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Singh M, Agarwal V, Pancham P, Jindal D, Agarwal S, Rai SN, Singh SK, Gupta V. A Comprehensive Review and Androgen Deprivation Therapy and Its Impact on Alzheimer's Disease Risk in Older Men with Prostate Cancer. Degener Neurol Neuromuscul Dis 2024; 14:33-46. [PMID: 38774717 PMCID: PMC11108066 DOI: 10.2147/dnnd.s445130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignancies affecting males worldwide. Despite reductions in mortality rates due to advances in early identification and treatment methods, PCa remains a major health concern. Recent research has shed light on a possible link between PCa and Alzheimer's disease (AD), which is a significant neurological ailment that affects older males all over the world. Androgen deprivation therapy (ADT), a cornerstone therapeutic method used in conjunction with radiation and palliative care in advanced metastatic PCa cases, is critical for disease management. Evidence reveals a relationship between ADT and cognitive impairment. Hormonal manipulation may cause long-term cognitive problems through processes such as amyloid beta (Aβ) aggregation and neurofibrillary tangles (NFTs). Fluctuations in basal androgen levels can upset the delicate balance of genes that are sensitive to androgen levels, contributing to cognitive impairment. This detailed review dives into the various aspects of PCa aetiology and its relationship with cognitive decline. It investigates the discovery of particular biomarkers, as well as microRNAs (miRNAs), which play important roles in pathogenic progression. The review attempts to identify potential biomarkers associated with ADT-induced cerebral changes, including Aβ oligomer buildup, NFT formation, and tauopathy, which can contribute to early-onset dementia and cognitive impairment. Besides it further aims to provide insights into innovative diagnostic and therapeutic avenues for alleviating PCa and ADT-related cognitive sequelae by unravelling these complicated pathways and molecular mechanisms.
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Affiliation(s)
- Manisha Singh
- Faculty of Health, Graduate School of Health, University of Technology Sydney, Sydney, Australia
- ARCCIM, School of Public Health, Faculty of Health, University of Technology Sydney, Sydney, Australia
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, Noida, Uttar Pradesh, India
| | - Vinayak Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, Noida, Uttar Pradesh, India
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Pranav Pancham
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, Noida, Uttar Pradesh, India
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Divya Jindal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, Noida, Uttar Pradesh, India
- Indian Institute of Technology Bombay Monash Research Academy, Mumbai, India
| | - Shriya Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, Noida, Uttar Pradesh, India
- Department of Molecular Science, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Sachchida Nand Rai
- Centre of Experimental Medicine and Surgery (CEMS), Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery (CEMS), Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Vivek Gupta
- Macquarie Medical School, Macquarie University, Sydney, Australia
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2
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Khan MS, Altwaijry N, Al-Bagmi MS, Alafaleq NO, Alokail MS, Shahwan M, Shamsi A. Structure-guided identification of potent inhibitors of ROS1 kinase for therapeutic development against non-small cell lung cancer. J Biomol Struct Dyn 2024; 42:3837-3847. [PMID: 37254309 DOI: 10.1080/07391102.2023.2217450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]
Abstract
Proto-oncogene tyrosine-protein kinase ROS (ROS1) is a member of the sevenless receptor, which affects epithelial cell differentiation and is highly expressed in a variety of tumor cells. The elevated expression and dysfunction of ROS1 have been involved in various malignancies, such as non-small cell lung cancer (NSCLC), stomach cancer, ovarian, breast cancer, cholangiocarcinoma, colorectal cancer, adenosarcoma, oesophageal cancer, etc. ROS1 has been postulated as a potential drug target in anticancer therapeutics. In this study, we carried out a virtual screening of phytochemicals against ROS1 to identify its potential inhibitors. The virtual screening process was performed on the ROS1 structure, where two phytochemicals, Helioscopinolide C and Taiwanin C, were identified. These compounds resulted from filters like Lipinski rule of five, PAINS filter, binding affinities values, and all-atom molecular dynamics (MD) simulations followed by principal component analysis (PCA) and essential dynamics. The findings of this study highlight the role of ROS1 in multiple physiological candidates and its therapeutic targeting using phytochemicals. This study suggests Helioscopinolide C and Taiwanin C as potential compounds for therapeutic development targeting ROS1-associated non-small cell lung cancer for clinical applications. Further in vitro and in vivo experiments are required to validate these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Nojood Altwaijry
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Moneera Saud Al-Bagmi
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Nouf Omar Alafaleq
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Majed S Alokail
- Department of Biochemistry, College of Science, King Saud University, KSA, Riyadh, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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3
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Al Assaad M, Michaud O, Semaan A, Sigouros M, Tranquille M, Phan A, Levine MF, Gundem G, Medina-Martínez JS, Papaemmanuil E, Manohar J, Wilkes D, Sboner A, Hoda SAF, Elemento O, Mosquera JM. Whole-Genome Sequencing Analysis of Male Breast Cancer Unveils Novel Structural Events and Potential Therapeutic Targets. Mod Pathol 2024; 37:100452. [PMID: 38369186 DOI: 10.1016/j.modpat.2024.100452] [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: 11/30/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly because of its low incidence rate, accounting for only 0.5% to 1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of 10 MaBC cases (n = 10) were delineated and correlated with clinical and histopathologic characteristics. Using fluorescence in situ hybridization, an additional cohort of 18 patients was interrogated to supplement WGS findings. The genomic landscape of MaBC uncovered significant genetic alterations that could influence diagnosis and treatment. We found common somatic mutations in key driver genes, such as FAT1, GATA3, SMARCA4, and ARID2. Our study also mapped out structural variants that impact cancer-associated genes, such as ARID1A, ESR1, GATA3, NTRK1, and NF1. Using a WGS-based classifier, homologous recombination deficiency (HRD) was identified in 2 cases, both presenting with deleterious variants in BRCA2. Noteworthy was the observation of FGFR1 amplification in 21% of cases. Altogether, we identified at least 1 potential therapeutic target in 8 of the 10 cases, including high tumor mutational burden, FGFR1 amplification, and HRD. Our study is the first WGS characterization of MaBC, which uncovered potentially relevant variants, including structural events in cancer genes, HRD signatures, and germline pathogenic mutations. Our results demonstrate unique genetic markers and potential treatment targets in MaBC, thereby underlining the necessity of tailoring treatment strategies for this understudied patient population. These WGS-based findings add to the growing knowledge of MaBC genomics and highlight the need to expand research on this type of cancer.
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Affiliation(s)
- Majd Al Assaad
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Michaud
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Département de Pathologie, Université Laval, Quebec City, Quebec, Canada
| | - Alissa Semaan
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Marvel Tranquille
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andy Phan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | | | | | | | | | - Jyothi Manohar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - David Wilkes
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Syed A F Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York; New York Genome Center, New York, New York.
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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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MacKeracher A, Arnoldo A, Siddaway R, Surrey LF, Somers GR. The Incidence of Multiple Fusions in a Series of Pediatric Soft Tissue and Bone Tumors. Pediatr Dev Pathol 2024; 27:3-12. [PMID: 37771132 PMCID: PMC10800079 DOI: 10.1177/10935266231199928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) has increased the detection of fusion genes in cancer. NGS has found multiple fusions in single tumor samples; however, the incidence of this in pediatric soft tissue and bone tumors (PSTBTs) is not well documented. The aim of this study is to catalogue the incidence of multiple fusions in a series of PSTBTs, and apply a modified gene fusion classification system to determine clinical relevance. METHODOLOGY RNA from 78 bone and soft tissue tumors and 7 external quality assessment samples were sequenced and analyzed using recently-described Metafusion (MF) software and classified using a modification of previously-published schema for fusion classification into 3 tiers: 1, strong clinical significance; 2, potential clinical significance; and 3, unknown clinical significance. RESULTS One-hundred forty-five fusions were detected in 85 samples. Fifty-five samples (65%) had a single fusion and 30 (35%) had more than 1 fusion. No samples contained more than 1 tier 1 fusion. There were 40 tier 1 (28%), 36 tier 2 (24%), and 69 (48%) tier 3 fusions. CONCLUSIONS A significant percentage of PSTBTs harbor more than 1 fusion, and by applying a modified fusion classification scheme, the potential clinical relevance of such fusions can be determined.
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Affiliation(s)
- Anastasia MacKeracher
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony Arnoldo
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Robert Siddaway
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Lea F. Surrey
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Gino R. Somers
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Xiang Y, Liu X, Sun Q, Liao K, Liu X, Zhao Z, Feng L, Liu Y, Wang B. The development of cancers research based on mitochondrial heat shock protein 90. Front Oncol 2023; 13:1296456. [PMID: 38098505 PMCID: PMC10720920 DOI: 10.3389/fonc.2023.1296456] [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: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondrial heat shock protein 90 (mtHsp90), including Tumor necrosis factor receptor-associated protein 1 (TRAP1) and Hsp90 translocated from cytoplasm, modulating cellular metabolism and signaling pathways by altering the conformation, activity, and stability of numerous client proteins, and is highly expressed in tumors. mtHsp90 inhibition results in the destabilization and eventual degradation of its client proteins, leading to interference with various tumor-related pathways and efficient control of cancer cell development. Among these compounds, gamitrinib, a specific mtHsp90 inhibitor, has demonstrated its safety and efficacy in several preclinical investigations and is currently undergoing evaluation in clinical trials. This review aims to provide a comprehensive overview of the present knowledge pertaining to mtHsp90, encompassing its structure and function. Moreover, our main emphasis is on the development of mtHsp90 inhibitors for various cancer therapies, to present a thorough overview of the recent pre-clinical and clinical advancements in this field.
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Affiliation(s)
- Yuchu Xiang
- West China Hospital of Sichuan University, Sichuan University, Chengdu, China
| | - Xudong Liu
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Qi Sun
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, Centre for Safe Medication Practice and Research, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaohan Liu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Zihui Zhao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lishuang Feng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yan Liu
- Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Bo Wang
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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Chen C, Qin F, Singh S, Tang Y, Li H. CTNNBIP1-CLSTN1 functions as a housekeeping chimeric RNA and regulates cell proliferation through SERPINE2. Cell Death Discov 2023; 9:369. [PMID: 37805599 PMCID: PMC10560238 DOI: 10.1038/s41420-023-01668-8] [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: 07/06/2023] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
The conventional understanding that chimeric RNAs are unique to carcinoma and are the products of chromosomal rearrangement is being challenged. However, experimental evidence supporting the function of chimeric RNAs in normal physiology is scarce. We decided to focus on one particular chimeric RNA, CTNNBIP1-CLSTN1. We examined its expression in various tissues and cell types and compared it quantitatively among cancer and noncancer cells. We further investigated its role in a panel of noncancer cells and investigated the functional mechanism. We found that this fusion transcript is expressed in almost all tissues and a wide range of cell types, including fibroblasts, epithelial cells, stem cells, vascular endothelial cells, and hepatocytes. In addition, the CTNNBIP1-CLSTN1 expression level in noncancerous cell lines was not evidently different from that in cancer cell lines. Furthermore, in at least three cell types, silencing CTNNBIP1-CLSTN1 significantly reduced the cell proliferation rate by inducing G2/M arrest and apoptosis. Importantly, rescue experiments confirmed that cell cycle arrest was restored by exogenous expression of the chimera but not the wild-type parental gene. Further evidence is provided that CTNNBIP1-CLSTN1 regulates cell proliferation through SERPINE2. Thus, CTNNBIP1-CLSTN1 is an example of a new class of fusion RNAs, dubbed "housekeeping chimeric RNAs".
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Affiliation(s)
- Chen Chen
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Department of Clinical Laboratory, Qilu Hospital of Shandong University Dezhou Hospital, Dezhou, 253000, Shandong, China
| | - Fujun Qin
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
- ICMR-Center for Research, Management and Control of Haemoglobinopathies (Unit of ICMR-National Institute of Immunohaematology, Mumbai), Chandrapur, Maharashtra, 442406, India
| | - Yue Tang
- School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
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Rafikova G, Gilyazova I, Enikeeva K, Pavlov V, Kzhyshkowska J. Prostate Cancer: Genetics, Epigenetics and the Need for Immunological Biomarkers. Int J Mol Sci 2023; 24:12797. [PMID: 37628978 PMCID: PMC10454494 DOI: 10.3390/ijms241612797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Epidemiological data highlight prostate cancer as a significant global health issue, with high incidence and substantial impact on patients' quality of life. The prevalence of this disease is associated with various factors, including age, heredity, and race. Recent research in prostate cancer genetics has identified several genetic variants that may be associated with an increased risk of developing the disease. However, despite the significance of these findings, genetic markers for prostate cancer are not currently utilized in clinical practice as reliable indicators of the disease. In addition to genetics, epigenetic alterations also play a crucial role in prostate cancer development. Aberrant DNA methylation, changes in chromatin structure, and microRNA (miRNA) expression are major epigenetic events that influence oncogenesis. Existing markers for prostate cancer, such as prostate-specific antigen (PSA), have limitations in terms of sensitivity and specificity. The cost of testing, follow-up procedures, and treatment for false-positive results and overdiagnosis contributes to the overall healthcare expenditure. Improving the effectiveness of prostate cancer diagnosis and prognosis requires either narrowing the risk group by identifying new genetic factors or enhancing the sensitivity and specificity of existing markers. Immunological biomarkers (both circulating and intra-tumoral), including markers of immune response and immune dysfunction, represent a potentially useful area of research for enhancing the diagnosis and prognosis of prostate cancer. Our review emphasizes the need for developing novel immunological biomarkers to improve the diagnosis, prognosis, and management of prostate cancer. We highlight the most recent achievements in the identification of biomarkers provided by circulating monocytes and tumor-associated macrophages (TAMs). We highlight that monocyte-derived and TAM-derived biomarkers can enable to establish the missing links between genetic predisposition, hormonal metabolism and immune responses in prostate cancer.
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Affiliation(s)
- Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450077 Ufa, Russia (K.E.); (V.P.)
| | - Irina Gilyazova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450077 Ufa, Russia (K.E.); (V.P.)
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450077 Ufa, Russia (K.E.); (V.P.)
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450077 Ufa, Russia (K.E.); (V.P.)
| | - Julia Kzhyshkowska
- Laboratory for Translational Cellular and Molecular Biomedicine, Tomsk State University, 634050 Tomsk, Russia
- Genetic Technology Laboratory, Siberian State Medical University, 634050 Tomsk, Russia
- Institute of Transfusion Medicine and Immunology, Mannheim Institute of Innate Immunosciences (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg—Hessen, 68167 Mannheim, Germany
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Salokas K, Dashi G, Varjosalo M. Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies. Cancers (Basel) 2023; 15:3678. [PMID: 37509339 PMCID: PMC10377698 DOI: 10.3390/cancers15143678] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Cancer-associated gene fusions, also known as oncofusions, have emerged as influential drivers of oncogenesis across a diverse range of cancer types. These genetic events occur via chromosomal translocations, deletions, and inversions, leading to the fusion of previously separate genes. Due to the drastic nature of these mutations, they often result in profound alterations of cellular behavior. The identification of oncofusions has revolutionized cancer research, with advancements in sequencing technologies facilitating the discovery of novel fusion events at an accelerated pace. Oncofusions exert their effects through the manipulation of critical cellular signaling pathways that regulate processes such as proliferation, differentiation, and survival. Extensive investigations have been conducted to understand the roles of oncofusions in solid tumors, leukemias, and lymphomas. Large-scale initiatives, including the Cancer Genome Atlas, have played a pivotal role in unraveling the landscape of oncofusions by characterizing a vast number of cancer samples across different tumor types. While validating the functional relevance of oncofusions remains a challenge, even non-driver mutations can hold significance in cancer treatment. Oncofusions have demonstrated potential value in the context of immunotherapy through the production of neoantigens. Their clinical importance has been observed in both treatment and diagnostic settings, with specific fusion events serving as therapeutic targets or diagnostic markers. However, despite the progress made, there is still considerable untapped potential within the field of oncofusions. Further research and validation efforts are necessary to understand their effects on a functional basis and to exploit the new targeted treatment avenues offered by oncofusions. Through further functional and clinical studies, oncofusions will enable the advancement of precision medicine and the drive towards more effective and specific treatments for cancer patients.
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Affiliation(s)
- Kari Salokas
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
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10
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Li H, Chen C, Tang Y, Qin F, Singh S. CTNNBIP1-CLSTN1 Functions as a Housekeeping Chimeric RNA, and Regulates Cell Proliferation through SERPINE2. RESEARCH SQUARE 2023:rs.3.rs-3112431. [PMID: 37503100 PMCID: PMC10371161 DOI: 10.21203/rs.3.rs-3112431/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The conventional wisdom that chimeric RNAs being peculiarity of carcinoma, and the products of chromosomal rearrangement is being challenged, However, experimental evidence supporting chimeric RNAs in normal physiology being functional is scarce. We decided to focus on one particular chimeric RNA, CTNNBIP1-CLSTN1 . We examined its expression among various tissues and cell types, and compared quantitatively among cancer and non-cancer cells. We further investigated its role in a panel of non-cancer cells and probed the functional mechanism. We found that this fusion transcript is expressed in almost all tissues, and a wide range of cell types including fibroblasts, epithelial, stem, vascular endothelial cells, and hepatocytes. The expression level in non-cancerous cell lines is also not evidently different from that in the cancer cell lines. Furthermore, silencing CTNNBIP1-CLSTN1 significantly reduces cell proliferation rate, by inducing G2/M arrest in cell cycle progress and apoptosis in at least three cell types. Importantly, rescue experiments confirmed that the cell cycle arrest can be regained by exogenous expression of the chimera, but not the wild type parental gene. Further evidence is provided that CTNNBIP1-CLSTN1 regulates cell proliferation through SERPINE2 . Thus, CTNNBIP1-CLSTN1 represents an example of a new class of fusion RNA, dubbed "housekeeping chimeric RNAs".
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11
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Zhu Y, Wu W, Qiao L, Ji J, Duan L, Gong L, Ren D, Li F, Wei L, Pan K. The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric cancer with MSS. BMC Gastroenterol 2023; 23:153. [PMID: 37189078 DOI: 10.1186/s12876-023-02765-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is maturely applied for gene fusion detection. Although tumor fusion burden (TFB) has been identified as an immune marker for cancer, the relationship between these fusions and the immunogenicity and molecular characteristics of gastric cancer (GC) patients remains unclear. GCs have different clinical significance depending on their subtypes, and thus, this study aimed to investigate the characteristics and clinical relevance of TFB in non-Epstein-Barr-virus-positive (EBV+) GC with microsatellite stability (MSS). METHODS A total of 319 GC patients from The Cancer Genome Atlas stomach adenocarcinoma (TCGA-STAD) and a cohort of 45-case from ENA (PRJEB25780) were included. The cohort characteristics and distribution of TFB among the patients were analyzed. Additionally, the correlations of TFB with mutation characteristics, pathway differences, relative abundance of immune cells, and prognosis were examined in the TCGA-STAD cohort of MSS and non-EBV (+) patients. RESULTS We observed that in the MSS and non-EBV (+) cohort, the TFB-low group exhibited significantly lower gene mutation frequency, gene copy number, loss of heterozygosity score, and tumor mutation burden than in the TFB-high group. Additionally, the TFB-low group exhibited a higher abundance of immune cells. Furthermore, the immune gene signatures were significantly upregulated in the TFB-low group, 2-year disease-specific survival was markedly increased in the TFB-low group compared with to the TFB-high group. The rates of TFB-low cases were significantly higher TFB-than high cases in durable clinical benefit (DCB) and response groups with pembrolizumab treatment. Low TFB may serve as a predictor of GC prognosis, and the TFB-low group exhibits higher immunogenicity. CONCLUSION In conclusion, this study reveals that the TFB-based classification of GC patient may be instructive for individualized immunotherapy regimens.
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Affiliation(s)
- Yongjun Zhu
- Department of Gastrointestinal surgery, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Weixin Wu
- Department of Oncology, Zhongshan Hospital affiliated to Xiamen University, Xiamen, 361004, China
| | - Liangliang Qiao
- Oncology Department I, Jinshazhou Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China
| | - Jingfen Ji
- Department of General Surgery, The Second Xiangya Hospital of Central South University, 410011, Changsha, China
| | - Lunxi Duan
- Department of General Surgery, The Second Xiangya Hospital of Central South University, 410011, Changsha, China
| | - Longlong Gong
- Department of Medicine, Genecast Biotechnology Co., Ltd, 214000, Wuxi, China
| | - Dandan Ren
- Department of Medicine, Genecast Biotechnology Co., Ltd, 214000, Wuxi, China
| | - Feifei Li
- Department of Medicine, Genecast Biotechnology Co., Ltd, 214000, Wuxi, China
| | - Lihui Wei
- Department of Medicine, Genecast Biotechnology Co., Ltd, 214000, Wuxi, China.
| | - Ke Pan
- Department of General Surgery, The Second Xiangya Hospital of Central South University, 410011, Changsha, China.
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12
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Spencer KR, Portal DE, Aisner J, Stein MN, Malhotra J, Shih W, Chan N, Silk AW, Ganesan S, Goodin S, Gounder M, Lin H, Li J, Cerchio R, Marinaro C, Chen S, Mehnert JM. A phase I trial of riluzole and sorafenib in patients with advanced solid tumors: CTEP #8850. Oncotarget 2023; 14:302-315. [PMID: 37036756 PMCID: PMC10085060 DOI: 10.18632/oncotarget.28403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/21/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Overexpression of metabotropic glutamate receptor 1 (GRM1) has been implicated in the pathogenesis of multiple cancers. Riluzole, an inhibitor of glutamate release, showed synergistic antitumor activity in combination with the multi-kinase inhibitor sorafenib in preclinical models. This phase I trial identified the toxicity profile, dose-limiting toxicities, maximum tolerated dose (MTD), and pharmacokinetic and pharmacodynamic properties of riluzole combined with sorafenib in patients with advanced cancers. PATIENTS AND METHODS Patients with refractory solid tumors were enrolled utilizing a 3+3 dose-escalation design. Riluzole was given at 100 mg PO BID in combination with sorafenib, beginning at 200 mg PO daily and escalating in 200 mg increments per level in 28-day cycles. Restaging evaluations were performed every 2 cycles. RESULTS 35 patients were enrolled over 4 dose levels. The MTD was declared at dose level 3 (riluzole: 100 mg PO BID; sorafenib: 400 mg AM/200 mg PM). Pharmacokinetic analyses did not reveal definitive evidence of drug-drug interactions. Consistent decreases in phospho-forms of ERK and AKT in tumor tissue analyses with accompanying decrease in GRM1 expression and increase in pro-apoptotic BIM suggest target engagement by the combination. Best responses included a partial response in 1 (2.9%) patient with pancreatic acinar cell carcinoma with a KANK4-RAF1 fusion, and stable disease in 11 (36%) patients. CONCLUSION Combination therapy with riluzole and sorafenib was safe and tolerable in patients with advanced solid tumors. The partial response in a patient with a RAF1 fusion suggests that further exploration in a genomically selected cohort may be warranted.
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Affiliation(s)
- Kristen R. Spencer
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Daniella E. Portal
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph Aisner
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Mark N. Stein
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Jyoti Malhotra
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Weichung Shih
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Biostatistics, School of Public Health, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Nancy Chan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Ann W. Silk
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Susan Goodin
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Murugesan Gounder
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hongxia Lin
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Jiadong Li
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Robert Cerchio
- Susan Lehman Cullman Laboratory for Cancer Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christina Marinaro
- Susan Lehman Cullman Laboratory for Cancer Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Suzie Chen
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- Susan Lehman Cullman Laboratory for Cancer Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Janice M. Mehnert
- Department of Medicine, New York University Grossman School of Medicine, Perlmutter Cancer Center of NYU Langone Health, NY 10016, USA
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13
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Jain P, Iyer S, Straka J, Surrey LF, Pogoriler J, Han H, Smith T, Busch C, Fox E, Li M, Waanders AJ, Resnick A, Davare MA. Discovery and functional characterization of the oncogenicity and targetability of a novel NOTCH1-ROS1 gene fusion in pediatric angiosarcoma. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006222. [PMID: 36307212 PMCID: PMC9632357 DOI: 10.1101/mcs.a006222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
Angiosarcomas are rare, malignant soft tissue tumors in children that arise in a wide range of anatomical locations and have limited targeted therapies available. Here, we report a rare case of a pediatric angiosarcoma (pAS) with Li-Fraumeni syndrome (LFS) expressing a novel NOTCH1-ROS1 gene fusion. Although both NOTCH1 and ROS1 are established proto-oncogenes, our study is the first to describe the mechanistic role of NOTCH1-ROS1 fusion arising via intrachromosomal rearrangement. NOTCH1-ROS1 displayed potent neoplastic transformation propensity in vitro, and harbors tumorigenic potential in vivo, where it induced oncogenic activation of the MAPK, PI3K/mTOR, and JAK-STAT signaling pathways in a murine allograft model. We found an unexpected contribution of the NOTCH1 extracellular region in mediating NOTCH1-ROS1 activation and oncogenic function, highlighting the contribution of both NOTCH1 and ROS1 fusion partners in driving tumorigenicity. Interestingly, neither membrane localization nor fusion protein dimerization were found to be essential for NOTCH1-ROS1 fusion oncogenicity. To target NOTCH1-ROS1-driven tumors, we tested both NOTCH1-directed inhibitors and ROS1-targeted tyrosine kinase inhibitors (TKI) in heterologous models (NIH3T3, Ba/F3). Although NOTCH1 inhibitors did not suppress NOTCH1-ROS1-driven oncogenic growth, we found that oral entrectinib treatment effectively suppressed the growth of NOTCH-ROS1-driven tumors. Taken together, we report the first known pAS case with a novel NOTCH1-ROS1 alteration along with a detailed report on the function and therapeutic targeting of NOTCH1-ROS1. Our study highlights the importance of genomic profiling of rare cancers such as pAS to reveal actionable drivers and improve patient outcomes.
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Affiliation(s)
- Payal Jain
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sudarshan Iyer
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon 97239, USA
| | - Joshua Straka
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lea F. Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jennifer Pogoriler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Harry Han
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Tiffany Smith
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Christine Busch
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth Fox
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Angela J. Waanders
- Department of Pediatrics, Feinberg School of Medicine Northwestern University, Chicago, Illinois 60611, USA;,Division of Hematology, Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Monika A. Davare
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon 97239, USA
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14
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Kim M, Seo AN. Molecular Pathology of Gastric Cancer. J Gastric Cancer 2022; 22:273-305. [PMID: 36316106 PMCID: PMC9633931 DOI: 10.5230/jgc.2022.22.e35] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/10/2022] [Indexed: 08/29/2023] Open
Abstract
Gastric cancer (GC) is one of the most common lethal malignant neoplasms worldwide, with limited treatment options for both locally advanced and/or metastatic conditions, resulting in a dismal prognosis. Although the widely used morphological classifications may be helpful for endoscopic or surgical treatment choices, they are still insufficient to guide precise and/or personalized therapy for individual patients. Recent advances in genomic technology and high-throughput analysis may improve the understanding of molecular pathways associated with GC pathogenesis and aid in the classification of GC at the molecular level. Advances in next-generation sequencing have enabled the identification of several genetic alterations through single experiments. Thus, understanding the driver alterations involved in gastric carcinogenesis has become increasingly important because it can aid in the discovery of potential biomarkers and therapeutic targets. In this article, we review the molecular classifications of GC, focusing on The Cancer Genome Atlas (TCGA) classification. We further describe the currently available biomarker-targeted therapies and potential biomarker-guided therapies. This review will help clinicians by providing an inclusive understanding of the molecular pathology of GC and may assist in selecting the best treatment approaches for patients with GC.
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Affiliation(s)
- Moonsik Kim
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - An Na Seo
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Korea.
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15
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Velaga R, Koo KM, Mainwaring PN. Harnessing gene fusion-derived neoantigens for 'cold' breast and prostate tumor immunotherapy. Immunotherapy 2022; 14:1165-1179. [PMID: 36043380 DOI: 10.2217/imt-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Breast and prostate cancers are generally considered immunologically 'cold' tumors due to multiple mechanisms rendering them unresponsive to immune checkpoint blockade therapies. With little success in garnering positive outcomes in modern immunotherapeutic clinical trials, it is prudent to re-examine the role of immunogenic neoantigens in these cold tumors. Gene fusions are driver mutations in hormone-driven cancers that can result in alternative mutation-specific neoantigens to promote immunotherapy sensitivity. This review focuses on 1) gene fusion formation mechanisms in neoantigen generation; 2) gene fusion neoantigens in cancer immunotherapeutic strategies and associated clinical trials; and 3) challenges and opportunities in computational and liquid biopsy technologies. This review is anticipated to initiate further research into gene fusion neoantigens of cold tumors for further experimental validation.
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Affiliation(s)
- Ravi Velaga
- Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kevin M Koo
- XING Technologies Pty Ltd, Brisbane, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD 4029, Australia
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16
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Zhou M, Ko M, Hoge AC, Luu K, Liu Y, Russell ML, Hannon WW, Zhang Z, Carrot-Zhang J, Beroukhim R, Van Allen EM, Choudhury AD, Nelson PS, Freedman M, Taplin ME, Meyerson M, Viswanathan SR, Ha G. Patterns of structural variation define prostate cancer across disease states. JCI Insight 2022; 7:161370. [PMID: 35943799 PMCID: PMC9536266 DOI: 10.1172/jci.insight.161370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
The complex genomic landscape of prostate cancer evolves across disease states under therapeutic pressure directed toward inhibiting androgen receptor (AR) signaling. While significantly altered genes in prostate cancer have been extensively defined, there have been fewer systematic analyses of how structural variation shapes the genomic landscape of this disease across disease states. We uniformly characterized structural alterations across 531 localized and 143 metastatic prostate cancers profiled by whole genome sequencing, 125 metastatic samples of which were also profiled via whole transcriptome sequencing. We observed distinct significantly recurrent breakpoints in localized and metastatic castration-resistant prostate cancers (mCRPC), with pervasive alterations in noncoding regions flanking the AR, MYC, FOXA1, and LSAMP genes enriched in mCRPC and TMPRSS2-ERG rearrangements enriched in localized prostate cancer. We defined 9 subclasses of mCRPC based on signatures of structural variation, each associated with distinct genetic features and clinical outcomes. Our results comprehensively define patterns of structural variation in prostate cancer and identify clinically actionable subgroups based on whole genome profiling.
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Affiliation(s)
- Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Minjeong Ko
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Anna Ch Hoge
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Kelsey Luu
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Yuzhen Liu
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Magdalena L Russell
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - William W Hannon
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Zhenwei Zhang
- Department of Pathology, University of Massachusetts Medical School, Worchester, United States of America
| | - Jian Carrot-Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Peter S Nelson
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana Faber Cancer Institute, Boston, United States of America
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States of America
| | - Gavin Ha
- Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, United States of America
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17
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Dathathri E, Isebia KT, Abali F, Lolkema MP, Martens JWM, Terstappen LWMM, Bansal R. Liquid Biopsy Based Circulating Biomarkers in Metastatic Prostate Cancer. Front Oncol 2022; 12:863472. [PMID: 35669415 PMCID: PMC9165750 DOI: 10.3389/fonc.2022.863472] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer is the most dominant male malignancy worldwide. The clinical presentation of prostate cancer ranges from localized indolent to rapidly progressing lethal metastatic disease. Despite a decline in death rate over the past years, with the advent of early diagnosis and new treatment options, challenges remain towards the management of metastatic prostate cancer, particularly metastatic castration sensitive prostate cancer (mCSPC) and castration resistant prostate cancer (mCRPC). Current treatments involve a combination of chemotherapy with androgen deprivation therapy and/or androgen receptor signalling inhibitors. However, treatment outcomes are heterogeneous due to significant tumor heterogeneity indicating a need for better prognostic biomarkers to identify patients with poor outcomes. Liquid biopsy has opened a plethora of opportunities from early diagnosis to (personalized) therapeutic disease interventions. In this review, we first provide recent insights about (metastatic) prostate cancer and its current treatment landscape. We highlight recent studies involving various circulating biomarkers such as circulating tumor cells, genetic markers, circulating nucleic acids, extracellular vesicles, tumor-educated platelets, and the secretome from (circulating) tumor cells and tumor microenvironment in metastatic prostate cancer. The comprehensive array of biomarkers can provide a powerful approach to understanding the spectrum of prostate cancer disease and guide in developing improved and personalized treatments for patients.
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Affiliation(s)
- Eshwari Dathathri
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Khrystany T. Isebia
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Fikri Abali
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Martijn P. Lolkema
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - John W. M. Martens
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Ruchi Bansal
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
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18
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Williams G, Llewelyn A, Thatcher R, Hardisty KM, Loddo M. Utilisation of semiconductor sequencing for the detection of predictive biomarkers in glioblastoma. PLoS One 2022; 17:e0245817. [PMID: 35324914 PMCID: PMC8947072 DOI: 10.1371/journal.pone.0245817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
The standard treatment for glioblastoma involves a combination of surgery, radiation and chemotherapy but have limited impact on survival. The exponential increase in targeted agents directed at pivotal oncogenic pathways now provide new therapeutic opportunities for this tumour type. However, lack of comprehensive precision oncology testing at diagnosis means such therapeutic opportunities are potentially overlooked. To investigate the role of semiconductor sequencing for detection of predictive biomarkers in routine glioblastoma samples we have undertaken analysis of test trending data generated by a clinically validated next generation sequencing platform designed to capture actionable genomic variants distributed across 505 genes. Analysis was performed across a cohort of 55 glioblastoma patients. Analysis of trending data has revealed a complex and rich actionable mutational landscape in which 166 actionable mutations were detected across 36 genes linked to 17 off label targeted therapy protocols and 111 clinical trials. The majority of patients harboured three or more actionable mutations affecting key cancer related regulatory networks including the PI3K/AKT/MTOR and RAS/RAF/MEK/MAPK signalling pathways, DNA-damage repair pathways and cell cycle checkpoints. Linkage with immunotherapy and PARP inhibitors was identified in 44% of glioblastoma patients as a consequence of alterations in DNA-damage repair genes. Taken together our data indicates that precision oncology testing utilising semiconductor sequencing can be used to identify a broad therapeutic armamentarium of targeted therapies and immunotherapies that can be potentially employed for the improved clinical management of glioblastoma patients.
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Affiliation(s)
- Gareth Williams
- Oncologica UK Ltd, Cambridge, United Kingdom
- * E-mail: (GW); (ML)
| | | | | | | | - Marco Loddo
- Oncologica UK Ltd, Cambridge, United Kingdom
- * E-mail: (GW); (ML)
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19
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Darabi S, Elliott A, Braxton DR, Zeng J, Hodges K, Poorman K, Swensen J, Shanthappa BU, Hinton JP, Gibney GT, Moser J, Phung T, Atkins MB, In GK, Korn WM, Eisenberg BL, Demeure MJ. Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions. Cancers (Basel) 2022; 14:cancers14061505. [PMID: 35326655 PMCID: PMC8946593 DOI: 10.3390/cancers14061505] [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: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Malignant melanoma is a complex disease that is estimated to claim over 7000 lives in the United States in 2021. Although recent advances in genomic technology have helped with the identification of driver variants, molecular studies and clinical trials have often focused on prevalent alterations, such as the BRAF-V600E mutation. With the inclusion of whole transcriptome sequencing, molecular profiling of melanomas has identified gene fusions and revealed gene expression profiles that are consistent with the activation of signaling pathways by common driver mutations. Patients harboring such fusions may benefit from currently approved targeted therapies and should be considered in the design of future clinical trials to further personalize treatments for patients with malignant melanoma. Abstract Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.
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Affiliation(s)
- Sourat Darabi
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Correspondence:
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - David R. Braxton
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
| | - Jia Zeng
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kurt Hodges
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kelsey Poorman
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Jeff Swensen
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Basavaraja U. Shanthappa
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - James P. Hinton
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Geoffrey T. Gibney
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Justin Moser
- Honor Health Research Institute, Scottsdale, AZ 85258, USA;
| | - Thuy Phung
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA;
| | - Michael B. Atkins
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Gino K. In
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Wolfgang M. Korn
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Burton L. Eisenberg
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Michael J. Demeure
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Translational Genomics Research Institution, Phoenix, AZ 85004, USA
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20
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Scott MA, Woolums AR, Swiderski CE, Thompson AC, Perkins AD, Nanduri B, Karisch BB, Goehl DR. Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle. BMC Vet Res 2022; 18:77. [PMID: 35197051 PMCID: PMC8864212 DOI: 10.1186/s12917-022-03178-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/17/2022] [Indexed: 01/21/2023] Open
Abstract
Background Transcriptomics has identified at-arrival differentially expressed genes associated with bovine respiratory disease (BRD) development; however, their use as prediction molecules necessitates further evaluation. Therefore, we aimed to selectively analyze and corroborate at-arrival mRNA expression from multiple independent populations of beef cattle. In a nested case-control study, we evaluated the expression of 56 mRNA molecules from at-arrival blood samples of 234 cattle across seven populations via NanoString nCounter gene expression profiling. Analysis of mRNA was performed with nSolver Advanced Analysis software (p < 0.05), comparing cattle groups based on the diagnosis of clinical BRD within 28 days of facility arrival (n = 115 Healthy; n = 119 BRD); BRD was further stratified for severity based on frequency of treatment and/or mortality (Treated_1, n = 89; Treated_2+, n = 30). Gene expression homogeneity of variance, receiver operator characteristic (ROC) curve, and decision tree analyses were performed between severity cohorts. Results Increased expression of mRNAs involved in specialized pro-resolving mediator synthesis (ALOX15, HPGD), leukocyte differentiation (LOC100297044, GCSAML, KLF17), and antimicrobial peptide production (CATHL3, GZMB, LTF) were identified in Healthy cattle. BRD cattle possessed increased expression of CFB, and mRNA related to granulocytic processes (DSG1, LRG1, MCF2L) and type-I interferon activity (HERC6, IFI6, ISG15, MX1). Healthy and Treated_1 cattle were similar in terms of gene expression, while Treated_2+ cattle were the most distinct. ROC cutoffs were used to generate an at-arrival treatment decision tree, which classified 90% of Treated_2+ individuals. Conclusions Increased expression of complement factor B, pro-inflammatory, and type I interferon-associated mRNA hallmark the at-arrival expression patterns of cattle that develop severe clinical BRD. Here, we corroborate at-arrival mRNA markers identified in previous transcriptome studies and generate a prediction model to be evaluated in future studies. Further research is necessary to evaluate these expression patterns in a prospective manner. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03178-8.
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Affiliation(s)
- Matthew A Scott
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, 79015, USA.
| | - Amelia R Woolums
- Department of Pathobiology and Population Medicine, Mississippi State University, Starkville, MS, 39762, USA
| | - Cyprianna E Swiderski
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Alexis C Thompson
- Department of Pathobiology and Population Medicine, Mississippi State University, Starkville, MS, 39762, USA
| | - Andy D Perkins
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, 39762, USA
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Brandi B Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Dan R Goehl
- Professional Beef Services, LLC, Canton, MO, 63435, USA
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21
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-Associated Carcinomas of the Breast: Diagnostic, Prognostic, and Therapeutic Significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent break-through cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include 1) ESR1-CCDC170 gene fusions in luminal B and endocrine resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC complex, 2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent ER transcriptional activity, 3) BCL2L14-ETV6 fusions in a more aggressive form of the triple negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, 4) the ETV6-NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, 5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB pathway, and 6) the NOTCH/MAST kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients that require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and on-going mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion positive disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan E Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA.,Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
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22
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Capone I, Bozzi F, Dagrada GP, Verderio P, Conca E, Busico A, Testi MA, Monti V, Duca M, Proto C, Damian S, Piccolo A, Perrone F, Tamborini E, Devecchi A, Collini P, Lorenzini D, Vingiani A, Agnelli L, Pruneri G. Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:582-597. [PMCID: PMC9630092 DOI: 10.37349/etat.2022.00102] [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: 04/29/2022] [Accepted: 08/02/2022] [Indexed: 11/07/2022] Open
Abstract
Aim: Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. The present study is aimed at assessing the overall accuracy of RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world diagnostics. Methods: Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex© Solid tumor kit through the manufacturer’s pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)]. Results: The combination of FusionPlex© Solid tumor with ArcherDX® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens. Conclusions: Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.
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Affiliation(s)
- Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Fabio Bozzi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Gian Paolo Dagrada
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Paolo Verderio
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Adele Busico
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Maria Adele Testi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Valentina Monti
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Matteo Duca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Claudia Proto
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Silvia Damian
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Alberta Piccolo
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Federica Perrone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Elena Tamborini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Devecchi
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Paola Collini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Daniele Lorenzini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Correspondence: Luca Agnelli, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy.
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy,Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, Italy
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23
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Bruford EA, Antonescu CR, Carroll AJ, Chinnaiyan A, Cree IA, Cross NCP, Dalgleish R, Gale RP, Harrison CJ, Hastings RJ, Huret JL, Johansson B, Le Beau M, Mecucci C, Mertens F, Verhaak R, Mitelman F. HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions. Leukemia 2021; 35:3040-3043. [PMID: 34615987 PMCID: PMC8550944 DOI: 10.1038/s41375-021-01436-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022]
Abstract
Gene fusions have been discussed in the scientific literature since they were first detected in cancer cells in the early 1980s. There is currently no standardized way to denote the genes involved in fusions, but in the majority of publications the gene symbols in question are listed either separated by a hyphen (-) or by a forward slash (/). Both types of designation suffer from important shortcomings. HGNC has worked with the scientific community to determine a new, instantly recognizable and unique separator-a double colon (::)-to be used in the description of fusion genes, and advocates its usage in all databases and articles describing gene fusions.
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Affiliation(s)
- Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Arul Chinnaiyan
- University of Michigan Medical School, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ian A Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Robert Peter Gale
- Centre for Haematology Research, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Rosalind J Hastings
- The Women's Centre, John Radcliffe Hospital, Oxford University Hospitals Foundation Trust, Oxford, UK
| | | | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michelle Le Beau
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Cristina Mecucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Roel Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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24
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Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes. Cancers (Basel) 2021; 13:cancers13194829. [PMID: 34638309 PMCID: PMC8507874 DOI: 10.3390/cancers13194829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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25
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Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Gragnano G, Conticelli F, Salatiello M, De Luca C, Girolami I, Eccher A, Iaccarino A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Methods for actionable gene fusion detection in lung cancer: now and in the future. Pharmacogenomics 2021; 22:833-847. [PMID: 34525844 DOI: 10.2217/pgs-2021-0048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although gene fusions occur rarely in non-small-cell lung cancer (NSCLC) patients, they represent a relevant target in treatment decision algorithms. To date, immunohistochemistry and fluorescence in situ hybridization are the two principal methods used in clinical trials. However, using these methods in routine clinical practice is often impractical and time consuming because they can only analyze single genes and the quantity of tissue material is often insufficient. Thus, novel technologies, able to test multiple genes in a single run with minimal sample input, are being under investigation. Here, we discuss the utility of next-generation sequencing and nCounter technologies in detecting simultaneous gene fusions in NSCLC patients.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology & Diagnostics, University & Hospital Trust of Verona, Verona, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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26
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Zhou Y, El-Bahrawy M. Gene fusions in tumourigenesis with particular reference to ovarian cancer. J Med Genet 2021; 58:789-795. [PMID: 34462289 DOI: 10.1136/jmedgenet-2021-108010] [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: 06/02/2021] [Accepted: 08/11/2021] [Indexed: 11/04/2022]
Abstract
Gene fusion, a genomic event that generates a novel gene from two independent genes, has long been known to be implicated in tumourigenesis and cancer progression. It has thus served as a diagnostic and prognostic biomarker in cancer, as well as an ideal therapeutic target in cancer therapy. Gene fusion can arise from chromosomal rearrangement and alternative splicing of transcripts, resulting in deregulation of proto-oncogenes or creation of an oncogenic novel gene. Largely facilitated by next generation sequencing technologies, a plethora of novel gene fusions have been identified in a variety of cancers, which leaves us the challenge of functionally characterising these candidate gene fusions. In this review, we summarise the molecular mechanisms, the oncogenic consequences and the therapeutic implications of verified gene fusions. We also discuss recent studies on gene fusions in both common and rare subtypes of ovarian tumours and how these findings can be translated to cancer therapies to benefit patients carrying these gene fusions.
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Affiliation(s)
- Yi Zhou
- Surgery and Cancer, Imperial College London, London, UK
| | - Mona El-Bahrawy
- Metabolism, Digestion and Reproduction, Imperial College London, London, UK .,Pathology, Alexandria University Faculty of Medicine, Alexandria, Egypt
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27
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Katerji M, Duerksen-Hughes PJ. DNA damage in cancer development: special implications in viral oncogenesis. Am J Cancer Res 2021; 11:3956-3979. [PMID: 34522461 PMCID: PMC8414375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/04/2021] [Indexed: 06/13/2023] Open
Abstract
DNA lesions arise from a combination of physiological/metabolic sources and exogenous environmental influences. When left unrepaired, these alterations accumulate in the cells and can give rise to mutations that change the function of important proteins (i.e. tumor suppressors, oncoproteins), or cause chromosomal rearrangements (i.e. gene fusions) that also result in the deregulation of key cellular molecules. Progressive acquisition of such genetic changes promotes uncontrolled cell proliferation and evasion of cell death, and hence plays a key role in carcinogenesis. Another less-studied consequence of DNA damage accumulating in the host genome is the integration of oncogenic DNA viruses such as Human papillomavirus, Merkel cell polyomavirus, and Hepatitis B virus. This critical step of viral-induced carcinogenesis is thought to be particularly facilitated by DNA breaks in both viral and host genomes. Therefore, the impact of DNA damage on carcinogenesis is magnified in the case of such oncoviruses via the additional effect of increasing integration frequency. In this review, we briefly present the various endogenous and exogenous factors that cause different types of DNA damage. Next, we discuss the contribution of these lesions in cancer development. Finally, we examine the amplified effect of DNA damage in viral-induced oncogenesis and summarize the limited data existing in the literature related to DNA damage-induced viral integration. To conclude, additional research is needed to assess the DNA damage pathways involved in the transition from viral infection to cancer. Discovering that a certain DNA damaging agent increases the likelihood of viral integration will enable the development of prophylactic and therapeutic strategies designed specifically to prevent such integration, with an ultimate goal of reducing or eliminating these viral-induced malignancies.
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Affiliation(s)
- Meghri Katerji
- Department of Basic Science, Loma Linda University School of Medicine Loma Linda, CA 92354, USA
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28
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Zhao R, Yao F, Xiang C, Zhao J, Shang Z, Guo L, Ding W, Ma S, Yu A, Shao J, Zhu L, Han Y. Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population. J Pathol Clin Res 2021; 7:375-384. [PMID: 33768710 PMCID: PMC8185368 DOI: 10.1002/cjp2.208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 12/30/2022]
Abstract
The molecular profile of neurotrophic tyrosine kinase receptor (NTRK) gene fusions in lung adenocarcinoma (LUAD) is not fully understood. Next-generation sequencing (NGS) and pan-tyrosine kinase receptor (TRK) immunohistochemistry (IHC) are powerful tools for NTRK fusion detection. In this study, a total of 4,619 LUAD formalin-fixed, paraffin-embedded tissues were collected from patients who underwent biopsy or resection at the Shanghai Chest Hospital during 2017-2019. All specimens were screened for NTRK1 rearrangements using DNA-based NGS. Thereafter, the cases with NTRK1 rearrangements and cases negative for common driver mutations were analyzed for NTRK1/2/3 fusions using total nucleic acid (TNA)-based NGS and pan-TRK IHC. Overall, four NTRK1/2 fusion events were identified, representing 0.087% of the original sample set. At the DNA level, seven NTRK1 rearrangements were identified, while only two TPM3-NTRK1 fusions were confirmed on TNA-based NGS as functional. In addition, two NTRK2 fusions (SQSTM1-NTRK2 and KIF5B-NTRK2) were identified by TNA-based NGS in 350 'pan-negative' cases. Two patients harboring NTRK1/2 fusions were diagnosed with invasive adenocarcinoma, while the other two were diagnosed with adenocarcinoma in situ and minimally invasive adenocarcinoma. All four samples with NTRK fusions were positive for the expression of pan-TRK. The two samples with NTRK2 fusions showed cytoplasmic staining alone, while the other two samples with NTRK1 fusions exhibited both cytoplasmic and membranous staining. In summary, functional NTRK fusions are found in early-stage LUAD; however, they are extremely rare. According to this study's results, they are independent oncogenic drivers, mutually exclusive with other driver mutations. We demonstrated that NTRK rearrangement analysis using a DNA-based approach should be verified with an RNA-based assay.
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Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Wenjie Ding
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengji Ma
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Anbo Yu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
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Fujita S, Masago K, Sasaki E, Tsukushi S, Horio Y, Kuroda H, Hida T. Weak-evidence Fusion Candidates Detected by a FusionPlex Assay Using the Ion Torrent System. In Vivo 2021; 35:993-998. [PMID: 33622894 DOI: 10.21873/invivo.12342] [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: 12/12/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The Archer FusionPlex platform is widely used for comprehensive fusion-gene detection in cancer tissues. This platform separately displays results for strong-evidence and weak-evidence fusion candidates (WEFCs). Distinctive fusion patterns are frequently found in the weak-evidence category and information about the patterns is clinically essential. PATIENTS AND METHODS We describe the type and frequency of WEFCs observed using the FusionPlex Sarcoma Panel (S Panel) and the FusionPlex ALK, RET, and ROS1 ver2 Panel (ARR Panel). RESULTS A total of 97 specimens were examined and 620 candidates were detected and categorized as WEFCs. A median of five WEFCs were detected per sample. In the S Panel group, there were 13 WEFCs with a frequency of more than 1%. In the ARR Panel group, a total of 16 WEFCs were detected with a frequency of more than 1%. CONCLUSION Specific WEFCs were detected according to the panel selected.
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Affiliation(s)
- Shiro Fujita
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan; .,Department of Respiratory Medicine, Kobe Central Hospital, Kobe, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Satoshi Tsukushi
- Department of Orthopaedic Surgery, Aichi Cancer Center, Nagoya, Japan
| | - Yoshitsugu Horio
- Department of Thoracic Oncology, Aichi Cancer Center, Nagoya, Japan
| | - Hiroaki Kuroda
- Department of Thoracic Surgery, Aichi Cancer Center, Nagoya, Japan
| | - Toyoaki Hida
- Department of Thoracic Oncology, Aichi Cancer Center, Nagoya, Japan
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30
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Bajpai M, Panda A, Birudaraju K, Van Gurp J, Chak A, Das KM, Javidian P, Aviv H. Recurring Translocations in Barrett's Esophageal Adenocarcinoma. Front Genet 2021; 12:674741. [PMID: 34178034 PMCID: PMC8220202 DOI: 10.3389/fgene.2021.674741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Barrett's esophagus (BE) is a premalignant metaplasia in patients with chronic gastroesophageal reflux disease (GERD). BE can progress to esophageal adenocarcinoma (EA) with less than 15% 5-year survival. Chromosomal aneuploidy, deletions, and duplication are early events in BE progression to EA, but reliable diagnostic assays to detect chromosomal markers in premalignant stages of EA arising from BE are lacking. Previously, we investigated chromosomal changes in an in vitro model of acid and bile exposure-induced Barrett's epithelial carcinogenesis (BEC). In addition to detecting changes already known to occur in BE and EA, we also reported a novel recurring chromosomal translocation t(10:16) in the BE cells at an earlier time point before they undergo malignant transformation. In this study, we refine the chromosomal event with the help of fluorescence microscopy techniques as a three-way translocation between chromosomes 2, 10, and 16, t(2:10;16) (p22;q22;q22). We also designed an exclusive fluorescent in situ hybridization for esophageal adenocarcinoma (FISH-EA) assay that detects these chromosomal breakpoints and fusions. We validate the feasibility of the FISH-EA assay to objectively detect these chromosome events in primary tissues by confirming the presence of one of the fusions in paraffin-embedded formalin-fixed human EA tumors. Clinical validation in a larger cohort of BE progressors and non-progressors will confirm the specificity and sensitivity of the FISH-EA assay in identifying malignant potential in the early stages of EA.
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Affiliation(s)
- Manisha Bajpai
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Kristen Birudaraju
- Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - James Van Gurp
- Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Kiron M Das
- Department of Medicine-Gastroenterology and Hepatology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Parisa Javidian
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
| | - Hana Aviv
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States.,Cytogenetics Laboratory, Department of Pathology, Rutgers-Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, New Brunswick, NJ, United States
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31
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Bertucci F, Gonçalves A, Guille A, Adelaïde J, Garnier S, Carbuccia N, Billon E, Finetti P, Sfumato P, Monneur A, Pécheux C, Khran M, Brunelle S, Mescam L, Thomassin-Piana J, Poizat F, Charafe-Jauffret E, Turrini O, Lambaudie E, Provansal M, Extra JM, Madroszyk A, Gilabert M, Sabatier R, Vicier C, Mamessier E, Chabannon C, Pakradouni J, Viens P, André F, Gravis G, Popovici C, Birnbaum D, Chaffanet M. Prospective high-throughput genome profiling of advanced cancers: results of the PERMED-01 clinical trial. Genome Med 2021; 13:87. [PMID: 34006291 PMCID: PMC8132379 DOI: 10.1186/s13073-021-00897-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The benefit of precision medicine based on relatively limited gene sets and often-archived samples remains unproven. PERMED-01 (NCT02342158) was a prospective monocentric clinical trial assessing, in adults with advanced solid cancer, the feasibility and impact of extensive molecular profiling applied to newly biopsied tumor sample and based on targeted NGS (t-NGS) of the largest gene panel to date and whole-genome array-comparative genomic hybridization (aCGH) with assessment of single-gene alterations and clinically relevant genomic scores. METHODS Eligible patients with refractory cancer had one tumor lesion accessible to biopsy. Extracted tumor DNA was profiled by t-NGS and aCGH. We assessed alterations of 802 "candidate cancer" genes and global genomic scores, such as homologous recombination deficiency (HRD) score and tumor mutational burden. The primary endpoint was the number of patients with actionable genetic alterations (AGAs). Secondary endpoints herein reported included a description of patients with AGA who received a "matched therapy" and their clinical outcome, and a comparison of AGA identification with t-NGS and aCGH versus whole-exome sequencing (WES). RESULTS Between November 2014 and September 2019, we enrolled 550 patients heavily pretreated. An exploitable complete molecular profile was obtained in 441/550 patients (80%). At least one AGA, defined in real time by our molecular tumor board, was found in 393/550 patients (71%, two-sided 90%CI 68-75%). Only 94/550 patients (17%, 95%CI 14-21) received an "AGA-matched therapy" on progression. The most frequent AGAs leading to "matched therapy" included PIK3CA mutations, KRAS mutations/amplifications, PTEN deletions/mutations, ERBB2 amplifications/mutations, and BRCA1/2 mutations. Such "matched therapy" improved by at least 1.3-fold the progression-free survival on matched therapy (PFS2) compared to PFS on prior therapy (PFS1) in 36% of cases, representing 6% of the enrolled patients. Within patients with AGA treated on progression, the use of "matched therapy" was the sole variable associated with an improved PFS2/PFS1 ratio. Objective responses were observed in 19% of patients treated with "matched therapy," and 6-month overall survival (OS) was 62% (95%CI 52-73). In a subset of 112 metastatic breast cancers, WES did not provide benefit in term of AGA identification when compared with t-NGS/aCGH. CONCLUSIONS Extensive molecular profiling of a newly biopsied tumor sample identified AGA in most of cases, leading to delivery of a "matched therapy" in 17% of screened patients, of which 36% derived clinical benefit. WES did not seem to improve these results. TRIAL REGISTRATION ID-RCB identifier: 2014-A00966-41; ClinicalTrials.gov identifier: NCT02342158 .
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Affiliation(s)
- François Bertucci
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.
| | - Anthony Gonçalves
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Arnaud Guille
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - José Adelaïde
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Séverine Garnier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Nadine Carbuccia
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Emilien Billon
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Patrick Sfumato
- Biostatistics Unit, Institut Paoli-Calmettes, Marseille, France
| | - Audrey Monneur
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Christophe Pécheux
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
| | - Martin Khran
- Department of Medical genetics, Hôpital Timone Enfants, AP-HM, Marseille, France
- Aix-Marseille University, Inserm, U1251-MMG, Marseille Medical Genetics, Marseille, France
| | - Serge Brunelle
- Department of Imaging, Institut Paoli-Calmettes, Marseille, France
| | - Lenaïg Mescam
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Flora Poizat
- Department of Biopathology, Institut Paoli-Calmettes, Marseille, France
| | | | - Olivier Turrini
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Jean-Marc Extra
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Anne Madroszyk
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Marine Gilabert
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Renaud Sabatier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Christian Chabannon
- Biobank, Department of Hematology, Institut Paoli-Calmettes, Marseille, France
| | - Jihane Pakradouni
- Department of Clinical Research and Innovation, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Fabrice André
- Department of Medical Oncology, Gustave Roussy Cancer Campus, UMR981 Inserm, Villejuif, France
- Paris Sud University, Orsay, France
| | - Gwenaelle Gravis
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Cornel Popovici
- Department of Oncogenetics, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
| | - Max Chaffanet
- Laboratory of Predictive Oncology, Department of Medical Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille University, 232 Boulevard Sainte-Marguerite, 13009, Marseille, France
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32
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Musicant AM, Parag-Sharma K, Gong W, Sengupta M, Chatterjee A, Henry EC, Tsai YH, Hayward MC, Sheth S, Betancourt R, Hackman TG, Padilla RJ, Parker JS, Giudice J, Flaveny CA, Hayes DN, Amelio AL. CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition. Cell Rep 2021; 34:108768. [PMID: 33626346 PMCID: PMC7955229 DOI: 10.1016/j.celrep.2021.108768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/22/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Mucoepidermoid carcinoma (MEC) is a life-threatening salivary gland cancer that is driven primarily by a transcriptional coactivator fusion composed of cyclic AMP-regulated transcriptional coactivator 1 (CRTC1) and mastermind-like 2 (MAML2). The mechanisms by which the chimeric CRTC1/MAML2 (C1/M2) oncoprotein rewires gene expression programs that promote tumorigenesis remain poorly understood. Here, we show that C1/M2 induces transcriptional activation of the non-canonical peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) splice variant PGC-1α4, which regulates peroxisome proliferator-activated receptor gamma (PPARγ)-mediated insulin-like growth factor 1 (IGF-1) expression. This mitogenic transcriptional circuitry is consistent across cell lines and primary tumors. C1/M2-positive tumors exhibit IGF-1 pathway activation, and small-molecule drug screens reveal that tumor cells harboring the fusion gene are selectively sensitive to IGF-1 receptor (IGF-1R) inhibition. Furthermore, this dependence on autocrine regulation of IGF-1 transcription renders MEC cells susceptible to PPARγ inhibition with inverse agonists. These results yield insights into the aberrant coregulatory functions of C1/M2 and identify a specific vulnerability that can be exploited for precision therapy.
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Affiliation(s)
- Adele M Musicant
- Graduate Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology and Physiology, Biological and Biomedical Sciences Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Weida Gong
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Monideepa Sengupta
- Graduate Curriculum in Pharmacological and Physiological Sciences, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Arindam Chatterjee
- Department of Pharmacology and Physiology, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Erin C Henry
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yi-Hsuan Tsai
- Bioinformatics Core, Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Siddharth Sheth
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Renee Betancourt
- Department of Pathology and Laboratory Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trevor G Hackman
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ricardo J Padilla
- Division of Diagnostic Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; McAllister Heart Institute, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colin A Flaveny
- Department of Pharmacology and Physiology, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - David N Hayes
- Lineberger Comprehensive Cancer Center, Cancer Genetics Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medical Oncology, University of Tennessee Health Sciences West Cancer Center, Memphis, TN, USA
| | - Antonio L Amelio
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, Cancer Cell Biology Program, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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El-Zaatari ZM, Thomas JS, Divatia MK, Shen SS, Ayala AG, Monroig-Bosque P, Shehabeldin A, Ro JY. Pleomorphic giant cell carcinoma of prostate: Rare tumor with unique clinicopathological, immunohistochemical, and molecular features. Ann Diagn Pathol 2021; 52:151719. [PMID: 33640702 DOI: 10.1016/j.anndiagpath.2021.151719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
Pleomorphic giant cell carcinoma (PGCC) of the prostate is a rare entity categorized as a variant of prostatic acinar adenocarcinoma in the 2016 World Health Organization (WHO) classification system. PGCC differs from conventional prostatic adenocarcinoma by having bizarre, markedly enlarged, and pleomorphic cells. It differs from high grade urothelial carcinoma by negativity for urothelial differentiation markers, and can be distinguished from sarcomatoid carcinoma by lack of spindle cells. Including two new cases described herein, there have been 51 cases of prostate PGCC reported in the English literature. Clinical features shared by cases of prostate PGCC include poor prognosis, occurrence in older patients, and frequent association with prior therapy. Pathologic features common to cases of prostate PGCC include admixture with a high-grade conventional prostate carcinoma component and absent or reduced expression of prostate differentiation markers. More recent studies have begun to elucidate the molecular characteristics of PGCC, detecting specific mutations and chromosomal translocations, and showing evidence of a high degree of molecular instability in these tumors. We report novel findings in two cases of PGCC including a PIK3CA p.His1047Arg mutation not previously described. One of our cases is the first to clearly demonstrate chronological loss of prostate markers during dedifferentiation from prior conventional prostate carcinoma to PGCC. Herein, we present our two new cases and comprehensively review the literature on all reported cases of PGCC with critical commentary on findings in cases of this rare tumor.
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Affiliation(s)
- Ziad M El-Zaatari
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Weill Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | - Mukul K Divatia
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Weill Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | - Steven S Shen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Weill Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | - Alberto G Ayala
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Weill Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | - Paloma Monroig-Bosque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Ahmed Shehabeldin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jae Y Ro
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Weill Medical College of Cornell University (WCMC), New York, NY 10065, USA.
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Scaravilli M, Koivukoski S, Latonen L. Androgen-Driven Fusion Genes and Chimeric Transcripts in Prostate Cancer. Front Cell Dev Biol 2021; 9:623809. [PMID: 33634124 PMCID: PMC7900491 DOI: 10.3389/fcell.2021.623809] [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: 10/30/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Androgens are steroid hormones governing the male reproductive development and function. As such, androgens and the key mediator of their effects, androgen receptor (AR), have a leading role in many diseases. Prostate cancer is a major disease where AR and its transcription factor function affect a significant number of patients worldwide. While disease-related AR-driven transcriptional programs are connected to the presence and activity of the receptor itself, also novel modes of transcriptional regulation by androgens are exploited by cancer cells. One of the most intriguing and ingenious mechanisms is to bring previously unconnected genes under the control of AR. Most often this occurs through genetic rearrangements resulting in fusion genes where an androgen-regulated promoter area is combined to a protein-coding area of a previously androgen-unaffected gene. These gene fusions are distinctly frequent in prostate cancer compared to other common solid tumors, a phenomenon still requiring an explanation. Interestingly, also another mode of connecting androgen regulation to a previously unaffected gene product exists via transcriptional read-through mechanisms. Furthermore, androgen regulation of fusion genes and transcripts is not linked to only protein-coding genes. Pseudogenes and non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) can also be affected by androgens and de novo functions produced. In this review, we discuss the prevalence, molecular mechanisms, and functional evidence for androgen-regulated prostate cancer fusion genes and transcripts. We also discuss the clinical relevance of especially the most common prostate cancer fusion gene TMPRSS2-ERG, as well as present open questions of prostate cancer fusions requiring further investigation.
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Affiliation(s)
- Mauro Scaravilli
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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Boija A, Klein IA, Young RA. Biomolecular Condensates and Cancer. Cancer Cell 2021; 39:174-192. [PMID: 33417833 PMCID: PMC8721577 DOI: 10.1016/j.ccell.2020.12.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
Malignant transformation is characterized by dysregulation of diverse cellular processes that have been the subject of detailed genetic, biochemical, and structural studies, but only recently has evidence emerged that many of these processes occur in the context of biomolecular condensates. Condensates are membrane-less bodies, often formed by liquid-liquid phase separation, that compartmentalize protein and RNA molecules with related functions. New insights from condensate studies portend a profound transformation in our understanding of cellular dysregulation in cancer. Here we summarize key features of biomolecular condensates, note where they have been implicated-or will likely be implicated-in oncogenesis, describe evidence that the pharmacodynamics of cancer therapeutics can be greatly influenced by condensates, and discuss some of the questions that must be addressed to further advance our understanding and treatment of cancer.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Zeng Y, Koo KM, Shen AG, Hu JM, Trau M. Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006370. [PMID: 33325632 DOI: 10.1002/smll.202006370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.
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Affiliation(s)
- Yi Zeng
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- XING Technologies Pty Ltd, Sinnamon Park, Brisbane, QLD, 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD, 4029, Australia
| | - Ai-Guo Shen
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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Forschner A, Forchhammer S, Bonzheim I. NTRK‐
Genfusionen beim Melanom: Diagnostik, Prävalenz und mögliche Therapierelevanz. J Dtsch Dermatol Ges 2020; 18:1387-1393. [PMID: 33373127 DOI: 10.1111/ddg.14160_g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 11/29/2022]
Abstract
Fusionen der neurotrophen Tyrosin-Rezeptor-Kinase (NTRK) sind bekannte Treiber der Onkogenese und treten, wenn auch sehr selten, ebenfalls beim Melanom auf. Eine besonders hohe Inzidenz von NTRK-Genfusionen wird beim infantilen Fibrosarkom (> 90 %) oder der sekretorischen Form des Mammakarzinoms (> 90 %) berichtet. Erst kürzlich wurde Larotrectinib, ein Tropomyosin-Rezeptor-Kinase (TRK)-Inhibitor, zugelassen, und wir fragten uns, ob TRK-Inhibitoren auch für Melanompatienten relevant sein könnten. Aus diesem Grund haben wir die Literatur gesichtet und sind zu relevanten Ergebnissen gekommen. Beim spitzoiden Melanom sind NTRK-Fusionen mit einer Prävalenz von 21-29 % relativ häufig, verglichen mit < 1 % beim kutanen oder mukosalen und 2,5 % beim akralen Melanom. Es scheint so zu sein, dass sich Fusionsproteine und andere onkogene Treiber wie BRAF oder NRAS gegenseitig ausschließen. Ein weiterer Anhaltspunkt für eine erhöhte Wahrscheinlichkeit, NTRK-positive Tumoren zu detektieren, könnte eine geringe Tumormutationslast sein. Da für Patienten mit NTRK-Fusionen bereits TRK-Inhibitoren zur Verfügung stehen, wird die Herausforderung darin bestehen, das Screening auf NTRK-Genfusionen in die klinische Praxis umzusetzen. Ein möglicher Ansatz könnte darin bestehen, BRAF-, NRAS- und KIT-Wildtyp-Melanom-Patienten mittels Next-Generation Sequencing zu screenen, sobald sie eine systemische Therapie benötigen oder aber spätestens dann, wenn sie kein Therapieansprechen auf Checkpoint-Inhibitoren zeigen.
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Affiliation(s)
| | - Stephan Forchhammer
- Mikroskopische und molekulare Dermatologie, Universitäts-Hautklinik Tübingen
| | - Irina Bonzheim
- Institut für Pathologie und Neuropathologie, Universitätsklinikum Tübingen
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [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: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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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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Mohammadi E, Benfeitas R, Turkez H, Boren J, Nielsen J, Uhlen M, Mardinoglu A. Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. Cancers (Basel) 2020; 12:E2694. [PMID: 32967266 PMCID: PMC7563533 DOI: 10.3390/cancers12092694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Modern drug discovery through de novo drug discovery entails high financial costs, low success rates, and lengthy trial periods. Drug repositioning presents a suitable approach for overcoming these issues by re-evaluating biological targets and modes of action of approved drugs. Coupling high-throughput technologies with genome-wide essentiality screens, network analysis, genome-scale metabolic modeling, and machine learning techniques enables the proposal of new drug-target signatures and uncovers unanticipated modes of action for available drugs. Here, we discuss the current issues associated with drug repositioning in light of curated high-throughput multi-omic databases, genome-wide screening technologies, and their application in systems biology/medicine approaches.
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Affiliation(s)
- Elyas Mohammadi
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden;
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, 25240 Erzurum, Turkey;
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden;
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden;
- BioInnovation Institute, DK-2200 Copenhagen N, Denmark
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
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De Luca A, Esposito Abate R, Rachiglio AM, Maiello MR, Esposito C, Schettino C, Izzo F, Nasti G, Normanno N. FGFR Fusions in Cancer: From Diagnostic Approaches to Therapeutic Intervention. Int J Mol Sci 2020; 21:E6856. [PMID: 32962091 PMCID: PMC7555921 DOI: 10.3390/ijms21186856] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are tyrosine kinase receptors involved in many biological processes. Deregulated FGFR signaling plays an important role in tumor development and progression in different cancer types. FGFR genomic alterations, including FGFR gene fusions that originate by chromosomal rearrangements, represent a promising therapeutic target. Next-generation-sequencing (NGS) approaches have significantly improved the discovery of FGFR gene fusions and their detection in clinical samples. A variety of FGFR inhibitors have been developed, and several studies are trying to evaluate the efficacy of these agents in molecularly selected patients carrying FGFR genomic alterations. In this review, we describe the most frequent FGFR aberrations in human cancer. We also discuss the different approaches employed for the detection of FGFR fusions and the potential role of these genomic alterations as prognostic/predictive biomarkers.
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Affiliation(s)
- Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Claudia Esposito
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Clorinda Schettino
- Clinical Trials Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Francesco Izzo
- Division of Surgical Oncology, Hepatobiliary Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Guglielmo Nasti
- SSD Innovative Therapies for Abdominal Cancers, 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; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
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Alhamar M, Tudor Vladislav I, Smith SC, Gao Y, Cheng L, Favazza LA, Alani AM, Ittmann MM, Riddle ND, Whiteley LJ, Gupta NS, Carskadon S, Gomez-Gelvez JC, Chitale DA, Palanisamy N, Hes O, Trpkov K, Williamson SR. Gene fusion characterisation of rare aggressive prostate cancer variants-adenosquamous carcinoma, pleomorphic giant-cell carcinoma, and sarcomatoid carcinoma: an analysis of 19 cases. Histopathology 2020; 77:890-899. [PMID: 32639612 DOI: 10.1111/his.14205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/12/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022]
Abstract
AIMS To evaluate the molecular underpinnings of the rare aggressive prostate cancer variants adenosquamous carcinoma, pleomorphic giant-cell carcinoma, and sarcomatoid carcinoma. METHODS AND RESULTS We retrieved 19 tumours with one or more variant(s), and performed ERG immunohistochemistry, a next-generation sequencing assay targeting recurrent gene fusions, and fluorescence in-situ hybridisation (FISH) for ERG and BRAF. Divergent differentiation included: sarcomatoid carcinoma (n = 10), adenosquamous carcinoma (n = 7), and pleomorphic giant-cell carcinoma (n = 7). Five patients had more than one variant. Four had variants only in metastases. ERG rearrangement was detected in nine (47%, seven via sequencing, showing TMPRSS2-ERG fusions and one GRHL2-ERG fusion, and two via FISH, showing rearrangement via deletion). ERG was immunohistochemically positive in the adenocarcinoma in eight of nine (89%) patients, but was immunohistochemically positive in the variant in only five of nine patients (56%, typically decreased). One patient had a false-positive ERG immunohistochemical result in the sarcomatoid component despite a negative FISH result. Two (11%) harboured BRAF fusions (FAM131A-BRAF and SND1-BRAF). CONCLUSIONS ERG fusions are present in these rare prostate cancer variants with a frequency close to that in conventional prostate cancer (9/19, 47%). ERG immunohistochemistry usually detects rearrangement in the adenocarcinoma, but is less sensitive for the variant histology, with weak to negative staining. Adenosquamous and sarcomatoid variants can, particularly, occur together. Molecular assessment may be an additional tool in selected cases to confirm the prostatic origin of unusual tumours. The presence of two BRAF rearrangements suggests that this gene fusion may be enriched in this setting, as RAF kinase fusions have been previously reported in 1-2% of prostate cancers.
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Affiliation(s)
- Mohamed Alhamar
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - I Tudor Vladislav
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Steven C Smith
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Yuan Gao
- Department of Pathology, Memorial University, St John's, Newfoundland, Canada
| | - Liang Cheng
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Laura A Favazza
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Ali M Alani
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Michael M Ittmann
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Nicole D Riddle
- Department of Pathology, USF Health, Ruffolo, Hooper, and Associates, Tampa, FL, USA
| | - Lisa J Whiteley
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Nilesh S Gupta
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Shannon Carskadon
- Department of Urology, Vattikutti Urology Institute, Henry Ford Health System, Detroit, MI, USA
| | - Juan C Gomez-Gelvez
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Dhananjay A Chitale
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA.,Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nallasivam Palanisamy
- Department of Urology, Vattikutti Urology Institute, Henry Ford Health System, Detroit, MI, USA
| | - Ondrej Hes
- Department of Pathology, Charles University Faculty of Medicine, Plzen, Czech Republic
| | - Kiril Trpkov
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sean R Williamson
- Department of Pathology and Laboratory Medicine and Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA.,Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
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Woo HY, Na K, Yoo J, Chang JH, Park YN, Shim HS, Kim SH. Glioblastomas harboring gene fusions detected by next-generation sequencing. Brain Tumor Pathol 2020; 37:136-144. [PMID: 32761533 DOI: 10.1007/s10014-020-00377-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
Oncogenic gene fusions have been reported in diffuse gliomas and may serve as potential therapeutic targets. Here, using next-generation sequencing analysis (Illumina TruSight Tumor 170 panel), we analyzed a total of 356 diffuse gliomas collected from 2017 to 2019 to evaluate clinical, pathological, and genetic features of gene fusion. We found 53 cases of glioblastomas harboring the following oncogenic gene fusions: MET (n = 18), EGFR (n = 14), FGFR (n = 12), NTRK (n = 5), RET (n = 2), AKT3 (n = 1), and PDGFRA fusions (n = 1). Gene fusions were consistently observed in both IDH-wildtype and IDH-mutant glioblastomas (8.8% and 9.4%, p = 1.000). PTPRZ1-MET fusion was the only fusion that genetically resembled secondary glioblastomas (i.e., high frequency of IDH mutation, ATRX loss, TP53 mutation, and absence of EGFR amplification), whereas other gene fusion types were similar to primary glioblastomas (i.e., high frequency of IDH-wildtype, TERT mutation, EGFR amplification, and PTEN mutation). In IDH-wildtype glioblastoma patients, multivariable analysis revealed that the PTPRZ1-MET fusion was associated with poor progression-free survival (HR [95% CI]: 5.42 (1.72-17.05), p = 0.004). Additionally, we described two novel cases of CCDC6-RET fusion in glioma. Collectively, our findings indicate that targetable gene fusions are associated with aggressive biological behavior and can aid the clinical treatment strategy for glioma patients.
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Affiliation(s)
- Ha Young Woo
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, 26 Kyungheedae-Ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Jihwan Yoo
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea.
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De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group. Ann Oncol 2020; 31:978-990. [PMID: 32610166 PMCID: PMC7885309 DOI: 10.1016/j.annonc.2020.05.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies. METHODS In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence. RESULTS A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies. CONCLUSIONS Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.
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Affiliation(s)
- L De Mattos-Arruda
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - M Vazquez
- Barcelona Supercomputing Center, Barcelona, Spain
| | - F Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - R Lepore
- Barcelona Supercomputing Center, Barcelona, Spain
| | - E Porta
- Barcelona Supercomputing Center, Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - J Hundal
- The McDonnell Genome Institute, Washington University in St Louis, USA
| | | | - C K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - A Valencia
- Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - J Carrillo
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - T A Chan
- Center for Immunotherapy and Precision-Immuno-Oncology, Cleveland Clinic, Cleveland, USA
| | - V Guallar
- Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - N McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College, London, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - J Blanco
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - M Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
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Forschner A, Forchhammer S, Bonzheim I. NTRK gene fusions in melanoma: detection, prevalence and potential therapeutic implications. J Dtsch Dermatol Ges 2020; 18:1387-1392. [PMID: 32656925 DOI: 10.1111/ddg.14160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
Fusions involving neurotrophic tyrosine receptor kinase (NTRK) are known drivers of oncogenesis and also occur in melanoma, although very rarely. A particularly high incidence of NTRK gene fusions is reported in infantile fibrosarcoma (> 90 %) or the secretory type of breast cancer (> 90 %). Recently, larotrectinib (a tropomyosin receptor kinase [TRK] inhibitor) was approved, and we wondered whether TRK inhibitors might also be helpful for melanoma patients. We therefore screened the literature and obtained relevant results. NTRK fusions are relatively common in spitzoid melanoma, with a prevalence of 21-29 % compared to < 1 % in cutaneous or mucosal melanoma and 2.5 % in acral melanoma. It appears that fusion proteins are mutually exclusive for most common oncogenic drivers such as BRAF or NRAS. A further indicator of an increased probability of detecting NTRK-positive tumors could be a low mutation load. Since TRK inhibitors are already available for patients with NTRK fusions, the challenge will be to implement screening for NTRK gene fusions in clinical practice. A possible approach could be to screen BRAF, NRAS and KIT wild-type melanoma patients with next-generation sequencing as soon as they need systemic treatment or at the latest when they have no tumor control on checkpoint inhibitors.
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Affiliation(s)
- Andrea Forschner
- Department of Dermatology, Center for Dermatooncology, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Forchhammer
- Department of Dermatology, Histopathology, University Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and neuropathology, University Hospital Tübingen, Tübingen, Germany
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Pisapia DJ, Ohara K, Bareja R, Wilkes DC, Hissong E, Croyle JA, Kim JH, Saab J, MacDonald TY, Beg S, O’Reilly C, Kudman S, Rubin MA, Elemento O, Sboner A, Greenfield J, Mosquera JM. Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta Neuropathol Commun 2020; 8:80. [PMID: 32493417 PMCID: PMC7271411 DOI: 10.1186/s40478-020-00951-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
BCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1-4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.
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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 DOI: 10.1097/pas.0000000000001377] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [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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48
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Heyer EE, Blackburn J. Sequencing Strategies for Fusion Gene Detection. Bioessays 2020; 42:e2000016. [DOI: 10.1002/bies.202000016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Erin E. Heyer
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
| | - James Blackburn
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
- Faculty of Medicine, St. Vincent's Clinical SchoolUNSW, St Vincent's Hospital Victoria Street Darlinghurst NSW 2010 Australia
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Singh S, Qin F, Kumar S, Elfman J, Lin E, Pham LP, Yang A, Li H. The landscape of chimeric RNAs in non-diseased tissues and cells. Nucleic Acids Res 2020; 48:1764-1778. [PMID: 31965184 PMCID: PMC7038929 DOI: 10.1093/nar/gkz1223] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/13/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Justin Elfman
- 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
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Amy Yang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - 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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Merging new-age biomarkers and nanodiagnostics for precision prostate cancer management. Nat Rev Urol 2020; 16:302-317. [PMID: 30962568 DOI: 10.1038/s41585-019-0178-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The accurate identification and stratified treatment of clinically significant early-stage prostate cancer have been ongoing concerns since the outcomes of large international prostate cancer screening trials were reported. The controversy surrounding clinical and cost benefits of prostate cancer screening has highlighted the lack of strategies for discriminating high-risk disease (that requires early treatment) from low-risk disease (that could be managed using watchful waiting or active surveillance). Advances in molecular subtyping and multiomics nanotechnology-based prostate cancer risk delineation can enable refinement of prostate cancer molecular taxonomy into clinically meaningful and treatable subtypes. Furthermore, the presence of intertumoural and intratumoural heterogeneity in prostate cancer warrants the development of novel nanodiagnostic technologies to identify clinically significant prostate cancer in a rapid, cost-effective and accurate manner. Circulating and urinary next-generation prostate cancer biomarkers for disease molecular subtyping and the newest complementary nanodiagnostic platforms for enhanced biomarker detection are promising tools for precision prostate cancer management. However, challenges in merging both aspects and clinical translation still need to be overcome.
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