIran
| | | | - Mohsen Aliakbarian
- Faculty of Medicine, Surgical Oncology Research CenterMashhad University of Medical SciencesMashhadIran
| | - Masoud Pezeshki Rad
- Faculty of Medicine, Department of RadiologyMashhad University of Medical SciencesMashhadIran
| | - Mohammad Amin Kerachian
- Medical Genetics Research CenterMashhad University of Medical SciencesMashhadIran,Faculty of Medicine, Department of Medical GeneticsMashhad University of Medical SciencesMashhadIran,Cancer Genetics Research UnitReza Radiotherapy and Oncology CenterMashhadIran
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16
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Talebi A, Rokni P, Kerachian MA. Transcriptome analysis of colorectal cancer liver metastasis: The importance of long non-coding RNAs and fusion transcripts in the disease pathogenesis. Mol Cell Probes 2022; 63:101816. [DOI: 10.1016/j.mcp.2022.101816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
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17
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Rahi H, Olave MC, Fritchie KJ, Greipp PT, Halling KC, Kipp BR, Graham RP. Gene Fusions in Gastrointestinal Tract cancers. Genes Chromosomes Cancer 2022; 61:285-297. [PMID: 35239225 DOI: 10.1002/gcc.23035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
Fusion genes have been identified a wide array of human neoplasms including hematologic and solid tumors, including gastrointestinal tract neoplasia. A fusion gene is the product of parts of two genes which are joined together following a deletion, translocation or chromosomal inversion. Together with single nucleotide variants, insertions, deletions, and amplification, fusion genes represent one of the key genomic mechanisms for tumor development. Detecting fusions in the clinic is accomplished by a variety of techniques including break-apart fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), and next-generation sequencing (NGS). Some recurrent gene fusions have been successfully targeted by small molecule or monoclonal antibody therapies (i.e. targeted therapies), while others are used for as biomarkers for diagnostic and prognostic purposes. The purpose of this review article is to discuss the clinical utility of detection of gene fusions in carcinomas and neoplasms arising primarily in the digestive system. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hamed Rahi
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Maria C Olave
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karen J Fritchie
- Division of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Patricia T Greipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
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18
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Klein Kranenbarg RAM, Vali AH, IJzermans JNM, Pisanic TR, Wang TH, Azad N, Sukumar S, Fackler MJ. High performance methylated DNA markers for detection of colon adenocarcinoma. Clin Epigenetics 2021; 13:218. [PMID: 34903270 PMCID: PMC8670296 DOI: 10.1186/s13148-021-01206-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Colon cancer (CC) is treatable if detected in its early stages. Improved CC detection assays that are highly sensitive, specific, and available at point of care are needed. In this study, we systematically selected and tested methylated markers that demonstrate high sensitivity and specificity for detection of CC in tissue and circulating cell-free DNA. METHODS Hierarchical analysis of 22 candidate CpG loci was conducted using The Cancer Genome Atlas (TCGA) COAD 450K HumanMethylation database. Methylation of 13 loci was analyzed using quantitative multiplex methylation-specific PCR (QM-MSP) in a training set of fresh frozen colon tissues (N = 53). Hypermethylated markers were identified that were highest in cancer and lowest in normal colon tissue using the 75th percentile in Mann-Whitney analyses and the receiver operating characteristic (ROC) statistic. The cumulative methylation status of the marker panel was assayed in an independent test set of fresh frozen colon tissues (N = 52) using conditions defined and locked in the training set. A minimal marker panel of 6 genes was defined based on ROC area under the curve (AUC). Plasma samples (N = 20 colorectal cancers, stage IV and N = 20 normal) were tested by cMethDNA assay to evaluate marker performance in liquid biopsy. RESULTS In the test set of samples, compared to normal tissue, a 6-gene panel showed 100% sensitivity and 90% specificity for detection of CC, and an AUC of 1.00 (95% CI 1.00, 1.00). In stage IV colorectal cancer plasma versus normal, an 8-gene panel showed 95% sensitivity, 100% specificity, and an AUC of 0.996 (95% CI 0.986, 1.00) while a 5-gene subset showed 100% sensitivity, 100% specificity, and an AUC of 1.00 (95% CI 1.00, 1.00), highly concordant with our observations in tissue. CONCLUSIONS We identified high performance methylated DNA marker panels for detection of CC. This knowledge has set the stage for development and implementation of novel, automated, self-contained CC detection assays in tissue and blood which can expeditiously and accurately detect colon cancer in both developed and underdeveloped regions of the world, enabling optimal use of limited resources in low- and middle-income countries.
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Affiliation(s)
- Romy A M Klein Kranenbarg
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Abdul Hussain Vali
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thomas R Pisanic
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Nilofer Azad
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Breast and Ovarian Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, CRB 1-Rm 144, Baltimore, MD, 21231, USA.
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Breast and Ovarian Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1650 Orleans Street, CRB 1-Rm 144, Baltimore, MD, 21231, USA.
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19
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ERAS, a Member of the Ras Superfamily, Acts as an Oncoprotein in the Mammary Gland. Cancers (Basel) 2021; 13:cancers13215588. [PMID: 34771750 PMCID: PMC8582886 DOI: 10.3390/cancers13215588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The genes of the RAS family are among the group of genes most frequently mutated in human cancer. ERAS is a relatively unknown gene of this family. Although ERAS is overexpressed in some tumoral samples and in several cancer cell lines of human origin, it is not known if its expression drives tumor formation or if, alternatively, its expression is a secondary event in tumoral transformation. In this report, in order to clarify the role of ERAS in mammary tumorigenesis, we studied transgenic mice expressing ERAS in myoepithelial cells of mammary and other exocrine glands and in basal cells of stratified epithelia. These mice displayed an altered development and function of the mammary glands, and suffered high-frequency tumoral lesions in the mammary glands resembling a rare human breast tumor named malignant adenomyoepithelioma. Our results clearly demonstrate that ERAS is a true oncogene able to produce mammary tumors when inappropriately expressed. Abstract ERAS is a relatively uncharacterized gene of the Ras superfamily. It is expressed in ES cells and in the first stages of embryonic development; later on, it is silenced in the majority of cell types and tissues. Although there are several reports showing ERAS expression in tumoral cell lines and human tumor samples, it is unknown if ERAS deregulated expression is enough to drive tumor development. In this report, we have generated transgenic mice expressing ERAS in myoepithelial basal cells of the mammary gland and in basal cells of stratified epithelia. In spite of the low level of ERAS expression, these transgenic mice showed phenotypic alterations resembling overgrowth syndromes caused by the activation of the AKT-PI3K pathway. In addition, their mammary glands present developmental and functional disabilities accompanied by morphological and biochemical alterations in the myoepithelial cells. These mice suffer from tumoral transformation in the mammary glands with high incidence. These mammary tumors resemble, both histologically and by the expression of differentiation markers, malignant adenomyoepitheliomas. In sum, our results highlight the importance of ERAS silencing in adult tissues and define a truly oncogenic role for ERAS in mammary gland cells when inappropriately expressed.
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20
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van den Berg I, Smid M, Coebergh van den Braak RRJ, van de Wiel MA, van Deurzen CHM, de Weerd V, Martens JWM, IJzermans JNM, Wilting SM. A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer. Mol Oncol 2021; 15:3348-3362. [PMID: 34510716 PMCID: PMC8637568 DOI: 10.1002/1878-0261.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/04/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). We aim to identify methylation markers to distinguish between CMS2 and CMS3 in patients with CRC, for which an easy test is currently lacking. To this aim, fresh‐frozen tumor tissue of 239 patients with stage I‐III CRC was analyzed. Methylation profiles were obtained using the Infinium HumanMethylation450 BeadChip. We performed adaptive group‐regularized logistic ridge regression with post hoc group‐weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3. The Cancer Genome Atlas (TCGA) data were used for validation. Group regularization of the probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier, resulting in two different prediction models and subsequently different marker panels. For both panels, even when using only five markers, accuracies were > 90% in our cohort and in the TCGA validation set. Our methylation marker panel accurately distinguishes between CMS2 and CMS3. This enables development of a targeted assay to provide a robust and clinically relevant classification tool for CRC patients.
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Affiliation(s)
- Inge van den Berg
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | | | - Mark A van de Wiel
- Department of Epidemiology & Data Science, Amsterdam University Medical Center, Amsterdam Public Health research institute, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
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21
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Russo A, Incorvaia L, Malapelle U, Del Re M, Capoluongo E, Vincenzi B, Chiari R, Cortesi L, Danesi R, Florena AM, Fontanini G, Gori S, Marchetti A, Normanno N, Pinto C, Sangiolo D, Silvestris N, Tagliaferri P, Tallini G, Cinieri S, Beretta GD. The Tumor-Agnostic Treatment For Patients with Solid Tumors: a Position Paper on behalf of the AIOM- SIAPEC/IAP-SIBIOC-SIF Italian Scientific Societies. Crit Rev Oncol Hematol 2021; 165:103436. [PMID: 34371157 DOI: 10.1016/j.critrevonc.2021.103436] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
The personalized medicine is in a rapidly evolving scenario. The identification of actionable mutations is revolutionizing the therapeutic landscape of tumors. The morphological and histological tumor features are enriched by the extensive genomic profiling, and the first tumor-agnostic drugs have been approved regardless of tumor histology, guided by predictive and druggable genetic alterations. This new paradigm of "mutational oncology", presents a great potential to change the oncologic therapeutic scenario, but also some critical aspects need to be underlined. A process governance is mandatory to ensure the genomic testing accuracy and homogeneity, the economic sustainability, and the regulatory issues, ultimately granting the possibility of translating this model in the "real world". In this position paper, based on experts' opinion, the AIOM-SIAPEC-IAP-SIBIOC-SIF Italian Scientific Societies revised the new agnostic biomarkers, the diagnostic technologies available, the current availability of agnostic drugs and their present indication.
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Affiliation(s)
- Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy.
| | - Lorena Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138, Naples, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, 80131, Naples, Italy; CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80131, Naples, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Campus Bio-Medico University, 00128, Rome, Italy
| | - Rita Chiari
- Medical Oncology, AULSS 6 Euganea, South Padova Hospital, Monselice, PD, Italy
| | - Laura Cortesi
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Ada Maria Florena
- Pathologic Anatomy Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Stefania Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Naples, Italy
| | - Carmine Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - Dario Sangiolo
- Department of Oncology, University of Torino, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Department of Internal Medicine and Oncology (DIMO), University of Bari, Bari, Italy
| | - Pierosandro Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100, Catanzaro, Italy
| | - Giovanni Tallini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna School of Medicine, Bologna, Italy
| | - Saverio Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
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22
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Hasegawa H, Miyo M, Mori K, Mano M, Ishida H, Mita E. A Rare BRAF Fusion in Advanced Rectal Cancer Treated with Anti-Epidermal Growth Factor Receptor Therapy. Case Rep Oncol 2021; 14:938-943. [PMID: 34267639 PMCID: PMC8261262 DOI: 10.1159/000517007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 11/19/2022] Open
Abstract
Recently, v-raf murine sarcoma viral oncogene homologue B (BRAF) fusions have been identified in multiple cancer types using comprehensive genomic profiling (CGP) assays. BRAF fusions are extremely rare, occurring in <0.5% of patients with metastatic colorectal cancer (mCRC). Until now, there is no standard treatment for mCRC with BRAF fusions. Here, we report a recurrent colorectal cancer case that harbored an EXOC4-BRAF fusion. A 40-year-old female patient with a 2-year history of type 2 diabetes was diagnosed with pathologically confirmed stage IV rectal adenocarcinoma with liver metastasis. She underwent R0 resection after neoadjuvant therapy; however, her disease recurred at multiple metastatic sites (lymph nodes, ovary, and peritoneal gland). A rectal cancer surgical specimen was submitted for CGP (Foundation One) to identify potential targets to develop treatment strategies. An EXOC4-BRAF fusion was identified, and she achieved partial response to FOLFOX + panitumumab which is a fully human antibody directed against epidermal growth factor receptor. No EXOC4-BRAF fusions in colorectal cancer cases have been reported to date. Further studies investigating molecular mechanisms and novel targeted therapy approaches are required.
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Affiliation(s)
- Hiroko Hasegawa
- Department of Gastroenterology and Hepatology, National Hospital Organization, Osaka National Hospital, Osaka, Japan
| | - Masaaki Miyo
- Department of Surgery, National Hospital Organization, Osaka National Hospital, Osaka, Japan
| | - Kiyoshi Mori
- Department of Pathology, National Hospital Organization, Osaka National Hospital, Osaka, Japan
| | - Masayuki Mano
- Department of Pathology, National Hospital Organization, Osaka National Hospital, Osaka, Japan
| | - Hisashi Ishida
- Department of Gastroenterology and Hepatology, National Hospital Organization, Osaka National Hospital, Osaka, Japan
| | - Eiji Mita
- Department of Gastroenterology and Hepatology, National Hospital Organization, Osaka National Hospital, Osaka, Japan
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23
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Chen W, Song J, Liu S, Tang B, Shen L, Zhu J, Fang S, Wu F, Zheng L, Qiu R, Chen C, Gao Y, Tu J, Zhao Z, Ji J. USP9X promotes apoptosis in cholangiocarcinoma by modulation expression of KIF1Bβ via deubiquitinating EGLN3. J Biomed Sci 2021; 28:44. [PMID: 34112167 PMCID: PMC8191029 DOI: 10.1186/s12929-021-00738-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Background Cholangiocarcinoma represents the second most common primary liver malignancy. The incidence rate has constantly increased over the last decades. Cholangiocarcinoma silent nature limits early diagnosis and prevents efficient treatment. Methods Immunoblotting and immunohistochemistry were used to assess the expression profiling of USP9X and EGLN3 in cholangiocarcinoma patients. ShRNA was used to silence gene expression. Cell apoptosis, cell cycle, CCK8, clone formation, shRNA interference and xenograft mouse model were used to explore biological function of USP9X and EGLN3. The underlying molecular mechanism of USP9X in cholangiocarcinoma was determined by immunoblotting, co-immunoprecipitation and quantitative real time PCR (qPCR). Results Here we demonstrated that USP9X is downregulated in cholangiocarcinoma which contributes to tumorigenesis. The expression of USP9X in cholangiocarcinoma inhibited cell proliferation and colony formation in vitro as well as xenograft tumorigenicity in vivo. Clinical data demonstrated that expression levels of USP9X were positively correlated with favorable clinical outcomes. Mechanistic investigations further indicated that USP9X was involved in the deubiquitination of EGLN3, a member of 2-oxoglutarate and iron-dependent dioxygenases. USP9X elicited tumor suppressor role by preventing degradation of EGLN3. Importantly, knockdown of EGLN3 impaired USP9X-mediated suppression of proliferation. USP9X positively regulated the expression level of apoptosis pathway genes de through EGLN3 thus involved in apoptosis of cholangiocarcinoma. Conclusion These findings help to understand that USP9X alleviates the malignant potential of cholangiocarcinoma through upregulation of EGLN3. Consequently, we provide novel insight into that USP9X is a potential biomarker or serves as a therapeutic or diagnostic target for cholangiocarcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00738-2.
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Affiliation(s)
- Weiqian Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jingjing Song
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Siyu Liu
- Clinical Laboratory, Lishui Central Hospital, Lishui, 323000, China
| | - Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Lin Shen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jinyu Zhu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Shiji Fang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Fazong Wu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Liyun Zheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Rongfang Qiu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Chunmiao Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Yang Gao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Jianfei Tu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China
| | - Zhongwei Zhao
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China.
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University/Affiliated Lishui Hospital of Zhejiang University/Clinical College of The Affiliated Central Hospital of Lishui University, Lishui, 323000, China.
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Fu Y, Li Z, Gao F, Yang J, Wu H, Zhang B, Pu X, Fan X. MLH1/PMS2 Expression Could Tell Classical NTRK Fusion in Fluorescence In Situ Hybridization Positive Colorectal Carcinomas. Front Oncol 2021; 11:669197. [PMID: 33996597 PMCID: PMC8117224 DOI: 10.3389/fonc.2021.669197] [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: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 12/19/2022] Open
Abstract
To gain insight into the clinicopathologic profile of colorectal carcinomas harboring oncogenic NTRK fusions based on eastern populations as well as make the best testing algorithm for the screen, we use pan-Trk immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) respectively to screen NTRK fusions in a large, unselected cohort of 819 colon cancers; either IHC or FISH positive cases were further detected by next-generation sequencing (NGS). IHC staining was observed in ten (1.22%) cases. FISH positive was observed in 13 (1.59%) cases, and finally, a total of 18 cases were under both a DNA-based and an RNA-based NGS assay. RNA-based NGS was positive in 13 of 18 cases, whereas DNA-based NGS was only positive in three of 18 cases. In total 13 RNA-based NGS NTRK fusion-positive cases, only six cases were pan-TRK IHC positive versus 12 were FISH positive. More important, in 13 RNA-based NGS cases only five cases contain the full length of NTRK tyrosine kinase (TK) domain and form the classical fusion chimeras, other six cases only maintain parts of the TK domain and form the sub-classical fusion chimeras, two cases totally miss the TK domain and form the non-classical fusions. For clinicopathologic characteristics, besides the MMR (mismatch repair) status (p = 0.001), there is no difference between the NTRK fusion-positive and negative cases. Nevertheless, classical fusion cases prefer low differentiation (p = 0.001) and different patterns of growth (p < 0.001). Besides, we found all five classical NTRK fusion cases, and only one sub-classical case was harboring MLH1/PMS2 deficiency. When combining FISH and MMR (Mismatch Repair) status, besides one sub-classical case, all five classical fusions were detected, which means MLH1/PMS2 expression could further narrow the classical fusions in FISH NTRK fusion positive cases. Given the low sensitivity and specificity of the pan-Trk antibody, it would be useless to use IHC to screen NTRK fusion-positive CRCs. Combining FISH and MLH1/PMS2 IHC would be a good testing algorithm for the screen effective NTRK fusions. Finally, if patients are going to undergo TRK-based targeted therapy, only RNA-based NGS for detection of the specific fusion could tell the precise rearrangement information.
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Affiliation(s)
- Yao Fu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Zheng Li
- Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Fuping Gao
- Department of Pathology, Gaochun People's Hospital, Nanjing, China
| | - Jun Yang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hongyan Wu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Biao Zhang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaohong Pu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiangshan Fan
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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25
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van den Berg I, Coebergh van den Braak RRJ, van Vugt JLA, Ijzermans JNM, Buettner S. Actual survival after resection of primary colorectal cancer: results from a prospective multicenter study. World J Surg Oncol 2021; 19:96. [PMID: 33820567 PMCID: PMC8022415 DOI: 10.1186/s12957-021-02207-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/19/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Colorectal cancer is the third most common type of cancer in the world. We characterize a cohort of patients who survived up to 5 years without recurrence and identify factors predicting the probability of cure. METHODS We analyzed data of patients who underwent curative intent surgery for stage I-III CRC between 2007 and 2012 and who had had been included in a large multicenter study in the Netherlands. Cure was defined as 5-year survival without recurrence. Survival data were retrieved from a national registry. RESULTS Analysis of data of 754 patients revealed a cure rate of 65% (n = 490). Patients with stage I disease and T1- and N0-tumor had the highest probability of cure (94%, 95% and 90%, respectively). Those with a T4-tumor or N2-tumor had the lowest probability of cure (62% and 50%, respectively). A peak in the mortality rate for older patients early in follow-up suggests early excess mortality as an explanation. A similar trend was observed for stage III disease, poor tumor grade, postoperative complications, sarcopenia, and R1 resections. Patients with stage III disease, poor tumor grade, postoperative complications, sarcopenia, and R1 resections show a similar trend for decrease in CSS deaths over time. CONCLUSION In the studied cohort, the probability of cure for patients with stage I-III CRC ranged from 50 to 95%. Even though most patients will be cured from CRC with standard therapy, standard therapy is insufficient for those with poor prognostic factors, such as high T- and N-stage and poor differentiation grade.
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Affiliation(s)
- Inge van den Berg
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands.
| | | | - Jeroen L A van Vugt
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands
| | - Stefan Buettner
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, Rotterdam, 3015 GD, The Netherlands
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26
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Zhang R, Dong L, Yu J. Concomitant Pathogenic Mutations and Fusions of Driver Oncogenes in Tumors. Front Oncol 2021; 10:544579. [PMID: 33520689 PMCID: PMC7844084 DOI: 10.3389/fonc.2020.544579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023] Open
Abstract
Driver oncogene alterations have always been one of leading causes in the process of occurrence and development of tumors. And the effects of driver oncogene alterations on tumorigenesis and progression in different kinds of tumors have been studied heatedly. And the roles that the driver oncogenes alterations play have been elucidated clearly in previous studies. The phenomenon of concomitant driver oncogenes mutations and driver genes fusions has gained much concentration in the past two decades. And a growing number of studies reported this phenomenon, either coexistence or mutually exclusivity. Here we reviewed on the phenomenon of concomitant mutations in three common types of carcinomas—lung cancer, thyroid cancer, and leukemia, which have been studied relatively more detailed and more general compared with others.
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Affiliation(s)
- Runjiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Li Dong
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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27
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Singh H, Li YY, Spurr LF, Shinagare AB, Abhyankar R, Reilly E, Brais LK, Nag A, Ducar MD, Thorner AR, Shapiro GI, Keller RB, Siletti C, Clark JW, Farago AF, Lin JJ, Demetri GD, Gujrathi R, Kulke MH, MacConaill LE, Ligon AH, Sicinska E, Meyerson ML, Meyerhardt JA, Cherniack AD, Wolpin BM, Ng K, Giannakis M, Hornick JL, Cleary JM. Molecular Characterization and Therapeutic Targeting of Colorectal Cancers Harboring Receptor Tyrosine Kinase Fusions. Clin Cancer Res 2021; 27:1695-1705. [PMID: 33414136 DOI: 10.1158/1078-0432.ccr-20-4073] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Receptor tyrosine kinase fusions in colorectal cancers are rare, but potentially therapeutically relevant. We describe clinical, molecular, and pathologic attributes of RTK fusion-associated colorectal cancer. EXPERIMENTAL DESIGN We identified all cases with RTK fusions in patients with colorectal cancer seen at Dana-Farber Cancer Institute (Boston, MA) who underwent OncoPanel testing between 2013 and 2018. Clinical, histologic, and molecular features were extracted from the patient charts and molecular testing results. RESULTS We identified 12 driver oncogenic fusions in various RTKs. These fusions occurred exclusively in BRAF and RAS wild-type tumors and were enriched in right-sided and mismatch repair-deficient (MMR-D) colorectal cancers. All of the MMR-D colorectal cancers with RTK fusions were found in tumors with acquired MMR-D due to MLH1 promoter hypermethylation and one was associated with a sessile serrated polyp. Molecular profiles of MMR-D colorectal cancer with RTK fusions largely resembled BRAF V600E-mutated MMR-D colorectal cancer, rather than those secondary to Lynch syndrome. We describe two patients with fusion-associated microsatellite stable (MSS) colorectal cancer who derived clinical benefit from therapeutic targeting of their translocation. The first harbored an ALK-CAD fusion and received sequential crizotinib and alectinib therapy for a total of 7.5 months until developing an ALK L1196Q gatekeeper mutation. The second patient, whose tumor contained an ROS1-GOPC fusion, continues to benefit from entrectinib after 9 months of therapy. CONCLUSIONS RTK fusions in colorectal cancer are a rare, but important disease subgroup that occurs in RAS and BRAF wild-type tumors. Despite enrichment in acquired MMR-D tumors, RTK fusions also occur in MSS colorectal cancer and provide an important therapeutic target.
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Affiliation(s)
- Harshabad Singh
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Liam F Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Atul B Shinagare
- Department of Radiology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Ritika Abhyankar
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Emma Reilly
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Lauren K Brais
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Anwesha Nag
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew D Ducar
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Early Drug Development Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rachel B Keller
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Cheta Siletti
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jeffrey W Clark
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Anna F Farago
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Division of Sarcoma, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rahul Gujrathi
- Department of Radiology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew H Kulke
- Department of Medical Oncology, Boston University Medical Center, Boston, Massachusetts
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Azra H Ligon
- Division of Clinical Cytogenetics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew L Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jeffrey A Meyerhardt
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Brian M Wolpin
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Kimmie Ng
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Marios Giannakis
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - James M Cleary
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
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28
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Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
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Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
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29
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Hong M, Tao S, Zhang L, Diao LT, Huang X, Huang S, Xie SJ, Xiao ZD, Zhang H. RNA sequencing: new technologies and applications in cancer research. J Hematol Oncol 2020; 13:166. [PMID: 33276803 PMCID: PMC7716291 DOI: 10.1186/s13045-020-01005-x] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past few decades, RNA sequencing has significantly progressed, becoming a paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing to single-molecular, single-cell and spatial transcriptome approaches has enabled increasingly accurate, individual cell resolution incorporated with spatial information. Cancer, a major malignant and heterogeneous lethal disease, remains an enormous challenge in medical research and clinical treatment. As a vital tool, RNA sequencing has been utilized in many aspects of cancer research and therapy, including biomarker discovery and characterization of cancer heterogeneity and evolution, drug resistance, cancer immune microenvironment and immunotherapy, cancer neoantigens and so on. In this review, the latest studies on RNA sequencing technology and their applications in cancer are summarized, and future challenges and opportunities for RNA sequencing technology in cancer applications are discussed.
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Affiliation(s)
- Mingye Hong
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Ling Zhang
- Health Science Center, The University of Texas, Houston, 77030, USA
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xuanmei Huang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Shaohui Huang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Shu-Juan Xie
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Hua Zhang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
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Agarwal S, Behring M, Kim H, Chandrashekar DS, Chakravarthi BVSK, Gupta N, Bajpai P, Elkholy A, Al Diffalha S, Datta PK, Heslin MJ, Varambally S, Manne U. TRIP13 promotes metastasis of colorectal cancer regardless of p53 and microsatellite instability status. Mol Oncol 2020; 14:3007-3029. [PMID: 33037736 PMCID: PMC7718953 DOI: 10.1002/1878-0261.12821] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Overexpression of TRIP13, a member of the AAA-ATPase family, is linked with various cancers, but its role in metastasis is unknown in colorectal cancer (CRC). In the current study, we investigated the role TRIP13 in experimental metastasis and its involvement in regulation of WNT/β-catenin and EGFR signaling pathways. Evaluation of formalin-fixed paraffin-embedded (FFPE) and frozen tissues of adenomas and CRCs, along with their corresponding normal samples, showed that TRIP13 was gradually increased in its phenotypic expression from adenoma to carcinoma and that its overexpression in CRCs was independent of patient's gender, age, race/ethnicity, pathologic stage, and p53 and microsatellite instability (MSI) status. Moreover, liver metastases of CRCs showed TRIP13 overexpression as compared to matched adjacent liver tissues, indicating the biological relevance of TRIP13 in CRC progression and metastasis. TRIP13 knockdown impeded colony formation, invasion, motility, and spheroid-forming capacity of CRC cells irrespective of their p53 and MSI status. Furthermore, xenograft studies demonstrated high expression of TRIP13 contributed to tumor growth and metastasis. Depletion of TRIP13 in CRC cells decreased metastasis and it was independent of the p53 and MSI status. Furthermore, TRIP13 interacted with a tyrosine kinase, FGFR4; this interaction could be essential for activation of the EGFR-AKT pathway. In addition, we demonstrated the involvement of TRIP13 in the Wnt signaling pathway and in the epithelial-mesenchymal transition. Cell-based assays revealed that miR-192 and PNPT1 regulate TRIP13 expression in CRC. Additionally, RNA sequencing of CRC cells with TRIP13 knockdown identified COL6A3, TREM2, SHC3, and KLK7 as downstream targets that may have functional relevance in TRIP13-mediated tumor growth and metastasis. In summary, our results demonstrated that TRIP13 promotes tumor growth and metastasis regardless of p53 and MSI status, and indicated that it is a target for therapy of CRC.
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Affiliation(s)
- Sumit Agarwal
- Department of PathologyUniversity of Alabama at BirminghamALUSA
| | - Michael Behring
- Department of PathologyUniversity of Alabama at BirminghamALUSA
| | - Hyung‐Gyoon Kim
- Department of PathologyUniversity of Alabama at BirminghamALUSA
| | | | | | - Nirzari Gupta
- Department of ChemistryUniversity of Alabama at BirminghamALUSA
| | - Prachi Bajpai
- Department of PathologyUniversity of Alabama at BirminghamALUSA
| | - Amr Elkholy
- Department of PathologyUniversity of Alabama at BirminghamALUSA
| | | | - Pran K. Datta
- Division of Hematology and OncologyDepartment of MedicineUniversity of Alabama at BirminghamALUSA
- Department of SurgeryUniversity of Alabama at BirminghamALUSA
- O'Neal Comprehensive Cancer CenterUniversity of Alabama at BirminghamALUSA
| | - Martin J. Heslin
- Department of SurgeryUniversity of Alabama at BirminghamALUSA
- O'Neal Comprehensive Cancer CenterUniversity of Alabama at BirminghamALUSA
| | - Sooryanarayana Varambally
- Department of PathologyUniversity of Alabama at BirminghamALUSA
- O'Neal Comprehensive Cancer CenterUniversity of Alabama at BirminghamALUSA
| | - Upender Manne
- Department of PathologyUniversity of Alabama at BirminghamALUSA
- Department of SurgeryUniversity of Alabama at BirminghamALUSA
- O'Neal Comprehensive Cancer CenterUniversity of Alabama at BirminghamALUSA
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Colorectal Adenocarcinomas Harboring ALK Fusion Genes: A Clinicopathologic and Molecular Genetic Study of 12 Cases and Review of the Literature. Am J Surg Pathol 2020; 44:1224-1234. [PMID: 32804454 DOI: 10.1097/pas.0000000000001512] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study determined the frequency and the clinicopathologic and genetic features of colorectal carcinomas driven by oncogenic fusions of the anaplastic lymphoma kinase gene (ALK). Of the 8150 screened tumors, 12 (0.15%) were immunohistochemically ALK-positive with D5F3 antibody. These cancers harbored CAD-ALK (n=1), DIAPH2-ALK (n=2), EML4-ALK (n=2), LOC101929227-ALK (n=1), SLMAP-ALK (n=1), SPTBN1-ALK (n=4), and STRN-ALK (n=1) fusions, as detected by an RNA-based next-generation sequencing assay. ALK fusion carcinomas were diagnosed mostly in older patients with a 9:3 female predominance (median age: 72 y). All tumors, except a rectal one, occurred in the right colon. Most tumors were stage T3 (n=7) or T4 (n=3). Local lymph node and distant metastases were seen at presentation in 9 and 2 patients. These tumors showed moderate (n=6) or poor (n=3) glandular differentiation, solid medullary growth pattern (n=2), and pure mucinous morphology (n=1). DNA mismatch repair-deficient phenotype was identified in 10 cases. Tumor-infiltrating lymphocytes were prominent in 9 carcinomas. In 4 carcinomas, tumor cells showed strong, focal (n=3), or diffuse programmed death-ligand 1 immunoreactivity. CDX2 expression and loss of CK20 and MUC2 expression were frequent. CK7 was expressed in 5 tumors. Four patients died of disease within 3 years, and 7 were alive with follow-up ranging from 1 to 8 years. No mutations in BRAF, RAS, and in genes encoding components of PI3K-AKT/MTOR pathway were identified. However, 1 tumor had a loss-of-function PTEN mutation. Aberration of p53 signaling, TP53 mutations, and/or nuclear accumulation of p53 protein was seen in 9 cases. ALK fusion colorectal carcinomas are a distinct and rare subtype of colorectal cancers displaying some features of mismatch repair-deficient tumors.
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Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21197120. [PMID: 32992457 PMCID: PMC7582694 DOI: 10.3390/ijms21197120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022] Open
Abstract
Fusion genes and epigenetic regulators (i.e., miRNAs and long non-coding RNAs) constitute essential pieces of the puzzle of the tumor genomic landscape, in particular in mechanisms behind the adenoma-to-carcinoma progression of colorectal cancer (CRC). In this work, we aimed to identify molecular signatures of the different steps of sporadic CRC development in eleven patients, of which synchronous samples of adenomas, tumors, and normal tissues were analyzed by RNA-Seq. At a functional level, tumors and adenomas were all characterized by increased activity of the cell cycle, cell development, cell growth, and biological proliferation functions. In contrast, organic survival and apoptosis-related functions were inhibited both in tumors and adenomas at different levels. At a molecular level, we found that three individuals shared a tumor-specific fusion named MRPS31-SUGT1, generated through an intra-chromosomal translocation on chromosome 13, whose sequence resulted in being 100% identical to the long non-coding RNA (lncRNA) MRPS31P5. Our analyses suggest that MRPS31P5 could take part to a competitive endogenous (ce)RNA network by acting as a miRNA sponge or/and as an interactor of other mRNAs, and thus it may be an important gene expression regulatory factor and could be used as a potential biomarker for the detection of early CRC events.
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Coebergh van den Braak RRJ, Ten Hoorn S, Sieuwerts AM, Tuynman JB, Smid M, Wilting SM, Martens JWM, Punt CJA, Foekens JA, Medema JP, IJzermans JNM, Vermeulen L. Interconnectivity between molecular subtypes and tumor stage in colorectal cancer. BMC Cancer 2020; 20:850. [PMID: 32887573 PMCID: PMC7473811 DOI: 10.1186/s12885-020-07316-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND There are profound individual differences in clinical outcomes between colorectal cancers (CRCs) presenting with identical stage of disease. Molecular stratification, in conjunction with the traditional TNM staging, is a promising way to predict patient outcomes. We investigated the interconnectivity between tumor stage and tumor biology reflected by the Consensus Molecular Subtypes (CMSs) in CRC, and explored the possible value of these insights in patients with stage II colon cancer. METHODS We performed a retrospective analysis using clinical records and gene expression profiling in a meta-cohort of 1040 CRC patients. The interconnectivity of tumor biology and disease stage was assessed by investigating the association between CMSs and TNM classification. In order to validate the clinical applicability of our findings we employed a meta-cohort of 197 stage II colon cancers. RESULTS CMS4 was significantly more prevalent in advanced stages of disease (stage I 9.8% versus stage IV 38.5%, p < 0.001). The observed differential gene expression between cancer stages is at least partly explained by the biological differences as reflected by CMS subtypes. Gene signatures for stage III-IV and CMS4 were highly correlated (r = 0.77, p < 0.001). CMS4 cancers showed an increased progression rate to more advanced stages (CMS4 compared to CMS2: 1.25, 95% CI: 1.08-1.46). Patients with a CMS4 cancer had worse survival in the high-risk stage II tumors compared to the total stage II cohort (5-year DFS 41.7% versus 100.0%, p = 0.008). CONCLUSIONS Considerable interconnectivity between tumor biology and tumor stage in CRC exists. This implies that the TNM stage, in addition to the stage of progression, might also reflect distinct biological disease entities. These insights can potentially be utilized to optimize identification of high-risk stage II colon cancers.
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Affiliation(s)
- R R J Coebergh van den Braak
- Department of Surgery, Erasmus MC University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - S Ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - A M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Cancer Genomics Center Netherlands, Amsterdam, The Netherlands
| | - J B Tuynman
- Department of Surgery, Amsterdam UMC, Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - M Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - S M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Cancer Genomics Center Netherlands, Amsterdam, The Netherlands
| | - C J A Punt
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CX, Utrecht, The Netherlands
| | - J A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J P Medema
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - J N M IJzermans
- Department of Surgery, Erasmus MC University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - L Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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Wu H, Singh S, Xie Z, Li X, Li H. Landscape characterization of chimeric RNAs in colorectal cancer. Cancer Lett 2020; 489:56-65. [PMID: 32534173 DOI: 10.1016/j.canlet.2020.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/31/2022]
Abstract
Gene fusions and their fusion products have been recognized as ideal biomarkers and drug targets for cancer. However, few recurrent gene fusions were found in colorectal cancer (CRC), despite comprehensive studies. We believe that chimeric RNAs, in the absence of chromosomal rearrangement, may represent a new repertoire of biomarkers and/or therapeutic targets in CRC. In this study, we aim to identify such recurrent chimeric RNAs, and investigate their clinical implications. To do so, we performed extensive data mining for chimeric RNAs using The Cancer Genome Atlas CRC RNA-Seq datasets. Multiple filtering criteria were applied, and the landscape of chimeric RNAs at multiple levels, from various angles, was analyzed. Eleven frequent, cancer biased chimeric RNAs were validated. The expression of RRM2-C2orf48 correlates with poor clinical outcomes, while the expression of parental RRM2 and C2orf48 correlates with positive clinical outcomes. Mechanistically, it is a product of cis-splicing between adjacent genes. Silencing of RRM2-C2orf48 resulted in reduced cellular proliferation in colon cancer cells, whereas overexpressed chimera promoted cell proliferation. These findings suggest that frequent chimeric RNAs are present in CRCs, and that chimeric RNAs may have different expression profiles and functions from parental genes, thus representing a new repertoire of biomarkers and therapeutic targets.
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Affiliation(s)
- Hao Wu
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, China; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
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35
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Vaňková B, Vaněček T, Ptáková N, Hájková V, Dušek M, Michal M, Švajdler P, Daum O, Daumová M, Michal M, Mezencev R, Švajdler M. Targeted next generation sequencing of MLH1-deficient, MLH1 promoter hypermethylated, and BRAF/RAS-wild-type colorectal adenocarcinomas is effective in detecting tumors with actionable oncogenic gene fusions. Genes Chromosomes Cancer 2020; 59:562-568. [PMID: 32427409 DOI: 10.1002/gcc.22861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Oncogenic gene fusions represent attractive targets for therapy of cancer. However, the frequency of actionable genomic rearrangements in colorectal cancer (CRC) is very low, and universal screening for these alterations seems to be impractical and costly. To address this problem, several large scale studies retrospectivelly showed that CRC with gene fusions are highly enriched in groups of tumors defined by MLH1 DNA mismatch repair protein deficiency (MLH1d), and hypermethylation of MLH1 promoter (MLH1ph), and/or the presence of microsatellite instability, and BRAF/KRAS wild-type status (BRAFwt/KRASwt). In this study, we used targeted next generation sequencing (NGS) to explore the occurence of potentially therapeutically targetable gene fusions in an unselected series of BRAFwt/KRASwt CRC cases that displayed MLH1d/MLH1ph. From the initially identified group of 173 MLH1d CRC cases, 141 cases (81.5%) displayed MLH1ph. BRAFwt/RASwt genotype was confirmed in 23 of 141 (~16%) of MLH1d/MLH1ph cases. Targeted NGS of these 23 cases identified oncogenic gene fusions in nine patients (39.1%; CI95: 20.5%-61.2%). Detected fusions involved NTRK (four cases), ALK (two cases), and BRAF genes (three cases). As a secondary outcome of NGS testing, we identified PIK3K-AKT-mTOR pathway alterations in two CRC cases, which displayed PIK3CA mutation. Altogether, 11 of 23 (~48%) MLH1d/MLH1ph/BRAFwt/RASwt tumors showed genetic alterations that could induce resistance to anti-EGFR therapy. Our study confirms that targeted NGS of MLH1d/MLH1ph and BRAFwt/RASwt CRCs could be a cost-effective strategy in detecting patients with potentially druggable oncogenic kinase fusions.
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Affiliation(s)
- Bohuslava Vaňková
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Tomáš Vaněček
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Nikola Ptáková
- Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic.,Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Martin Dušek
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Michael Michal
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | | | - Ondřej Daum
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Magdaléna Daumová
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Michal Michal
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Roman Mezencev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marián Švajdler
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
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36
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Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing. Nat Commun 2020; 11:2861. [PMID: 32504042 PMCID: PMC7275081 DOI: 10.1038/s41467-020-16641-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. Here, we develop FUDGE (FUsion Detection from Gene Enrichment) to accurately and impartially identify fusions. FUDGE couples target-selected and strand-specific CRISPR-Cas9 activity for fusion gene driver enrichment — without prior knowledge of fusion partner or breakpoint-location — to long read nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints within 2 days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay for diagnostic pan-cancer fusion detection. Fusion genes are a hallmarks of cancer, though breakpoint-position promiscuity restricts diagnostic detection. Here, the authors present FUDGE, a CRISPR-Cas9-based enrichment strategy for nanopore sequencing to identify target fusions irrespective of genomic breakpoint or fusion partner.
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37
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38
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RET Gene Fusions in Malignancies of the Thyroid and Other Tissues. Genes (Basel) 2020; 11:genes11040424. [PMID: 32326537 PMCID: PMC7230609 DOI: 10.3390/genes11040424] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/05/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023] Open
Abstract
Following the identification of the BCR-ABL1 (Breakpoint Cluster Region-ABelson murine Leukemia) fusion in chronic myelogenous leukemia, gene fusions generating chimeric oncoproteins have been recognized as common genomic structural variations in human malignancies. This is, in particular, a frequent mechanism in the oncogenic conversion of protein kinases. Gene fusion was the first mechanism identified for the oncogenic activation of the receptor tyrosine kinase RET (REarranged during Transfection), initially discovered in papillary thyroid carcinoma (PTC). More recently, the advent of highly sensitive massive parallel (next generation sequencing, NGS) sequencing of tumor DNA or cell-free (cfDNA) circulating tumor DNA, allowed for the detection of RET fusions in many other solid and hematopoietic malignancies. This review summarizes the role of RET fusions in the pathogenesis of human cancer.
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39
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Chan AWH, Pan Y, Tong JHM, Lung RWM, Kwan JSH, Chow C, Tin EKY, Chung LY, Li H, Wong SSY, Chau SL, Chan YY, Mak TWC, Ng SSM, To KF. Receptor tyrosine kinase fusions act as a significant alternative driver of the serrated pathway in colorectal cancer development. J Pathol 2020; 251:74-86. [PMID: 32162306 DOI: 10.1002/path.5418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 02/06/2023]
Abstract
Serrated polyps are a clinically and molecularly heterogeneous group of lesions that can contribute to the development of colorectal cancers (CRCs). However, the molecular mechanism underlying the development of serrated lesions is still not well understood. Here, we combined multiple approaches to analyze the genetic alterations in 86 colorectal adenomas (including 35 sessile serrated lesions, 15 traditional adenomas, and 36 conventional adenomatous polyps). We also investigated the in vitro and in vivo oncogenic properties of a novel variant of the NCOA4-RET fusion gene. Molecular profiling revealed that sessile serrated lesions and traditional serrated adenomas have distinct clinicopathological and molecular features. Moreover, we identified receptor tyrosine kinase translocations exclusively in sessile serrated lesions (17%), and the observation was validated in a separate cohort of 34 sessile serrated lesions (15%). The kinase fusions as well as the BRAF and KRAS mutations were mutually exclusive to each other. Ectopic expression of a novel variant of the NCOA4-RET fusion gene promoted cell proliferation in vitro and in vivo, and the proliferation was significantly suppressed by RET kinase inhibitors. All of these underscored the importance of mitogen-activated protein kinase (MAPK) pathway activation in the serrated pathway of colorectal tumorigenesis. In addition, we demonstrated that the kinase fusion may occur early in the precursor lesion and subsequent loss of TP53 may drives the transformation to carcinoma during serrated tumorigenesis. In conclusion, we identified kinase fusions as a significant alternative driver of the serrated pathway in colorectal cancer development, and detecting their presence may serve as a biomarker for the diagnosis of sessile serrated lesions. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Anthony W-H Chan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Yi Pan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, PR China.,Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Joanna H-M Tong
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Raymond W-M Lung
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Johnny S-H Kwan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Chit Chow
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Edith K-Y Tin
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Lau-Ying Chung
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Hui Li
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Shela S-Y Wong
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Shuk-Ling Chau
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Yuk Yu Chan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Tony W-C Mak
- Division of Colorectal Surgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Simon Siu-Man Ng
- Division of Colorectal Surgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Sir Y.K. Pao Cancer Center, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, PR China.,Institute of Digestive Disease, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, PR China
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40
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Rachiglio AM, Sacco A, Forgione L, Esposito C, Chicchinelli N, Normanno N. Colorectal cancer genomic biomarkers in the clinical management of patients with metastatic colorectal carcinoma. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:53-70. [PMID: 36046264 PMCID: PMC9400741 DOI: 10.37349/etat.2020.00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal carcinoma (CRC) is an heterogeneous disease in which different genetic alterations play a role in its pathogenesis and progression and offer potential for therapeutic intervention. The research on predictive biomarkers in metastatic CRC (mCRC) mainly focused on the identification of biomarkers of response or resistance to anti-epidermal growth factor receptor monoclonal antibodies. In this respect, international guidelines suggest testing mCRC patients only for KRAS, NRAS and BRAF mutations and for microsatellite instability. However, the use of novel testing methods is raising relevant issue related to these biomarkers, such as the presence of sub-clonal RAS mutations or the clinical interpretation of rare no-V600 BRAF variants. In addition, a number of novel biomarkers is emerging from recent studies including amplification of ERBB2, mutations in ERBB2, MAP2K1 and NF1 and rearrangements of ALK, ROS1, NTRK and RET. Mutations in POLE and the levels of tumor mutation burden also appear as possible biomarkers of response to immunotherapy in CRC. Finally, the consensus molecular subtypes classification of CRC based on gene expression profiling has prognostic and predictive implications. Integration of all these information will be likely necessary in the next future in order to improve precision/personalized medicine in mCRC patients.
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Affiliation(s)
- Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Laura Forgione
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Claudia Esposito
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Nicoletta Chicchinelli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
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41
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Lasota J, Chłopek M, Lamoureux J, Christiansen J, Kowalik A, Wasąg B, Felisiak-Gołąbek A, Agaimy A, Biernat W, Canzonieri V, Centonze G, Chmielik E, Daum O, Dubová M, Dziuba I, Goertz S, Góźdź S, Guttmejer-Nasierowska A, Haglund C, Hałoń A, Hartmann A, Inaguma S, Iżycka-Świeszewska E, Kaczorowski M, Kita P, Kołos M, Kopczyński J, Michal M, Milione M, Okoń K, Pęksa R, Pyzlak M, Ristimaki A, Ryś J, Szostak B, Szpor J, Szumiło J, Teresiński L, Waloszczyk P, Wejman J, Wesołowski W, Miettinen M. Colonic Adenocarcinomas Harboring NTRK Fusion Genes: A Clinicopathologic and Molecular Genetic Study of 16 Cases and Review of the Literature. Am J Surg Pathol 2020; 44:162-173. [PMID: 31567189 PMCID: PMC8170835 DOI: 10.1097/pas.0000000000001377] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study was undertaken to determine the frequency, and the clinicopathologic and genetic features, of colon cancers driven by neurotrophic receptor tyrosine kinase (NTRK) gene fusions. Of the 7008 tumors screened for NTRK expression using a pan-Trk antibody, 16 (0.23%) had Trk immunoreactivity. ArcherDx assay detected TPM3-NTRK1 (n=9), LMNA-NTRK1 (n=3), TPR-NTRK1 (n=2) and EML4-NTRK3 (n=1) fusion transcripts in 15 cases with sufficient RNA quality. Patients were predominantly women (median age: 63 y). The tumors involved the right (n=12) and left colon unequally and were either stage T3 (n=12) or T4. Local lymph node and distant metastases were seen at presentation in 6 and 1 patients, respectively. Lymphovascular invasion was present in all cases. Histologically, tumors showed moderate to poor (n=11) differentiation with a partly or entirely solid pattern (n=5) and mucinous component (n=10), including 1 case with sheets of signet ring cells. DNA mismatch repair-deficient phenotype was seen in 13 cases. Tumor-infiltrating CD4/CD8 lymphocytes were prominent in 9 cases. Programmed death-ligand 1 positive tumor-infiltrating immune cells and focal tumor cell positivity were seen in the majority of cases. CDX2 expression and loss of CK20 and MUC2 expression were frequent. CK7 was expressed in 5 cases. No mutations in BRAF, RAS, and PIK3CA were identified. However, other genes of the PI3K-AKT/MTOR pathway were mutated. In several cases, components of Wnt/β-catenin (APC, AMER1, CTNNB1), p53, and TGFβ (ACVR2A, TGFBR2) pathways were mutated. However, no SMAD4 mutations were found. Two tumors harbored FBXW7 tumor suppressor gene mutations. NTRK fusion tumors constitute a distinct but rare subgroup of colorectal carcinomas.
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MESH Headings
- Adenocarcinoma/diagnosis
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Colonic Neoplasms/diagnosis
- Colonic Neoplasms/genetics
- Colonic Neoplasms/pathology
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Humans
- Immunohistochemistry
- Male
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Middle Aged
- Neoplasm Staging
- Oncogene Fusion
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor, trkA/genetics
- Receptor, trkA/metabolism
- Receptor, trkB/genetics
- Receptor, trkB/metabolism
- Receptor, trkC/genetics
- Receptor, trkC/metabolism
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Affiliation(s)
- Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland
| | - Małgorzata Chłopek
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland
- Department of Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | | | | | - Artur Kowalik
- Department of Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Abbas Agaimy
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Vincenzo Canzonieri
- Division of Pathology, National Cancer Institute, Aviano, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Ewa Chmielik
- Diagnostic Histopathology Laboratory, Opole, Poland
| | - Ondrej Daum
- Sikl’s Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Magdalena Dubová
- Sikl’s Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Ireneusz Dziuba
- Health Sciences and Physical Education, University of Technology and Humanities, Radom Poland
| | - Sebastian Goertz
- Department of Pathomorphology Copernicus Hospital Gdańsk, Gdańsk, Poland
| | - Stanisław Góźdź
- Department of Clinical Oncology, Holycross Cancer Center, Kielce, Poland
- Faculty of Health Sciences, Jan Kochanowski University, Kielce, Poland
| | | | - Caj Haglund
- Department of Surgery, University of Helsinki, Helsinki, Finland
| | - Agnieszka Hałoń
- Division of Pathomorphology and Oncological Cytology, Wrocław Medical University, Wrocław, Poland
| | - Arndt Hartmann
- Institute of Pathology, University Hospital of Erlangen, Erlangen, Germany
| | - Shingo Inaguma
- Department of Pathology, Aichi Medical University School of Medicine, Nagakute, Japan
| | | | - Maciej Kaczorowski
- Division of Pathomorphology and Oncological Cytology, Wrocław Medical University, Wrocław, Poland
| | - Paweł Kita
- Diagnostic Histopathology Laboratory, Opole, Poland
| | - Małgorzata Kołos
- Department of Pathology, Central Clinical Hospital of the Ministry of Interior, Warszawa, Poland
| | - Janusz Kopczyński
- Department of Surgical Pathology, Holycross Cancer Center, Kielce, Poland
| | - Michal Michal
- Sikl’s Department of Pathology, University Hospital, Charles University in Prague, Medical Faculty in Plzeň, Plzeň, Czech Republic
| | - Massimo Milione
- Department of Pathology and Laboratory Medicine, Milan, Italy
| | - Krzysztof Okoń
- Department of Pathomorphology, Jagiellonian University, Kraków, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Pyzlak
- Department of Pathology, Prof. Orłowski-Memorial, Independent, Public, Clinical Hospital and Center for Medical Postgraduate Education, Warszawa, Poland
| | | | - Janusz Ryś
- Department of Tumor Pathology, Centre of Oncology, Maria Skłodowska-Curie Memorial Institute, Kraków Branch, Poland
| | - Blażej Szostak
- Department of Pathomorphology, Provincial Hospital, Olsztyn, Poland
| | - Joanna Szpor
- Department of Pathomorphology, Jagiellonian University, Kraków, Poland
| | - Justyna Szumiło
- Department of Clinical Pathomorphology, Medical University of Lublin, Lublin, Poland
| | - Leszek Teresiński
- Department of Pathomorphology, Provincial Hospital, Gorzów Wielkopolski, Poland
| | | | - Jaroslaw Wejman
- Department of Pathology, Prof. Orłowski-Memorial, Independent, Public, Clinical Hospital and Center for Medical Postgraduate Education, Warszawa, Poland
| | | | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland
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42
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Kawasaki K, Fujii M, Sugimoto S, Ishikawa K, Matano M, Ohta Y, Toshimitsu K, Takahashi S, Hosoe N, Sekine S, Kanai T, Sato T. Chromosome Engineering of Human Colon-Derived Organoids to Develop a Model of Traditional Serrated Adenoma. Gastroenterology 2020; 158:638-651.e8. [PMID: 31622618 DOI: 10.1053/j.gastro.2019.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Traditional serrated adenomas (TSAs) are rare colorectal polyps with unique histologic features. Fusions in R-spondin genes have been found in TSAs, but it is not clear whether these are sufficient for TSA development, due to the lack of a chromosome engineering platform for human tissues. We studied the effects of fusions in R-spondin genes and other genetic alterations found in TSA using CRISPR-Cas9-mediated chromosome and genetic modification of human colonic organoids. METHODS We introduced chromosome rearrangements that involve R-spondin genes into human colonic organoids, with or without disruption of TP53, using CRISPR-Cas9 (chromosome-engineered organoids). We then knocked a mutation into BRAF encoding the V600E substitution and overexpressed the GREM1 transgene; the organoids were transplanted into colons of NOG mice and growth of xenograft tumors was measured. Colon tissues were collected and analyzed by immunohistochemistry or in situ hybridization. We also established 2 patient-derived TSA organoid lines and characterized their genetic features and phenotypes. We inserted a bicistronic cassette expressing a dimerizer-inducible suicide gene and fluorescent marker downstream of the LGR5 gene in the chromosome-engineered organoids; addition of the dimerizer eradicates LGR5+ cells. Some tumor-bearing mice were given intraperitoneal injections of the dimerizer to remove LGR5-expressing cells. RESULTS Chromosome engineering of organoids required disruption of TP53 or culture in medium containing IGF1 and FGF2. In colons of mice, organoids that expressed BRAFV600E and fusions in R-spondin genes formed flat serrated lesions. Patient-derived TSA organoids grew independent of exogenous R-spondin, and 1 line grew independent of Noggin. Organoids that overexpressed GREM1, in addition to BRAFV600E and fusions in R-spondin genes, formed polypoid tumors in mice that had histologic features similar to TSAs. Xenograft tumors persisted after loss of LGR5-expressing cells. CONCLUSIONS We demonstrated efficient chromosomal engineering of human normal colon organoids. We introduced genetic and chromosome alterations into human colon organoids found in human TSAs; tumors grown from these organoids in mice had histopathology features of TSAs. This model might be used to study progression of human colorectal tumors with RSPO fusion gene and GREM1 overexpression.
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Affiliation(s)
- Kenta Kawasaki
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Fujii
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Sugimoto
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ishikawa
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yuki Ohta
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kohta Toshimitsu
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Sirirat Takahashi
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan; Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan.
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43
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Post JB, Roodhart JML, Snippert HJG. Colorectal Cancer Modeling with Organoids: Discriminating between Oncogenic RAS and BRAF Variants. Trends Cancer 2020; 6:111-129. [PMID: 32061302 DOI: 10.1016/j.trecan.2019.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
RAS and BRAF proteins are frequently mutated in colorectal cancer (CRC) and have been associated with therapy resistance in metastatic CRC patients. RAS isoforms are considered to act as redundant entities in physiological and pathological settings. However, there is compelling evidence that mutant variants of RAS and BRAF have different oncogenic potentials and therapeutic outcomes. In this review we describe similarities and differences between various RAS and BRAF oncogenes in CRC development, histology, and therapy resistance. In addition, we discuss the potential of patient-derived tumor organoids for personalized therapy, as well as CRC modeling using genome editing in preclinical model systems to study similarities and discrepancies between the effects of oncogenic MAPK pathway mutations on tumor growth and drug response.
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Affiliation(s)
- Jasmin B Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, CX Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands
| | - Jeanine M L Roodhart
- Department of Medical Oncology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, CX Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands.
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44
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Stangl C, Post JB, van Roosmalen MJ, Hami N, Verlaan-Klink I, Vos HR, van Es RM, Koudijs MJ, Voest EE, Snippert HJG, Kloosterman WP. Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity. Mol Cancer Res 2020; 18:537-548. [PMID: 31911540 DOI: 10.1158/1541-7786.mcr-19-0529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/13/2019] [Accepted: 01/02/2020] [Indexed: 11/16/2022]
Abstract
Fusion genes can be oncogenic drivers in a variety of cancer types and represent potential targets for targeted therapy. The BRAF gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2%-3% throughout different cancers. However, BRAF fusions rarely occur in the same gene configuration, potentially challenging personalized therapy design. In particular, the impact of the wide variety of fusion partners on the oncogenic role of BRAF during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare BRAF fusions containing various partner genes (AGAP3, DLG1, and TRIM24) with respect to cellular behavior, downstream signaling activation, and response to targeted therapies. We demonstrate that 5' fusion partners mainly promote canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region. In addition, the 5' partner of BRAF fusions influences their subcellular localization and intracellular signaling capacity, revealing distinct subsets of affected signaling pathways and altered gene expression. Presence of the different BRAF fusions resulted in varying sensitivities to combinatorial inhibition of MEK and the EGF receptor family. However, all BRAF fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that BRAF fusions should be screened alongside other MAPK pathway alterations to identify patients with metastatic colorectal cancer to exclude from anti-EGFR-targeted treatment. IMPLICATIONS: Although intracellular signaling and sensitivity to targeted therapies of BRAF fusion genes are influenced by their 5' fusion partner, we show that all investigated BRAF fusions confer resistance to clinically relevant EGFR inhibition.
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Affiliation(s)
- Christina Stangl
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Division of Molecular Oncology, Netherlands Cancer Institute, and Oncode Institute, Amsterdam, the Netherlands
| | - Jasmin B Post
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, the Netherlands
| | - Nizar Hami
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Ingrid Verlaan-Klink
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Marco J Koudijs
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands.,Center for Personalized Cancer Treatment, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emile E Voest
- Division of Molecular Oncology, Netherlands Cancer Institute, and Oncode Institute, Amsterdam, the Netherlands.
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, and Oncode Institute, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands
| | - W P Kloosterman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, Utrecht, the Netherlands. .,Cyclomics, Utrecht, the Netherlands.,Frame Cancer Therapeutics, Amsterdam, the Netherlands
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45
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Sveen A, Kopetz S, Lothe RA. Biomarker-guided therapy for colorectal cancer: strength in complexity. Nat Rev Clin Oncol 2020; 17:11-32. [PMID: 31289352 PMCID: PMC7577509 DOI: 10.1038/s41571-019-0241-1] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
The number of molecularly stratified treatment options available to patients with colorectal cancer (CRC) is increasing, with a parallel rise in the use of biomarkers to guide prognostication and treatment decision-making. The increase in both the number of biomarkers and their use has resulted in a progressively complex situation, evident both from the extensive interactions between biomarkers and from their sometimes complex associations with patient prognosis and treatment benefit. Current and emerging biomarkers also reflect the genomic complexity of CRC, and include a wide range of aberrations such as point mutations, amplifications, fusions and hypermutator phenotypes, in addition to global gene expression subtypes. In this Review, we provide an overview of current and emerging clinically relevant biomarkers and their role in the management of patients with CRC, illustrating the intricacies of biomarker interactions and the growing treatment opportunities created by the availability of comprehensive molecular profiling.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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46
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Pietrantonio F, Di Nicolantonio F, Schrock AB, Lee J, Morano F, Fucà G, Nikolinakos P, Drilon A, Hechtman JF, Christiansen J, Gowen K, Frampton GM, Gasparini P, Rossini D, Gigliotti C, Kim ST, Prisciandaro M, Hodgson J, Zaniboni A, Chiu VK, Milione M, Patel R, Miller V, Bardelli A, Novara L, Wang L, Pupa SM, Sozzi G, Ross J, Di Bartolomeo M, Bertotti A, Ali S, Trusolino L, Falcone A, de Braud F, Cremolini C. RET fusions in a small subset of advanced colorectal cancers at risk of being neglected. Ann Oncol 2019. [PMID: 29538669 DOI: 10.1093/annonc/mdy090] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Recognition of rare molecular subgroups is a challenge for precision oncology and may lead to tissue-agnostic approval of targeted agents. Here we aimed to comprehensively characterize the clinical, pathological and molecular landscape of RET rearranged metastatic colorectal cancer (mCRC). Patients and methods In this case series, we compared clinical, pathological and molecular characteristics of 24 RET rearranged mCRC patients with those of a control group of 291 patients with RET negative tumors. RET rearranged and RET negative mCRCs were retrieved by systematic literature review and by taking advantage of three screening sources: (i) Ignyta's phase 1/1b study on RXDX-105 (NCT01877811), (ii) cohorts screened at two Italian and one South Korean Institutions and (iii) Foundation Medicine Inc. database. Next-generation sequencing data were analyzed for RET rearranged cases. Results RET fusions were more frequent in older patients (median age of 66 versus 60 years, P = 0.052), with ECOG PS 1-2 (90% versus 50%, P = 0.02), right-sided (55% versus 32%, P = 0.013), previously unresected primary tumors (58% versus 21%, P < 0.001), RAS and BRAF wild-type (100% versus 40%, P < 0.001) and MSI-high (48% versus 7%, P < 0.001). Notably, 11 (26%) out of 43 patients with right-sided, RAS and BRAF wild-type tumors harbored a RET rearrangement. At a median follow-up of 45.8 months, patients with RET fusion-positive tumors showed a significantly worse OS when compared with RET-negative ones (median OS 14.0 versus 38.0 months, HR: 4.59; 95% CI, 3.64-32.66; P < 0.001). In the multivariable model, RET rearrangements were still associated with shorter OS (HR: 2.97; 95% CI, 1.25-7.07; P = 0.014), while primary tumor location, RAS and BRAF mutations and MSI status were not. Conclusions Though very rare, RET rearrangements define a new subtype of mCRC that shows poor prognosis with conventional treatments and is therefore worth of a specific management.
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Affiliation(s)
- F Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
| | - F Di Nicolantonio
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A B Schrock
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - J Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - F Morano
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Fucà
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - P Nikolinakos
- Medical Oncology, University Cancer & Blood Center, Athens
| | - A Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - K Gowen
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - G M Frampton
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - P Gasparini
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - D Rossini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Gigliotti
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - S T Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - M Prisciandaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - J Hodgson
- Medical Oncology, University Cancer & Blood Center, Athens
| | - A Zaniboni
- Department of Medical Oncology, Fondazione Poliambulanza, Brescia, Italy
| | - V K Chiu
- Department of Internal Medicine, University of New Mexico, Albuquerque, USA
| | - M Milione
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - R Patel
- Department of Diagnostics, Ignyta, Inc., San Diego, USA
| | - V Miller
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - A Bardelli
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - L Novara
- ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - L Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, USA
| | - S M Pupa
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Sozzi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - J Ross
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - M Di Bartolomeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A Bertotti
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - S Ali
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - L Trusolino
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A Falcone
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - F de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Amatu A, Sartore-Bianchi A, Bencardino K, Pizzutilo EG, Tosi F, Siena S. Tropomyosin receptor kinase (TRK) biology and the role of NTRK gene fusions in cancer. Ann Oncol 2019; 30:viii5-viii15. [PMID: 31738427 PMCID: PMC6859819 DOI: 10.1093/annonc/mdz383] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The tropomyosin receptor kinase (TRK) family of receptor tyrosine kinases are encoded by NTRK genes and have a role in the development and normal functioning of the nervous system. Since the discovery of an oncogenic NTRK gene fusion in colorectal cancer in 1986, over 80 different fusion partner genes have been identified in a wide array of adult and paediatric tumours, providing actionable targets for targeted therapy. This review describes the normal function and physiology of TRK receptors and the biology behind NTRK gene fusions and how they act as oncogenic drivers in cancer. Finally, an overview of the incidence and prevalence of NTRK gene fusions in various types of cancers is discussed.
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Affiliation(s)
- A Amatu
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
| | - A Sartore-Bianchi
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
- Department of Oncology and Hemato- Oncology, Università degli Studi di Milano, Milan, Italy
| | - K Bencardino
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
| | - E G Pizzutilo
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
- Department of Oncology and Hemato- Oncology, Università degli Studi di Milano, Milan, Italy
| | - F Tosi
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
- Department of Oncology and Hemato- Oncology, Università degli Studi di Milano, Milan, Italy
| | - S Siena
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan
- Department of Oncology and Hemato- Oncology, Università degli Studi di Milano, Milan, Italy
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Pagani F, Randon G, Guarini V, Raimondi A, Prisciandaro M, Lobefaro R, Di Bartolomeo M, Sozzi G, de Braud F, Gasparini P, Pietrantonio F. The Landscape of Actionable Gene Fusions in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20215319. [PMID: 31731495 PMCID: PMC6861915 DOI: 10.3390/ijms20215319] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
The treatment scenario of metastatic colorectal cancer (mCRC) has been rapidly enriched with new chemotherapy combinations and biological agents that lead to a remarkable improvement in patients’ outcome. Kinase gene fusions account for less than 1% of mCRC overall but are enriched in patients with high microsatellite instability, RAS/BRAF wild-type colorectal cancer. mCRC patients harboring such alterations show a poor prognosis with standard treatments that could be reversed by adopting novel therapeutic strategies. Moving forward to a positive selection of mCRC patients suitable for targeted therapy in the era of personalized medicine, actionable gene fusions, although rare, represent a peculiar opportunity to disrupt a tumor alteration to achieve therapeutic goal. Here we summarize the current knowledge on potentially actionable gene fusions in colorectal cancer available from retrospective experiences and promising preliminary results of new basket trials.
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Affiliation(s)
- Filippo Pagani
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Giovanni Randon
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Vincenzo Guarini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Alessandra Raimondi
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Michele Prisciandaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Riccardo Lobefaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Maria Di Bartolomeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Gabriella Sozzi
- Unit of Molecular Cytogenetics, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milano, Italy; (G.S.); (P.G.)
| | - Filippo de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Patrizia Gasparini
- Unit of Molecular Cytogenetics, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milano, Italy; (G.S.); (P.G.)
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
- Correspondence:
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Takashima Y, Kawaguchi A, Yamanaka R. Promising Prognosis Marker Candidates on the Status of Epithelial-Mesenchymal Transition and Glioma Stem Cells in Glioblastoma. Cells 2019; 8:cells8111312. [PMID: 31653034 PMCID: PMC6912254 DOI: 10.3390/cells8111312] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022] Open
Abstract
Multivariable analyses of global expression profiling are valid indicators of the prognosis of various diseases including brain cancers. To identify the candidates for markers of prognosis of glioblastoma, we performed multivariable analyses on the status of epithelial (EPI)-mesenchymal (MES) transition (EMT), glioma (GLI) stem cells (GSCs), molecular target therapy (MTT), and potential glioma biomarkers (PGBs) using the expression data and clinical information from patients. Random forest survival and Cox proportional hazards regression analyses indicated significant variable values for DSG3, CLDN1, CDH11, FN1, HDAC3/7, PTEN, L1CAM, OLIG2, TIMP4, IGFBP2, and GFAP. The analyses also comprised prognosis prediction formulae that could distinguish between the survival curves of the glioblastoma patients. In addition to the genes mentioned above, HDAC1, FLT1, EGFR, MGMT, PGF, STAT3, SIRT1, and GADD45A constituted complex genetic interaction networks. The calculated status scores obtained by principal component analysis indicated that GLI genes covered the status of EPI, GSC, and MTT-related genes. Moreover, survival tree analyses indicated that MEShigh, MEShighGLIlow, GSChighGLIlow, MEShighMTTlow, and PGBhigh showed poor prognoses and MESmiddle, GSClow, and PGBlow showed good prognoses, suggesting that enhanced EMT and GSC are associated with poor survival and that lower expression of EPI markers and the pre-stages of EMT are relatively less malignant in glioblastoma. These results demonstrate that the assessment of EMT and GSC enables the prediction of the prognosis of glioblastoma that would help develop novel therapeutics and de novo marker candidates for the prognoses of glioblastoma.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan.
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
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50
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ANKRD26-RET - A novel gene fusion involving RET in papillary thyroid carcinoma. Cancer Genet 2019; 238:10-17. [DOI: 10.1016/j.cancergen.2019.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/13/2019] [Accepted: 07/01/2019] [Indexed: 12/14/2022]
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