1
|
Carillo AM, De Luca C, Pisapia P, Vigliar E, Ikenberg K, Freiberger SN, Troncone G, Rupp NJ, Bellevicine C. Molecular testing in salivary gland cytopathology: A practical overview in conjunction with the Milan system. Cytopathology 2024; 35:330-343. [PMID: 38308401 DOI: 10.1111/cyt.13363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Recently, significant advances in the molecular characterization of salivary gland neoplasms have facilitated the classification and diagnosis of specific diagnostic entities. In the highly challenging diagnostic scenario of salivary malignancies, molecular testing is increasingly being adopted in routine practice to refine the cytological diagnosis of salivary lesions. Here, we reviewed the most recent evidence in the field of salivary glands molecular cytopathology.
Collapse
Affiliation(s)
- Anna Maria Carillo
- 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
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Kristian Ikenberg
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Sandra N Freiberger
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| |
Collapse
|
2
|
Pan E, Bai Y. Insight into NSCLC through novel analysis of gene interactions and characteristics. Am J Clin Exp Immunol 2024; 13:58-67. [PMID: 38765019 PMCID: PMC11101995 DOI: 10.62347/anlv4963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Around 80 to 85% of all lung cancers are non-small cell lung cancer (NSCLC). Previous research has aimed at exploring the genetic basis of NSCLC through individual approaches, but studies have yet to investigate the results of combining them. Here we show that analyzing NSCLC genetics through three approaches simultaneously creates unique insights into our understanding of the disease. Through a combination of previous research and bioinformatics tools, we determined 35 NSCLC candidate genes. We analyzed these genes in 3 different approaches. First, we found the gene fusions between these candidate genes. Second, we found the common superfamilies between genes. Finally, we identified mutational signatures that are possibly associated with NSCLC. Each approach has its individual, unique results. Fusion relationships identify specific gene fusion targets, common superfamilies identify possible avenues to determine novel target genes, and identifying NSCLC associated mutational signatures has diagnostic and prognostic benefits. Combining the approaches, we found that gene CD74 has significant fusion relationships, but it has no association with the other two approaches, suggesting that CD74 is associated with NSCLC mainly because of its fusion relationships. Targeting the gene fusions of CD74 may be an alternative NSCLC treatment. This genetic analysis has indeed created unique insight into NSCLC genes. Both the results from each of the approaches separately and combined allow pursuit of more effective treatment strategies for this cancer. The methodology presented can also apply to other cancers, creating insights that current analytical methods could not find.
Collapse
Affiliation(s)
- Eric Pan
- Debakey High SchoolHouston, TX 77030, USA
| | - Yongsheng Bai
- Next-Gen Intelligent Science TrainingAnn Arbor, MI 48105, USA
| |
Collapse
|
3
|
Daruish M, Ambrogio F, Colagrande A, Marzullo A, Alaggio R, Trilli I, Ingravallo G, Cazzato G. Kinase Fusions in Spitz Melanocytic Tumors: The Past, the Present, and the Future. Dermatopathology (Basel) 2024; 11:112-123. [PMID: 38390852 PMCID: PMC10885070 DOI: 10.3390/dermatopathology11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
In recent years, particular interest has developed in molecular biology applied to the field of dermatopathology, with a focus on nevi of the Spitz spectrum. From 2014 onwards, an increasing number of papers have been published to classify, stratify, and correctly frame molecular alterations, including kinase fusions. In this paper, we try to synthesize the knowledge gained in this area so far. In December 2023, we searched Medline and Scopus for case reports and case series, narrative and systematic reviews, meta-analyses, observational studies-either longitudinal or historical, case series, and case reports published in English in the last 15 years using the keywords spitzoid neoplasms, kinase fusions, ALK, ROS1, NTRK (1-2-3), MET, RET, MAP3K8, and RAF1. ALK-rearranged Spitz tumors and ROS-1-rearranged tumors are among the most studied and characterized entities in the literature, in an attempt (although not always successful) to correlate histopathological features with the probable molecular driver alteration. NTRK-, RET-, and MET-rearranged Spitz tumors present another studied and characterized entity, with several rearrangements described but as of yet incomplete information about their prognostic significance. Furthermore, although rarer, rearrangements of serine-threonine kinases such as BRAF, RAF1, and MAP3K8 have also been described, but more cases with more detailed information about possible histopathological alterations, mechanisms of etiopathogenesis, and also prognosis are needed. The knowledge of molecular drivers is of great interest in the field of melanocytic diagnostics, and it is important to consider that in addition to immunohistochemistry, molecular techniques such as FISH, PCR, and/or NGS are essential to confirm and classify the different patterns of mutation. Future studies with large case series and molecular sequencing techniques are needed to allow for a more complete and comprehensive understanding of the role of fusion kinases in the spitzoid tumor family.
Collapse
Affiliation(s)
- Maged Daruish
- Dorset County Hospital NHS Foundation Trust, Dorchester DT1 2JY, UK
| | - Francesca Ambrogio
- Section of Dermatology and Venereology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Anna Colagrande
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Andrea Marzullo
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Irma Trilli
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giuseppe Ingravallo
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Gerardo Cazzato
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| |
Collapse
|
4
|
Gomez RS, El Mouatani A, Duarte-Andrade FF, Pereira TDSF, Guimarães LM, Gayden T, Faury D, Nakada EM, Langlois S, Sinnett D, de Castro WH, Diniz MG, Jabado N, Gomes CC. Comprehensive Genomic Analysis of Cemento-Ossifying Fibroma. Mod Pathol 2024; 37:100388. [PMID: 37995913 DOI: 10.1016/j.modpat.2023.100388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
Cemento-ossifying fibroma (COF) of the jaws is currently classified as a benign mesenchymal odontogenic tumor, and only targeted approaches have been used to assess its genetic alterations. A minimal proportion of COFs harbor CDC73 somatic mutations, and copy number alterations (CNAs) involving chromosomes 7 and 12 have recently been reported in a small proportion of cases. However, the genetic background of COFs remains obscure. We used a combination of whole-exome sequencing and RNA sequencing to assess somatic mutations, fusion transcripts, and CNAs in a cohort of 12 freshly collected COFs. No recurrent fusions have been identified among the 5 cases successfully analyzed by RNA sequencing, with in-frame fusions being detected in 2 cases (MARS1::GOLT1B and PARG::BMS1 in one case and NCLN::FZR1 and NFIC::SAMD1 in the other case) and no candidate fusions identified for the remaining 3 cases. No recurrent pathogenic mutations were detected in the 11 cases that had undergone whole-exome sequencing. A KRAS p.L19F missense variant was detected in one case, and 2 CDC73 deletions were detected in another case. The other variants were of uncertain significance and included variants in PC, ACTB, DOK6, HACE1, and COL1A2 and previously unreported variants in PTPN14, ATP5F1C, APOBEC1, HDAC5, ATF7IP, PARP2, and ACTR3B. The affected genes do not clearly converge on any signaling pathway. CNAs were detected in 5/11 cases (45%), with copy gains involving chromosome 12 occurring in 3/11 cases (27%). In conclusion, no recurrent fusions or pathogenic variants have been detected in the present COF cohort, with copy gains involving chromosome 12 occurring in 27% of cases.
Collapse
Affiliation(s)
- Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil; Medical School, Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Filipe Fideles Duarte-Andrade
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Thais Dos Santos Fontes Pereira
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Letícia Martins Guimarães
- Department of Human Genetics, McGill University, Montreal, Canada; Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Damien Faury
- Department of Pediatrics, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Emily M Nakada
- Department of Pediatrics, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Sylvie Langlois
- Division of Hematology-Oncology, Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Canada; Department of Pediatrics, Université de Montreal, Montreal, Canada
| | - Wagner Henriques de Castro
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Marina Gonçalves Diniz
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Canada; Department of Pediatrics, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Canada
| | - Carolina Cavalieri Gomes
- Department of Human Genetics, McGill University, Montreal, Canada; Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.
| |
Collapse
|
5
|
Güllülü Ö, Mayer BE, Toplek FB. Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita. Int J Mol Sci 2024; 25:1606. [PMID: 38338888 PMCID: PMC10855549 DOI: 10.3390/ijms25031606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Dyskeratosis Congenita (DC) is a multisystem disorder intrinsically associated with telomere dysfunction, leading to bone marrow failure (BMF). Although the pathology of DC is largely driven by mutations in telomere-associated genes, the implications of gene fusions, which emerge due to telomere-induced genomic instability, remain unexplored. We meticulously analyzed gene fusions in RNA-Seq data from DC patients to provide deeper insights into DC's progression. The most significant DC-specific gene fusions were subsequently put through in silico assessments to ascertain biophysical and structural attributes, including charge patterning, inherent disorder, and propensity for self-association. Selected candidates were then analyzed using deep learning-powered structural predictions and molecular dynamics simulations to gauge their potential for forming higher-order oligomers. Our exploration revealed that genes participating in fusion events play crucial roles in upholding genomic stability, facilitating hematopoiesis, and suppressing tumors. Notably, our analysis spotlighted a particularly disordered polyampholyte fusion protein that exhibits robust higher-order oligomerization dynamics. To conclude, this research underscores the potential significance of several high-confidence gene fusions in the progression of BMF in DC, particularly through the dysregulation of genomic stability, hematopoiesis, and tumor suppression. Additionally, we propose that these fusion proteins might hold a detrimental role, specifically in inducing proteotoxicity-driven hematopoietic disruptions.
Collapse
Affiliation(s)
- Ömer Güllülü
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin E. Mayer
- Computational Biology & Simulation, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Fran Bačić Toplek
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| |
Collapse
|
6
|
Erdoğdu İH, Örenay-Boyacıoğlu S, Boyacıoğlu O, Kahraman-Çetin N, Kacar-Döger F, Yavaşoğlu İ, Bolaman AZ. Evaluation of New Generation Sequencing (NGS)-Based Somatic Gene Variations and Real-Time Polymerase Chain Reaction (PCR)-Based Gene Fusions in Elderly and Young Acute Leukemia Patients: A Retrospective View. J Pers Med 2024; 14:140. [PMID: 38392574 PMCID: PMC10890296 DOI: 10.3390/jpm14020140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Malignant diseases occurring in elderly patients follow a different course from younger patients and show different genetic structures. Therefore, in this retrospective study, the somatic gene variant profile and fusion gene profiles of elderly and young acute leukemia patients were determined to draw attention to the existing genetic difference, and the results were compared. In this study, the records of 204 acute leukemia patients aged 18+ who were referred to the Molecular Pathology Laboratory from the Hematology Clinic between 2018 and 2022 were reviewed retrospectively. Fusion gene detection in patients was performed with the HemaVision®-28Q Panel. The NGS Myeloid Neoplasms Panel was conducted using the MiniSEQ NGS platform according to the manufacturer's protocol. When all cases are evaluated together, the most frequently diagnosed acute leukemia is acute myeloid leukemia (85.8%). Both groups had a similar fusion gene profile; however, the fusion burden was higher in the elderly group. When the groups were evaluated in terms of somatic gene variations, there were differences between the groups, and the variation load was higher in the elderly group. Considering the different somatic gene variation profiles, it is understood that the genetic structure of tumor cells is different in elderly patients compared to young cases.
Collapse
Affiliation(s)
- İbrahim Halil Erdoğdu
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Seda Örenay-Boyacıoğlu
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Olcay Boyacıoğlu
- Faculty of Engineering, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Nesibe Kahraman-Çetin
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Füruzan Kacar-Döger
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - İrfan Yavaşoğlu
- Department of Hematology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Ali Zahit Bolaman
- Department of Hematology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| |
Collapse
|
7
|
Watrowski R, Palumbo M, Guerra S, Gallo A, Zizolfi B, Giampaolino P, Bifulco G, Di Spiezio Sardo A, De Angelis MC. Uterine Tumors Resembling Ovarian Sex Cord Tumors (UTROSCTs): A Scoping Review of 511 Cases, Including 2 New Cases. Medicina (Kaunas) 2024; 60:179. [PMID: 38276058 PMCID: PMC10820159 DOI: 10.3390/medicina60010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
Uterine Tumors Resembling Ovarian Sex Cord Tumors (UTROSCTs) are rare uterine mesenchymal neoplasms with uncertain biological potential. These tumors, which affect both premenopausal and postmenopausal women, usually have a benign clinical course. Nevertheless, local recurrences and distant metastases have been described. By analyzing 511 cases retrieved from individual reports and cases series, we provide here the most comprehensive overview of UTROSCT cases available in the literature, supplemented by two new cases of UTROSCTs. Case 1 was an asymptomatic 31-year-old woman who underwent a laparoscopic resection of a presumed leiomyoma. Case 2 was a 58-year-old postmenopausal woman with abnormal vaginal bleeding who underwent an outpatient hysteroscopic biopsy of a suspicious endometrial area. In both cases, immunohistochemical positivity for Calretinin and Inhibin was noted, typical for a sex cord differentiation. In both cases, total laparoscopic hysterectomy with bilateral salpingo-oophorectomy was performed. In light of the available literature, no pathognomonic clinical or imaging finding can be attributed to UTROSCT. Patients usually present with abnormal uterine bleeding or pelvic discomfort, but 20% of them are asymptomatic. In most cases, a simple hysterectomy appears to be the appropriate treatment, but for women who wish to become pregnant, uterus-preserving approaches should be discussed after excluding risk factors. Age, tumor size, lymphovascular space invasion, nuclear atypia, and cervical involvement are not reliable prognostic factors in UTROSCT. The current research suggests that aggressive cases (with extrauterine spread or recurrence) can be identified based on a distinct genetic and immunohistochemical phenotype. For instance, UTROSCTs characterized by GREB1::NCOA1-3 fusions and PD-L1 molecule expression appear to be predisposed to more aggressive behaviors and recurrence, with GREB1::NCOA2 being the most common gene fusion in recurrent tumors. Hence, redefining the criteria for UTROSCTs may allow a better selection of women suitable for fertility-sparing treatments or requiring more aggressive treatments in the future.
Collapse
Affiliation(s)
- Rafał Watrowski
- Department of Obstetrics and Gynecology, Helios Hospital Müllheim, 79379 Müllheim, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mario Palumbo
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Serena Guerra
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Alessandra Gallo
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Brunella Zizolfi
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Pierluigi Giampaolino
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Giuseppe Bifulco
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Attilio Di Spiezio Sardo
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| | - Maria Chiara De Angelis
- Department of Public Health, School of Medicine, University of Naples Federico II, 80138 Naples, Italy; (M.P.); (S.G.); (A.G.); (B.Z.); (P.G.); (G.B.); (A.D.S.S.); (M.C.D.A.)
| |
Collapse
|
8
|
Diks J, Tang Z, Altan M, Anderson S, Chen H, Rashid A, Yang RK, Routbort MJ, Patel KP, Toruner GA, Medeiros LJ, Tang G, Luthra R, Roy-Chowdhuri S. Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence in situ hybridization. Cancer Cytopathol 2024; 132:41-49. [PMID: 37747438 DOI: 10.1002/cncy.22766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing. METHODS A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH. RESULTS Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n = 2) and SLC34A2::ROS1 (n = 1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively. CONCLUSION RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.
Collapse
Affiliation(s)
- John Diks
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Anderson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Kenneth Yang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
9
|
Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2023. [PMID: 38117001 DOI: 10.1002/iub.2801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
Collapse
Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| |
Collapse
|
10
|
Cipri S, Fabozzi F, Del Baldo G, Milano GM, Boccuto L, Carai A, Mastronuzzi A. Targeted therapy for pediatric central nervous system tumors harboring mutagenic tropomyosin receptor kinases. Front Oncol 2023; 13:1235794. [PMID: 38144536 PMCID: PMC10748602 DOI: 10.3389/fonc.2023.1235794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
The family of the neurotrophic tyrosine kinase receptor (NTRK) gene encodes for members of the tropomyosin receptor kinase (TRK) family. Rearrangements involving NTRK1/2/3 are rare oncogenic factors reported with variable frequencies in an extensive range of cancers in pediatrics and adult populations, although they are more common in the former than in the latter. The alterations in these genes are causative of the constitutive activation of TRKs that drive carcinogenesis. In 2017, first-generation TRK inhibitor (TRKi) larotrectinib was granted accelerated approval from the FDA, having demonstrated histologic-agnostic activity against NTRKs fusions tumors. Since this new era has begun, resistance to first-generation TRKi has been described and has opened the development of second-generation molecules, such as selitrectinib and repotrectinib. In this review, we provide a brief overview of the studies on NTRK alterations found in pediatric central nervous system tumors and first and second-generation TRKi useful in clinical practice.
Collapse
Affiliation(s)
- Selene Cipri
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Fabozzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Giada Del Baldo
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Maria Milano
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, United States
| | - Andrea Carai
- Department of Neurosciences, Neurosurgery Unit, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Mastronuzzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| |
Collapse
|
11
|
Cuello M, García-Rivello H, Huamán-Garaicoa F, Irigoyen-Piñeiros P, Lara-Torres CO, Rizzo MM, Ticona-Castro M, Trejo R, Zoroquiain P. Detection of NTRK gene fusions in solid tumors: recommendations from a Latin American group of oncologists and pathologists. Future Oncol 2023; 19:2669-2682. [PMID: 38088163 DOI: 10.2217/fon-2023-0552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
NTRK gene fusions have been detected in more than 25 types of tumors and their prevalence is approximately 0.3% in solid tumors. This low prevalence makes identifying patients who could benefit from TRK inhibitors a considerable challenge. Furthermore, while numerous papers on the evaluation of NTRK fusion genes are available, not all countries have guidelines that are suitable for their setting, as is the case with Latin America. Therefore, a group of oncologists and pathologists from several countries in Latin America (Argentina, Chile, Ecuador, Mexico, Peru and Uruguay) met to discuss and reach consensus on how to identify patients with NTRK gene fusions in solid tumors. To do so, they developed a practical algorithm, considering their specific situation and limitations.
Collapse
Affiliation(s)
- Mauricio Cuello
- Academic Unit of Oncology, Hospital de Clínicas Dr. Manuel Quintela, Montevideo, Uruguay
| | - Hernán García-Rivello
- Departmento of Clinical Pathology, Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), Hospital Italiano, Buenos Aires, Argentina
| | - Fuad Huamán-Garaicoa
- Instituto de Salud Integral (ISAIN), Universidad Católica, Santiago de Guayaquil (Ecuador), Department of Pathology, Sociedad de Lucha Contra el Cáncer del Ecuador (SOLCA), Guayaquil, Ecuador
| | | | - César O Lara-Torres
- Laboratory of Molecular Pathology, Instituto Nacional de Cancerología, Ciudad de México, México
| | - Manglio M Rizzo
- Cancer Immunobiology Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), Facultad de Ciencias Biomédicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Austral, Derqui-Pilar, Argentina
- Department of Medical Oncology, Hospital Universitario Austral, Derqui-Pilar, Argentina
| | - Miguel Ticona-Castro
- Service of Medical Oncology, Hospital Nacional Edgardo Rebagliati Martins, EsSalud - Jesús María, Lima (Perú), Clínica Montefiori, La Molina, Lima, Perú
| | - Rogelio Trejo
- Department of Medical Oncology, Centro Médico Nacional Siglo XXI, Ciudad de México, México
| | - Pablo Zoroquiain
- Pathology Department, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
12
|
Chou A, Qiu MR, Crayton H, Wang B, Ahadi MS, Turchini J, Clarkson A, Sioson L, Sheen A, Singh N, Clifton-Bligh RJ, Robinson BG, Gild ML, Tsang V, Leong D, Sidhu SB, Sywak M, Delbridge L, Aniss A, Wright D, Graf N, Kumar A, Rathi V, Benitez-Aguirre P, Glover AR, Gill AJ. A Detailed Histologic and Molecular Assessment of the Diffuse Sclerosing Variant of Papillary Thyroid Carcinoma. Mod Pathol 2023; 36:100329. [PMID: 37716505 DOI: 10.1016/j.modpat.2023.100329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Diffuse sclerosing variant papillary thyroid carcinoma (DS-PTC) is characterized clinically by a predilection for children and young adults, bulky neck nodes, and pulmonary metastases. Previous studies have suggested infrequent BRAFV600E mutation but common RET gene rearrangements. Using strict criteria, we studied 43 DS-PTCs (1.9% of unselected PTCs in our unit). Seventy-nine percent harbored pathogenic gene rearrangements involving RET, NTRK3, NTRK1, ALK, or BRAF; with the remainder driven by BRAFV600E mutations. All 10 pediatric cases were all gene rearranged (P = .02). Compared with BRAFV600E-mutated tumors, gene rearrangement was characterized by psammoma bodies involving the entire lobe (P = .038), follicular predominant or mixed follicular architecture (P = .003), pulmonary metastases (24% vs none, P = .04), and absent classical, so-called "BRAF-like" atypia (P = .014). There was no correlation between the presence of gene rearrangement and recurrence-free survival. Features associated with persistent/recurrent disease included pediatric population (P = .030), gene-rearranged tumors (P = .020), microscopic extrathyroidal extension (P = .009), metastases at presentation (P = .007), and stage II disease (P = .015). We conclude that DS-PTC represents 1.9% of papillary thyroid carcinomas and that actionable gene rearrangements are extremely common in DS-PTC. DS-PTC can be divided into 2 distinct molecular subtypes and all BRAFV600E-negative tumors (1.5% of papillary thyroid carcinomas) are driven by potentially actionable oncogenic fusions.
Collapse
Affiliation(s)
- Angela Chou
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia.
| | - Min Ru Qiu
- Department of Anatomical Pathology, SydPATH, St Vincent's Hospital, Darlinghurst, New South Wales, Australia; University of NSW, Randwick, New South Wales, Australia
| | - Henry Crayton
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Bin Wang
- Department of Anatomical Pathology, SydPATH, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Mahsa S Ahadi
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia
| | - John Turchini
- Department of Anatomical Pathology, Douglass Hanly Moir Pathology (A Sonic Healthcare Practice), Macquarie Park, New South Wales, Australia; Discipline of Pathology, Macquarie Medical School, Macquarie University, New South Wales, Australia
| | - Adele Clarkson
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia
| | - Loretta Sioson
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia
| | - Amy Sheen
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia
| | - Nisha Singh
- NSW Health Pathology, Cytogenetics Department, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Roderick J Clifton-Bligh
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Bruce G Robinson
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Matti L Gild
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Venessa Tsang
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Department of Endocrinology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - David Leong
- Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia
| | - Stanley B Sidhu
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia
| | - Mark Sywak
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia
| | - Leigh Delbridge
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia
| | - Ahmad Aniss
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia
| | - Dale Wright
- Cytogenetics Department, Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genome Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Nicole Graf
- Histopathology Department, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Amit Kumar
- Diagnostic Genomics, Monash Health Pathology, Monash Health, Clayton, Victoria, Australia
| | - Vivek Rathi
- LifeStrands Genomics, Mount Waverley, Victoria, Australia
| | - Paul Benitez-Aguirre
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Anthony R Glover
- Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, University of Sydney, New South Wales, Australia; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales, Australia.
| | - Anthony J Gill
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Faculty of Medicine and Health Sciences and Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia; Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, New South Wales, Australia.
| |
Collapse
|
13
|
Hahn E, Xu B, Katabi N, Dogan S, Smith SM, Perez-Ordonez B, Patel PB, MacMillan C, Lubin DJ, Gagan J, Weinreb I, Bishop JA. Comprehensive Molecular Characterization of Polymorphous Adenocarcinoma, Cribriform Subtype: Identifying Novel Fusions and Fusion Partners. Mod Pathol 2023; 36:100305. [PMID: 37595638 DOI: 10.1016/j.modpat.2023.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Polymorphous adenocarcinoma (PAC) is a common, usually low-grade salivary gland carcinoma. While conventional PACs are most associated with PRKD1 p.E710D hotspot mutations, the cribriform subtype is often associated with gene fusions in PRKD1, PRKD2, or PRKD3. These fusions have been primarily identified by fluorescence in situ hybridization (FISH) analysis, with a minority evaluated by next-generation sequencing (NGS). Many of the reported fusions were detected by break-apart FISH probes and therefore have unknown partners or were negative by FISH altogether. In this study, we aimed to further characterize the fusions associated with PAC with NGS. Fifty-four PACs (exclusively cribriform and mixed/intermediate types to enrich the study for fusion-positive cases) were identified and subjected to NGS. Fifty-one cases were successfully sequenced, 28 of which demonstrated gene fusions involving PRKD1, PRKD2, or PRKD3. There were 10 cases with the PRKD1 p.E710D mutation. We identified a diverse group of fusion partners, including 13 novel partners, 3 of which were recurrent. The most common partners for the PRKD genes were ARID1A and ARID1B. The wide variety of involved genes is unlike in other salivary gland malignancies and warrants a broader strategy of sequencing for molecular confirmation for particularly challenging cases, as our NGS study shows.
Collapse
Affiliation(s)
- Elan Hahn
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
| | - Bin Xu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | | | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Daniel J Lubin
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ilan Weinreb
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| |
Collapse
|
14
|
Chiosea S, Hodak SP, Yip L, Abraham D, Baldwin C, Baloch Z, Gulec SA, Hannoush ZC, Haugen BR, Joseph L, Kargi AY, Khanafshar E, Livhits MJ, McIver B, Patel K, Patel SG, Randolph GW, Shaha AR, Sharma J, Stathatos N, van Zante A, Carty SE, Nikiforov YE, Nikiforova MN. Molecular Profiling of 50 734 Bethesda III-VI Thyroid Nodules by ThyroSeq v3: Implications for Personalized Management. J Clin Endocrinol Metab 2023; 108:2999-3008. [PMID: 37071871 PMCID: PMC10583990 DOI: 10.1210/clinem/dgad220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023]
Abstract
CONTEXT Comprehensive genomic analysis of thyroid nodules for multiple classes of molecular alterations detected in a large series of fine needle aspiration (FNA) samples has not been reported. OBJECTIVE To determine the prevalence of clinically relevant molecular alterations in Bethesda categories III-VI (BCIII-VI) thyroid nodules. METHODS This retrospective analysis of FNA samples, tested by ThyroSeq v3 using Genomic Classifier and Cancer Risk Classifier at UPMC Molecular and Genomic Pathology laboratory, analyzed the prevalence of diagnostic, prognostic, and targetable genetic alterations in a total of 50 734 BCIII-VI nodules from 48 225 patients. RESULTS Among 50 734 informative FNA samples, 65.3% were test-negative, 33.9% positive, 0.2% positive for medullary carcinoma, and 0.6% positive for parathyroid. The benign call rate in BCIII-IV nodules was 68%. Among test-positive samples, 73.3% had mutations, 11.3% gene fusions, and 10.8% isolated copy number alterations. Comparing BCIII-IV nodules with BCV-VI nodules revealed a shift from predominantly RAS-like alterations to BRAF V600E-like alterations and fusions involving receptor tyrosine kinases (RTK). Using ThyroSeq Cancer Risk Classifier, a high-risk profile, which typically included TERT or TP53 mutations, was found in 6% of samples, more frequently BCV-VI. RNA-Seq confirmed ThyroSeq detection of novel RTK fusions in 98.9% of cases. CONCLUSION In this series, 68% of BCIII-IV nodules were classified as negative by ThyroSeq, potentially preventing diagnostic surgery in this subset of patients. Specific genetic alterations were detected in most BCV-VI nodules, with a higher prevalence of BRAF and TERT mutations and targetable gene fusions compared to BCIII-IV nodules, offering prognostic and therapeutic information for patient management.
Collapse
Affiliation(s)
- Simion Chiosea
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Steven P Hodak
- NYU Robert I. Grossman School of Medicine, NYU Langone Health, New York, NY 12297, USA
| | - Linwah Yip
- Division of Endocrine Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Devaprabu Abraham
- Division of Endocrinology, Department of Internal Medicine, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Chelsey Baldwin
- Division of Endocrinology & Metabolism, George Washington University, Washington, DC 20037, USA
| | - Zubair Baloch
- Perelman School of Medicine Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Seza A Gulec
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Zeina C Hannoush
- Division of Endocrinology, Diabetes and Metabolism. University of Miami, Miller School of Medicine, Miami, FL 33146, USA
| | - Bryan R Haugen
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lija Joseph
- Lowell General Hospital, Boston University and Tufts University, Lowell, MA 01854, USA
| | - Atil Y Kargi
- Division of Endocrinology, Diabetes and Metabolism. University of Miami, Miller School of Medicine, Miami, FL 33146, USA
| | - Elham Khanafshar
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Masha J Livhits
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | | | - Kepal Patel
- NYU Robert I. Grossman School of Medicine, NYU Langone Health, New York, NY 12297, USA
| | - Snehal G Patel
- Department of Surgery, Emory University School of Medicine, Atlanta, GA 30342, USA
| | | | - Ashok R Shaha
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jyotirmay Sharma
- Department of Surgery, Emory University School of Medicine, Atlanta, GA 30342, USA
| | | | - Annemieke van Zante
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sally E Carty
- Division of Endocrine Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| |
Collapse
|
15
|
Giménez‐Capitán A, Sánchez‐Herrero E, Robado de Lope L, Aguilar‐Hernández A, Sullivan I, Calvo V, Moya‐Horno I, Viteri S, Cabrera C, Aguado C, Armiger N, Valarezo J, Mayo‐de‐las‐Casas C, Reguart N, Rosell R, Provencio M, Romero A, Molina‐Vila MA. Detecting ALK, ROS1, and RET fusions and the METΔex14 splicing variant in liquid biopsies of non-small-cell lung cancer patients using RNA-based techniques. Mol Oncol 2023; 17:1884-1897. [PMID: 37243883 PMCID: PMC10483610 DOI: 10.1002/1878-0261.13468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 05/29/2023] Open
Abstract
ALK, ROS1, and RET fusions and MET∆ex14 variant associate with response to targeted therapies in non-small-cell lung cancer (NSCLC). Technologies for fusion testing in tissue must be adapted to liquid biopsies, which are often the only material available. In this study, circulating-free RNA (cfRNA) and extracellular vesicle RNA (EV-RNA) were purified from liquid biopsies. Fusion and MET∆ex14 transcripts were analyzed by nCounter (Nanostring) and digital PCR (dPCR) using the QuantStudio® System (Applied Biosystems). We found that nCounter detected ALK, ROS1, RET, or MET∆ex14 aberrant transcripts in 28/40 cfRNA samples from positive patients and 0/16 of control individuals (70% sensitivity). Regarding dPCR, aberrant transcripts were detected in the cfRNA of 25/40 positive patients. Concordance between the two techniques was 58%. Inferior results were obtained when analyzing EV-RNA, where nCounter often failed due to a low amount of input RNA. Finally, results of dPCR testing in serial liquid biopsies of five patients correlated with response to targeted therapy. We conclude that nCounter can be used for multiplex detection of fusion and MET∆ex14 transcripts in liquid biopsies, showing a performance comparable with next-generation sequencing platforms. dPCR could be employed for disease follow-up in patients with a known alteration. cfRNA should be preferred over EV-RNA for these analyses.
Collapse
Affiliation(s)
- Ana Giménez‐Capitán
- Pangaea Oncology, Laboratory of OncologyDexeus University HospitalBarcelonaSpain
| | - Estela Sánchez‐Herrero
- Atrys HealthBarcelonaSpain
- Liquid Biopsy LaboratoryBiomedical Sciences Research Institute Puerta de Hierro‐MajadahondaMadridSpain
| | - Lucía Robado de Lope
- Liquid Biopsy LaboratoryBiomedical Sciences Research Institute Puerta de Hierro‐MajadahondaMadridSpain
| | | | - Ivana Sullivan
- Dr Rosell Oncology InstituteQuirón Dexeus University HospitalBarcelonaSpain
- Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Virginia Calvo
- Medical Oncology DepartmentHospital Universitario Puerta de Hierro‐MajadahondaSpain
| | - Irene Moya‐Horno
- Hospital Universitario General de Cataluña Grupo QuirónSant Cugat del VallésSpain
| | | | | | - Cristina Aguado
- Pangaea Oncology, Laboratory of OncologyDexeus University HospitalBarcelonaSpain
| | - Noelia Armiger
- Pangaea Oncology, Laboratory of OncologyDexeus University HospitalBarcelonaSpain
| | - Joselyn Valarezo
- Pangaea Oncology, Laboratory of OncologyDexeus University HospitalBarcelonaSpain
| | | | | | - Rafael Rosell
- Dr Rosell Oncology InstituteQuirón Dexeus University HospitalBarcelonaSpain
- Hospital Germans Trias i PujolHealth Sciences Institute and Hospital (IGTP)BarcelonaSpain
| | - Mariano Provencio
- Medical Oncology DepartmentHospital Universitario Puerta de Hierro‐MajadahondaSpain
| | - Atocha Romero
- Liquid Biopsy LaboratoryBiomedical Sciences Research Institute Puerta de Hierro‐MajadahondaMadridSpain
- Medical Oncology DepartmentHospital Universitario Puerta de Hierro‐MajadahondaSpain
| | | |
Collapse
|
16
|
Zhong X, Luan J, Yu A, Lee-Hassett A, Miao Y, Yang L. SFyNCS detects oncogenic fusions involving non-coding sequences in cancer. bioRxiv 2023:2023.04.03.535462. [PMID: 37066382 PMCID: PMC10104044 DOI: 10.1101/2023.04.03.535462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fusion genes are well-known cancer drivers. However, very few known oncogenic fusions involve non-coding sequences. We develop SFyNCS with superior performance to detect fusions of both protein-coding genes and non-coding sequences from transcriptomic sequencing data. We validate fusions using somatic structural variations detected from the genomes. This allows us to comprehensively evaluate various fusion detection and filtering strategies and parameters. We detect 165,139 fusions in 9,565 tumor samples across 33 tumor types in the Cancer Genome Atlas cohort. Among them, 72% of the fusions involve non-coding sequences and many are recurrent. We discover two long non-coding RNAs recurrently fused with various partner genes in 32% of dedifferentiated liposarcomas and experimentally validated the oncogenic functions in mouse model.
Collapse
Affiliation(s)
- Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Jingyun Luan
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Anqi Yu
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Anna Lee-Hassett
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
| | - Yuxuan Miao
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago IL, USA
| |
Collapse
|
17
|
Schubert L, Le AT, Hinz TK, Navarro A, Nelson-Taylor SK, Nemenoff RA, Heasley LE, Doebele RC. A Rapid, Functional sgRNA Screening Method for Generating Murine RET and NTRK1 Fusion Oncogenes. bioRxiv 2023:2023.04.06.535912. [PMID: 37066347 PMCID: PMC10104125 DOI: 10.1101/2023.04.06.535912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
CRISPR/Cas9 gene editing technology is an indispensable and powerful tool in the field of cancer biology. To conduct successful CRISPR-based experiments, it is crucial that sgRNAs generate their designed alterations. Here, we describe a simple and efficient sgRNA screening method for validating sgRNAs that generate oncogenic gene rearrangements. We used IL3-independence in Ba/F3 cells as an assay to identify sgRNA pairs that generate fusion oncogenes involving the Ret and Ntrk1 tyrosine kinases. We confirmed these rearrangements with PCR or RT-PCR as well as sequencing. Ba/F3 cells harboring Ret or Ntrk1 rearrangements acquired sensitivity to RET and TRK inhibitors, respectively. Adenoviruses encoding Cas9 and sgRNAs that catalyze the Kif5b-Ret and Trim24-Ret rearrangements were intratracheally instilled into mice and yielded lung adenocarcinomas. A cell line (TR.1) was established from a Trim24-Ret positive tumor that exhibited high in vitro sensitivity to RET-specific TKIs. Moreover, orthotopic transplantation of TR.1 cells into the left lung yielded well-defined tumors that shrank in response to LOXO-292 treatment. The method offers an efficient means to validate sgRNAs that successfully target their intended loci for the generation of novel murine oncogene-driven tumor models.
Collapse
Affiliation(s)
- Laura Schubert
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Anh T. Le
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Trista K. Hinz
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Andre Navarro
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Raphael A. Nemenoff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lynn E. Heasley
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
- Eastern Colorado VA Healthcare System, Rocky Mountain Regional VA Medical Center, Aurora, CO
| | - Robert C. Doebele
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
18
|
Dermawan JK, Dashti N, Chiang S, Turashvili G, Dickson BC, Ellenson LH, Kirchner M, Stenzinger A, Mechtersheimer G, Agaimy A, Antonescu CR. Expanding the molecular spectrum of gene fusions in endometrial stromal sarcoma: Novel subunits of the chromatin remodeling complexes PRC2 and NuA4/TIP60 as alternative fusion partners. Genes Chromosomes Cancer 2023; 62:152-160. [PMID: 36445224 PMCID: PMC9825654 DOI: 10.1002/gcc.23109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2022] Open
Abstract
Endometrial stromal sarcomas (ESS) are morphologically and molecularly heterogeneous. We report novel gene fusions (EPC1::EED, EPC1::EZH2, ING3::PHF1) identified by targeted RNA sequencing in five cases. The ING3::PHF1-fusion positive ESS presented in a 58-year-old female as extrauterine mesocolonic, ovarian masses, and displayed large, monomorphic ovoid-to-epithelioid cells arranged in solid sheets. The patient remained alive with disease 13 months after surgery. The three ESS with EPC1::EED occurred in the uterine corpus in patients with a median age of 58 years (range 27-62 years). One tumor showed a uniform epithelioid nested morphology, while the other two were composed of monomorphic spindle cells in fascicles with elevated mitotic figures, focal tumor cell necrosis, and lymphovascular invasion. At a median follow-up of 20 months, two patients developed local recurrence, including one with concomitant distant metastasis, while one patient remained free of disease. All three patients were alive at the last follow-up. The EPC1::EZH2-fusion positive ESS presented in a 52-year-old female in the uterus, and displayed uniform spindled cells arranged in short fascicles, with focally elevated mitotic activity but without necrosis. The patient remained free of disease 3 months after surgery. All cases were diffusely positive for CD10; four diffusely express estrogen and progesterone receptors. Our study expands the molecular spectrum of EPC1 and PHF1-related gene fusions in ESS to include additional novel subunits of the PRC2 and/or NuA4/TIP60 complexes. These cases displayed a monomorphic epithelioid or spindled phenotype, spanning low-grade and high-grade cytomorphology, all expressing CD10 and commonly ER and PR, and are prone to local and/or distant spread.
Collapse
Affiliation(s)
- Josephine K. Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nooshin Dashti
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sarah Chiang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Brendan C. Dickson
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Lora H. Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Abbas Agaimy
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg, Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Cristina R. Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
19
|
Kao YC, Yoshida A, Hsieh TH, Nord KH, Saba KH, Ichikawa H, Tsai JW, Huang HY, Chih-Hsueh Chen P, Fletcher CDM, Lee JC. Identification of COL1A1/2 Mutations and Fusions With Noncoding RNA Genes in Bizarre Parosteal Osteochondromatous Proliferation (Nora Lesion). Mod Pathol 2023; 36:100011. [PMID: 36853784 DOI: 10.1016/j.modpat.2022.100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/14/2022] [Accepted: 09/16/2022] [Indexed: 01/11/2023]
Abstract
Bizarre parosteal osteochondromatous proliferation (BPOP) (Nora lesion) is a benign bone surface lesion, which most commonly occurs in the digits of young patients and has a high rate of recurrence. Histologically, it is composed of a mixture of disorganized bone, cartilage, and spindle cells in variable proportions and characterized by amorphous "blue bone" mineralization. Recurrent chromosomal abnormalities, including t(1;17)(q32-42;q21-23) and inv(7)(q21.1-22q31.3-32), have been reported in BPOP. However, the exact genes involved in the rearrangements remain unknown. In this study, we analyzed 8 BPOP cases affecting the fingers, toe, ulna, radius, and fibula of 5 female and 3 male patients, aged 5 to 68 years. RNA sequencing of 5 cases identified genetic fusions between COL1A2 and LINC-PINT in 3 cases and COL1A1::MIR29B2CHG fusion in 1, both validated using fluorescence in situ hybridization and reverse transcription (RT)-PCR. The remaining fusion-negative case harbored 3 COL1A1 mutations as revealed by whole-exome sequencing and confirmed using Sanger sequencing. All these genetic alterations were predicted to cause frameshift and/or truncation of COL1A1/2. The chromosomal locations of COL1A2 (7q21.3), LINC-PINT (7q32.3), COL1A1 (17q21.33), and MIR29B2CHG (1q32.2) were consistent with the breakpoints identified in the previous cytogenetic studies. Subsequent screening of 3 BPOPs using fluorescence in situ hybridization identified 1 additional case each with COL1A1 or COL1A2 rearrangement. Our findings are consistent with reported chromosomal abnormalities and implicate the disruption of type I collagen, and perhaps of either noncoding RNA gene as a tumor suppressor, in the tumorigenesis of BPOP. The prevalence and tumorigenic mechanisms of these COL1A1/2 alterations in BPOP require further investigation.
Collapse
Affiliation(s)
- Yu-Chien Kao
- Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hitoshi Ichikawa
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Jen-Wei Tsai
- Department of Pathology, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | | | | | - Jen-Chieh Lee
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
| |
Collapse
|
20
|
Mandahl N, Mitelman F. Giemsa-negative chromosome bands preferentially recombine in cancer-associated translocations and gene fusions. Genes Chromosomes Cancer 2023; 62:61-74. [PMID: 36116030 PMCID: PMC10092824 DOI: 10.1002/gcc.23095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022] Open
Abstract
Chromosome abnormalities, in particular translocations, and gene fusions are hallmarks of neoplasia. Although both have been recognized as important drivers of cancer for decades, our knowledge of the characterizing features of the cytobands involved in recombinations is poorly understood. The present study, based on a comparative analysis of 10 442 translocation breakpoints and 30 762 gene fusions comprising 13 864 protein-coding genes, is the most comprehensive evaluation of the interactions of cytobands participating in the formation of such rearrangements in cancer. The major conclusion is that although large G-negative, gene-rich bands are most frequently involved, the greatest impact was seen for staining properties. Thus, 60% of the recombinations leading to the formation of both translocations and fusion genes take place between two G-negative bands whereas only about 10% involve two G-positive bands. There is compelling evidence that G-negative bands contain more genes than dark staining bands and it has previously been shown that breakpoints involved in structural chromosome rearrangements and in gene fusions preferentially affect gene-rich bands. The present study not only corroborates these findings but in addition demonstrates that the recombination processes favor the joining of two G-negative cytobands and that this feature may be a stronger factor than gene content. It is reasonable to assume that the formation of translocations and fusion genes in cancer cells, irrespective of whether they have a pathogenetically significant impact or not, may be mediated by some underlying mechanisms that either favor the origin or provide a selective advantage for recombinations of G-negative cytobands.
Collapse
Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Mitelman
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| |
Collapse
|
21
|
Tang YF, An PG, Gu BX, Yi S, Hu X, Wu WJ, Zhang J. Transcriptomic insights into adenoid cystic carcinoma via RNA sequencing. Front Genet 2023; 14:1144945. [PMID: 37152992 PMCID: PMC10160386 DOI: 10.3389/fgene.2023.1144945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Background: The aim of this study was to investigate the underlying mechanisms of adenoid cystic carcinoma (ACC) at the transcriptome level. Materials and methods: We obtained paired tumor and normal salivary gland tissues from 15 ACC patients, which were prepared for RNA sequencing. Results: Gene enrichment analysis revealed that the upregulated pathways were mainly involved in axonogenesis, and the downregulated pathways were mainly related to leukocyte migration, the adaptive immune response, lymphocyte-mediated immunity, and the humoral immune response. T-cells, B-cells and NK cells showed low infiltration in ACC tissues. In addition to the gene fusions MYB-NFIB and MYBL1-NFIB, a new gene fusion, TVP23C-CDRT4, was also detected in 3 ACC tissues. PRAME was significantly upregulated in ACC tissues, while antigen-presenting human leukocyte antigen (HLA) genes were downregulated. Conclusion: We found a new gene fusion, TVP23C-CDRT4, that was highly expressed in ACC. PRAME may be an attractive target for ACC immunotherapy.
Collapse
Affiliation(s)
- Yu-Fang Tang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
- Department of Stomatology, Xinqiao Hospital (the Second Affiliated Hospital), Army Medical University, Chongqing, China
| | - Pu-Gen An
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Bao-Xin Gu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Shu Yi
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Xiao Hu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Wen-Jie Wu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
- *Correspondence: Wen-Jie Wu, ; Jie Zhang,
| | - Jie Zhang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
- National Center of Stomatology and National Clinical Research Center for Oral Diseases, Beijing, China
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
- *Correspondence: Wen-Jie Wu, ; Jie Zhang,
| |
Collapse
|
22
|
Dazio G, Epistolio S, Frattini M, Saletti P. Recent and Future Strategies to Overcome Resistance to Targeted Therapies and Immunotherapies in Metastatic Colorectal Cancer. J Clin Med 2022; 11. [PMID: 36556139 DOI: 10.3390/jcm11247523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide, and 20% of patients with CRC present at diagnosis with metastases. The treatment of metastatic CRC is based on a fluoropyrimidine-based chemotherapy plus additional agents such as oxaliplatin and irinotecan. To date, on the basis of the molecular background, targeted therapies (e.g., monoclonal antibodies against epidermal growth factor receptor or inhibiting angiogenesis) are administered to improve the treatment of metastatic CRC. In addition, more recently, immunological agents emerged as effective in patients with a defective mismatch repair system. The administration of targeted therapies and immunotherapy lead to a significant increase in the survival of patients; however these drugs do not always prove effective. In most cases the lack of effectiveness is due to the development of primary resistance, either a resistance-inducing factor is already present before treatment or resistance is acquired when it occurs after treatment initiation. In this review we describe the most relevant targeted therapies and immunotherapies and expand on the reasons for resistance to the different approved or under development targeted drugs. Then we showed the possible mechanisms and drugs that may lead to overcoming the primary or acquired resistance in metastatic CRC.
Collapse
|
23
|
Yuen LC, Baker ML, Sin JM, Linos K, Kerr DA. A Rare Case of Primary Epithelioid Hemangioma of Bone with WWTR1::FOSB Fusion: A Benign Lesion with the Potential to Mimic Malignancy. Int J Surg Pathol 2022:10668969221117438. [PMID: 35946109 DOI: 10.1177/10668969221117438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epithelioid hemangioma of bone is a rare benign, locally aggressive vascular tumor that can be particularly challenging to diagnose given its frequent multifocality, non-specific imaging findings, and wide range of morphologic appearances. Additionally, some epithelioid hemangiomas demonstrate atypical histologic features including increased cellularity, necrosis, and moderate cytologic atypia - characteristics that may raise concern for malignancy. Molecular studies can serve as a powerful, objective tool in the differential diagnosis of diagnostically challenging epithelioid vascular tumors. Importantly, FOS and FOSB gene rearrangements have been identified as the genetic hallmarks of osseous epithelioid hemangioma, present in greater than 70% of cases. FOSB-fusion-positive epithelioid hemangioma, in particular, may display atypical histologic features. While ZFP36 is the typical FOSB fusion partner in epithelioid hemangioma, we herein present a case of epithelioid hemangioma of bone with a rare WWTR1::FOSB fusion. This case demonstrates the diagnostic challenges associated with epithelioid hemangioma, especially in the setting of FOSB gene rearrangements, and the importance of genomic studies in the work up of these vascular tumors.
Collapse
Affiliation(s)
- Leslie C Yuen
- 12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Michael L Baker
- 12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Pathology and Laboratory Medicine, 22916Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jessica M Sin
- 12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Radiology, 22916Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Konstantinos Linos
- 12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Pathology and Laboratory Medicine, 22916Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Darcy A Kerr
- 12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Pathology and Laboratory Medicine, 22916Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| |
Collapse
|
24
|
Wang H, Li ZW, Ou Q, Wu X, Nagasaka M, Shao Y, Ou SHI, Yang Y. NTRK fusion positive colorectal cancer is a unique subset of CRC with high TMB and microsatellite instability. Cancer Med 2022; 11:2541-2549. [PMID: 35506567 PMCID: PMC9249987 DOI: 10.1002/cam4.4561] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 01/20/2023] Open
Abstract
TRK fusions are rare but targetable mutations which occur across a wide variety of cancer types. We report the prevalence of approximately 0.7% for NTRK‐positive colorectal cancer (CRC) by genetically profiling 2519 colonic and rectal tumors. The aberrations of APC and TP53 frequently co‐occurred with NTRK gene fusions, whereas RAS/BRAF oncogenic alterations and NTRK fusions were almost always mutually exclusive. NTRK‐driven colorectal cancer patients demonstrated increased TMB (median = 53 mut/MB, 95% CI: 36.8–68.0 mut/MB), high microsatellite instability, and an enrichment for POLE/POLD1 mutations when compared to molecularly unstratified colorectal cancer population. These data shed light on possible future approach of multimodality treatment regimen including TRK‐targeted therapy and immune checkpoint inhibitor therapy in NTRK‐positive CRCs.
Collapse
Affiliation(s)
- Hui Wang
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi-Wei Li
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Misako Nagasaka
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California, USA
| | - Yu Yang
- Department of Oncology, the Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| |
Collapse
|
25
|
Thomas J, Sonpavde G. Molecularly Targeted Therapy towards Genetic Alterations in Advanced Bladder Cancer. Cancers (Basel) 2022; 14:1795. [PMID: 35406567 PMCID: PMC8997162 DOI: 10.3390/cancers14071795] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 01/27/2023] Open
Abstract
Despite the introduction of immune checkpoint inhibitors and antibody-drug conjugates to the management of advanced urothelial carcinoma, the disease is generally incurable. The increasing incorporation of next-generation sequencing of tumor tissue into the characterization of bladder cancer has led to a better understanding of the somatic genetic aberrations potentially involved in its pathogenesis. Genetic alterations have been observed in kinases, such as FGFRs, ErbBs, PI3K/Akt/mTOR, and Ras-MAPK, and genetic alterations in critical cellular processes, such as chromatin remodeling, cell cycle regulation, and DNA damage repair. However, activating mutations or fusions of FGFR2 and FGFR3 remains the only validated therapeutically actionable alteration, with erdafitinib as the only targeted agent currently approved for this group. Bladder cancer is characterized by genomic heterogeneity and a high tumor mutation burden. This review highlights the potential relevance of aberrations and discusses the current status of targeted therapies directed at them.
Collapse
Affiliation(s)
- Jonathan Thomas
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
- Division of Medical Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Guru Sonpavde
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
| |
Collapse
|
26
|
Raspin K, O'Malley DE, Marthick JR, Donovan S, Malley RC, Banks A, Redwig F, Skala M, Dickinson JL, FitzGerald LM. Analysis of a large prostate cancer family identifies novel and recurrent gene fusion events providing evidence for inherited predisposition. Prostate 2022; 82:540-550. [PMID: 34994974 DOI: 10.1002/pros.24300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/27/2021] [Accepted: 12/21/2021] [Indexed: 11/12/2022]
Abstract
There is strong interest in the characterisation of gene fusions and their use to enhance clinical practices in prostate cancer (PrCa). Significantly, ~50% of prostate tumours harbour a gene fusion. Inherited factors are thought to predispose to these events but, to date, only one study has investigated gene fusions in a familial context. Here, we examined the prevalence and diversity of gene fusions in 14 tumours from a single large PrCa family, PcTas9, using the TruSight® RNA Fusion Panel and Sanger sequencing validation. These fusions were then explored in The Cancer Genome Atlas (TCGA) PrCa data set (n = 494). Overall, 64.3% of PcTas9 tumours harboured a gene fusion, including known erythroblast transformation-specific (ETS) fusions involving ERG and ETV1, and two novel gene fusions, C19orf48:ETV4 and RYBP:FOXP1. Although 3' ETS genes were overexpressed in PcTas9 and TCGA tumour samples, 3' fusion of FOXP1 did not appear to alter its expression. In addition, PcTas9 fusion carriers were more likely to have lower-grade disease than noncarriers (p = 0.02). Likewise, TCGA tumours with high-grade disease were less likely to harbour fusions (p = 0.03). Our study further implicates an inherited predisposition to PrCa gene fusion events, which are associated with less aggressive tumours. This knowledge could lead to clinical strategies to predict men at risk for fusion-positive PrCa and, thus, identify patients who are more or less at risk of aggressive disease and/or responsive to particular therapies.
Collapse
Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Dannielle E O'Malley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Roslyn C Malley
- Hobart Pathology, Hobart, TAS, Australia
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Frank Redwig
- Department of Urology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Marketa Skala
- WP Holman Clinic, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| |
Collapse
|
27
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
28
|
Chouvarine P, Antić Ž, Lentes J, Schröder C, Alten J, Brüggemann M, Carrillo-de Santa Pau E, Illig T, Laguna T, Schewe D, Stanulla M, Tang M, Zimmermann M, Schrappe M, Schlegelberger B, Cario G, Bergmann AK. Transcriptional and Mutational Profiling of B-Other Acute Lymphoblastic Leukemia for Improved Diagnostics. Cancers (Basel) 2021; 13:5653. [PMID: 34830809 DOI: 10.3390/cancers13225653] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common cancer in children, and significant progress has been made in diagnostics and the treatment of this disease based on the subtypes of BCP-ALL. However, in a large proportion of cases (B-other), recurrent BCP-ALL-associated genomic alterations remain unidentifiable by current diagnostic procedures. In this study, we performed RNA sequencing and analyzed gene fusions, expression profiles, and mutations in diagnostic samples of 185 children with BCP-ALL. Gene expression clustering showed that a subset of B-other samples partially clusters with some of the known subgroups, particularly DUX4-positive. Mutation analysis coupled with gene expression profiling revealed the presence of distinctive BCP-ALL subgroups, characterized by the presence of mutations in known ALL driver genes, e.g., PAX5 and IKZF1. Moreover, we identified novel fusion partners of lymphoid lineage transcriptional factors ETV6, IKZF1 and PAX5. In addition, we report on low blast count detection thresholds and show that the use of EDTA tubes for sample collection does not have adverse effects on sequencing and downstream analysis. Taken together, our findings demonstrate the applicability of whole-transcriptome sequencing for personalized diagnostics in pediatric ALL, including tentative classification of the B-other cases that are difficult to diagnose using conventional methods.
Collapse
|
29
|
Antonescu CR, Dickson BC, Zhang L, Sung YS, Fletcher CD. Unclassified low grade spindle cell sarcoma with storiform pattern characterized by recurrent novel EWSR1/FUS-NACC1 fusions. Mod Pathol 2021; 34:1541-1546. [PMID: 33859361 PMCID: PMC8298288 DOI: 10.1038/s41379-021-00805-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
Despite extraordinary advances in the molecular characterization of soft tissue tumors as a result of the widespread application of next generation sequencing in clinical practice, a subset of lesions remain difficult to diagnose. In this study we describe 3 unclassified spindle cell sarcomas with a monomorphic cytomorphology and distinctive storiform growth, characterized by novel fusions between EWSR1 or FUS1, and NACC1 genes. The tumors occurred in 3 young adult females (age range: 29-31) involving deep soft tissues, two located in the lower extremity and one in the abdominal wall. All three tumors showed patchy positivity for S100 protein, while being negative for SOX10 and retained H3K27me3 expression. All cases were negative for epithelial or muscle markers. As the findings were non-specific, molecular studies using targeted panels of RNA sequencing were performed, including one case tested by TruSight RNA Fusion Panel and 2 cases by Archer FusionPlex. The results showed 2 cases were positive for FUS-NACC1 and one for EWSR1-NACC1 fusions. These findings were further confirmed by FISH using custom BAC probes for a dual-color fusion assay. These results suggest the possibility of a previously undescribed soft tissue neoplasm characterized by a uniform spindle cell phenotype arranged in a storiform and fascicular pattern, expressing S100 protein and harboring NACC1-related fusions. The biologic behavior of this tumor remains to be determined.
Collapse
Affiliation(s)
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Shao Sung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | |
Collapse
|
30
|
Abstract
Cytology samples are suitable for the study of genotypic and phenotypic changes observed in different tumors. Being a minimally invasive technique, cytology sampling has been used as an acceptable alternative to track the alterations associated with tumor progression. Although the detection of gene mutations is well-established on cytology, in the last few years, gene fusion detections are becoming mandatory, especially in some tumor types such as lung cancer. Different technologies are available such as immunocytochemistry, fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, and massive parallel sequencing approaches. Considering that many new drugs targeted fusion proteins, cytological samples can be of use to detect gene fusions in solid and lymphoproliferative tumor patients. In this article, we revised the use of several techniques utilized to check gene fusions in cytological material.
Collapse
Affiliation(s)
- Fernando Schmitt
- Medical Faculty of Porto University, Porto, Portugal.,Unit of Molecular Pathology of Institute of Molecular Pathology and Immunology of University of Porto, Porto, Portugal.,CIntesis@RISE, Porto, Portugal
| | | | | |
Collapse
|
31
|
Berrino E, Bragoni A, Annaratone L, Fenocchio E, Carnevale-Schianca F, Garetto L, Aglietta M, Sarotto I, Casorzo L, Venesio T, Sapino A, Marchiò C. Pursuit of Gene Fusions in Daily Practice: Evidence from Real-World Data in Wild-Type and Microsatellite Instable Patients. Cancers (Basel) 2021; 13:3376. [PMID: 34282766 DOI: 10.3390/cancers13133376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
Agnostic biomarkers such as gene fusions allow to address cancer patients to targeted therapies; however, the low prevalence of these alterations across common malignancies poses challenges and needs a feasible and sensitive diagnostic process. RNA-based targeted next generation sequencing was performed on 125 samples of patients affected either by colorectal carcinoma, melanoma, or lung adenocarcinoma lacking genetic alterations in canonical driver genes, or by a colorectal carcinoma with microsatellite instability. Gene fusion rates were compared with in silico data from MSKCC datasets. For NTRK gene fusion detection we also employed a multitarget qRT-PCR and pan-TRK immunohistochemistry. Gene fusions were detected in 7/55 microsatellite instable colorectal carcinomas (12.73%), and in 4/70 of the "gene driver free" population (5.71%: 3/28 melanomas, 10.7%, and 1/12 lung adenocarcinomas, 8.3%). Fusion rates were significantly higher compared with the microsatellite stable and "gene driver positive" MSKCC cohorts. Pan-TRK immunohistochemistry showed 100% sensitivity, 91.7% specificity, and the occurrence of heterogeneous and/or subtle staining patterns. The enrichment of gene fusions in this "real-world" cohort highlights the feasibility of a workflow applicable in clinical practice. The heterogeneous expression in NTRK fusion positive tumours unveils challenging patterns to recognize and raises questions on the effective translation of the chimeric protein.
Collapse
|
32
|
Kao YC, Bennett JA, Suurmeijer AJH, Dickson BC, Swanson D, Wanjari P, Zhang L, Lee JC, Antonescu CR. Recurrent MEIS1-NCOA2/1 fusions in a subset of low-grade spindle cell sarcomas frequently involving the genitourinary and gynecologic tracts. Mod Pathol 2021; 34:1203-12. [PMID: 33574497 DOI: 10.1038/s41379-021-00744-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/13/2022]
Abstract
Sarcomas with MEIS1-NCOA2 fusions have been so far reported in 2 cases each of primitive renal sarcomas and intraosseous pelvic rhabdomyosarcomas. Their histologic spectrum, anatomic distribution, and clinical behavior remain poorly defined. In this study, we report 6 additional spindle cell sarcomas with MEIS1-NCOA2 or NCOA1 fusions that fall into the same disease spectrum with the previously reported renal sarcomas. The patients' age range was wide (20-76 years, mean 46) and all except one were female. The tumors arose in the kidney (n = 2), and one each in the uterine corpus, vagina, scrotum, and para-rectal region. The consistent morphology was that of monomorphic spindle to ovoid cells in a storiform, whorling, or solid pattern. Alternating cellularity, myxoid stroma, and microcystic changes were seen in some cases. Mitotic activity varied greatly (<1-33/10 high power fields). The immunophenotype was nonspecific, with most cases expressing variable degrees of TLE1, WT1, cyclin D1, CD56, and CD10. Using various platforms of RNA-based targeted sequencing, MEIS1-NCOA2 fusions were recurrently identified in 5 cases, and a novel MEIS1-NCOA1 fusion was found in one renal tumor. The gene fusions were validated by fluorescence in situ hybridization using custom BAC probes. Of the 5 patients with available follow-up (5 months to 8 years), all experienced local recurrences, but no distant spread or death from disease. Our results expand the clinicopathologic spectrum of sarcomas with MEIS1-NCOA2/1 fusions, providing evidence of an undifferentiated spindle cell phenotype with nonspecific immunoprofile and low-grade clinical behavior.
Collapse
|
33
|
Ducker C, Shaw PE. Ubiquitin-Mediated Control of ETS Transcription Factors: Roles in Cancer and Development. Int J Mol Sci 2021; 22:5119. [PMID: 34066106 PMCID: PMC8151852 DOI: 10.3390/ijms22105119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Genome expansion, whole genome and gene duplication events during metazoan evolution produced an extensive family of ETS genes whose members express transcription factors with a conserved winged helix-turn-helix DNA-binding domain. Unravelling their biological roles has proved challenging with functional redundancy manifest in overlapping expression patterns, a common consensus DNA-binding motif and responsiveness to mitogen-activated protein kinase signalling. Key determinants of the cellular repertoire of ETS proteins are their stability and turnover, controlled largely by the actions of selective E3 ubiquitin ligases and deubiquitinases. Here we discuss the known relationships between ETS proteins and enzymes that determine their ubiquitin status, their integration with other developmental signal transduction pathways and how suppression of ETS protein ubiquitination contributes to the malignant cell phenotype in multiple cancers.
Collapse
Affiliation(s)
- Charles Ducker
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Peter E. Shaw
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| |
Collapse
|
34
|
Liu Z, Chen X, Roberts R, Huang R, Mikailov M, Tong W. Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma. Front Pharmacol 2021; 12:608778. [PMID: 33967751 PMCID: PMC8105087 DOI: 10.3389/fphar.2021.608778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
High-risk neuroblastoma (NB) remains a significant therapeutic challenge facing current pediatric oncology patients. Structural variants such as gene fusions have shown an initial promise in enhancing mechanistic understanding of NB and improving survival rates. In this study, we performed a comprehensive in silico investigation on the translational ability of gene fusions for patient stratification and treatment development for high-risk NB patients. Specifically, three state-of-the-art gene fusion detection algorithms, including ChimeraScan, SOAPfuse, and TopHat-Fusion, were employed to identify the fusion transcripts in a RNA-seq data set of 498 neuroblastoma patients. Then, the 176 high-risk patients were further stratified into four different subgroups based on gene fusion profiles. Furthermore, Kaplan-Meier survival analysis was performed, and differentially expressed genes (DEGs) for the redefined high-risk group were extracted and functionally analyzed. Finally, repositioning candidates were enriched in each patient subgroup with drug transcriptomic profiles from the LINCS L1000 Connectivity Map. We found the number of identified gene fusions was increased from clinical the low-risk stage to the high-risk stage. Although the technical concordance of fusion detection algorithms was suboptimal, they have a similar biological relevance concerning perturbed pathways and regulated DEGs. The gene fusion profiles could be utilized to redefine high-risk patient subgroups with significant onset age of NB, which yielded the improved survival curves (Log-rank p value ≤ 0.05). Out of 48 enriched repositioning candidates, 45 (93.8%) have antitumor potency, and 24 (50%) were confirmed with either on-going clinical trials or literature reports. The gene fusion profiles have a discrimination power for redefining patient subgroups in high-risk NB and facilitate precision medicine-based drug repositioning implementation.
Collapse
Affiliation(s)
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Xi Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, United Kingdom.,University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Mike Mikailov
- Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| |
Collapse
|
35
|
Abstract
Orthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artifacts. In this article, we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups, and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultrafast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm. Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups. Tested on two benchmark data sets, Broccoli outperforms current orthology pipelines. In addition, Broccoli is scalable, with runtimes similar to those of recent distance-based pipelines. Given its high level of performance and efficiency, this new pipeline represents a suitable choice for comparative genomic studies. Broccoli is freely available at https://github.com/rderelle/Broccoli.
Collapse
Affiliation(s)
- Romain Derelle
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France.,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, QC, Canada
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
36
|
Cai L, Chen Y, Tong X, Wu X, Bao H, Shao Y, Luo Z, Wang X, Cao Y. The genomic landscape of young and old lung cancer patients highlights age-dependent mutation frequencies and clinical actionability in young patients. Int J Cancer 2021; 149:883-892. [PMID: 33811322 DOI: 10.1002/ijc.33583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 11/09/2022]
Abstract
The aim of the study was to investigate age-dependent tendency of genomic alterations in lung cancer, and also to examine mutational profiles and its association with clinical treatment outcomes in young adenocarcinoma patients. By studying 7858 lung cancer samples using targeted-gene sequencing, we investigated genomic differences and clinical on-treatment time (OTT) to different therapies between young (≤ 45 years) and old (> 45 years) patients. The age-dependent trend test for genomic alterations in all patients revealed steady increases in tumor mutation burden and alterations in a number of genes with age, including KRAS, MET, CDKN2A, PIK3CA and MDM2, while the frequencies of ALK, ROS1 and RET fusions and ERBB2 mutations were decreasing. The highest rate of EGFR alterations was observed in the 45 ~ 50 years age group. Comparisons of young and old adenocarcinoma patients found that young patients were characterized by a higher prevalence of ALK, ROS1 and RET fusions, and ERBB2 exon-20 insertions and EGFR exon-19 deletions. Actionable mutations were highly prevalent in young adenocarcinoma patients, with 88% of patients harboring at least one actionable genetic alteration. First-line therapies in EGFR-positive patients (n = 979) by EGFR tyrosine kinase inhibitors or chemotherapy resulted in similar OTT between young and old patients. Somatic interaction analyses implied that young EGFR-positive patients were more likely to also have PIK3CA, MET, TP53 and RB1 mutations than old patients. Lung cancer in young patients, and especially those with adenocarcinoma, exhibited different clinical features and genomic attributes compared to old patients, which should be considered for therapeutic decision-making purposes.
Collapse
Affiliation(s)
- Lei Cai
- Department of Thoracic Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Zhejiang, Hangzhou, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou, China
| | - Yong Chen
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Xiaoling Tong
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Ontario, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Ontario, Canada
| | - Hua Bao
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Ontario, Canada
| | - Yang Shao
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhuang Luo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunan, China
| | - Xuming Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunan, China
| | - Yang Cao
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| |
Collapse
|
37
|
Yang SR, Aypar U, Rosen EY, Mata DA, Benayed R, Mullaney K, Jayakumaran G, Zhang Y, Frosina D, Drilon A, Ladanyi M, Jungbluth AA, Rekhtman N, Hechtman JF. A Performance Comparison of Commonly Used Assays to Detect RET Fusions. Clin Cancer Res 2021; 27:1316-1328. [PMID: 33272981 PMCID: PMC8285056 DOI: 10.1158/1078-0432.ccr-20-3208] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 01/02/2023]
Abstract
PURPOSE Selpercatinib and pralsetinib induce deep and durable responses in patients with advanced RET fusion-positive lung and thyroid cancer. RET fusion testing strategies with rapid and reliable results are critical given recent FDA approval. Here, we assess various clinical assays in a large pan-cancer cohort. EXPERIMENTAL DESIGN Tumors underwent DNA-based next-generation sequencing (NGS) with reflex to RNA-based NGS if no mitogenic driver or if a RET structural variant of unknown significance (SVUS) were present. Canonical DNA-level RET fusions and RNA-confirmed RET fusions were considered true fusions. Break-apart FISH and IHC performance were assessed in subgroups. RESULTS A total of 171 of 41,869 patients with DNA NGS harbored RET structural variants, including 139 canonical fusions and 32 SVUS. Twelve of 32 (37.5%) SVUS were transcribed into RNA-level fusions, resulting in 151 oncogenic RET fusions. The most common RET fusion-positive tumor types were lung (65.6%) and thyroid (23.2%). The most common partners were KIF5B (45%), CCDC6 (29.1%), and NCOA4 (13.3%). DNA NGS showed 100% (46/46) sensitivity and 99.6% (4,459/4,479) specificity. FISH showed 91.7% (44/48) sensitivity, with lower sensitivity for NCOA4-RET (66.7%, 8/12). A total of 87.5% (7/8) of RET SVUS negative for RNA-level fusions demonstrated rearrangement by FISH. The sensitivity of IHC varied by fusion partner: KIF5B sensitivity was highest (100%, 31/31), followed by CCDC6 (88.9%, 16/18) and NCOA4 (50%, 6/12). Specificity of RET IHC was 82% (73/89). CONCLUSIONS Although DNA sequencing has high sensitivity and specificity, RNA sequencing of RET SVUS is necessary. Both FISH and IHC demonstrated lower sensitivity for NCOA4-RET fusions.
Collapse
Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
38
|
Abstract
Introduction: Characteristic of some rare pediatric and adult malignancies, addiction to the NTRK oncogene family is also observed in a small fraction of common cancers. Inhibition of their protein products, the Trk kinases, proved a successful treatment strategy for these tumors.Areas covered: The current paper reviews the clinical development of larotrectinib, a selective inhibitor of the Trk kinase family, for the treatment of NTRK fusion-positive cancers. The manuscript includes an overview of the efficacy, safety, pharmacokinetics and pharmacodynamics. The authors sum up by providing the reader with their expert opinion on larotrectinib and its potential future use.Expert opinion: Larotrectinib showed tolerability and high efficacy, regardless of the primary site. In 2018, larotrectinib was granted by the Food and Drug Administration a tissue-agnostic approval for the treatment of solid tumors harboring an NTRK fusion. The major challenges will be the implementation of the screening for NTRK fusions in the general oncologic population, and the incorporation of larotrectinib into the therapeutic algorithms.
Collapse
Affiliation(s)
- Roberto Filippi
- Medical Oncology 1 - AOU Città Della Salute E Della Scienza Di Torino; Candiolo Cancer Institute, FPO - IRCCS Candiolo; Department of Oncology, University of Turin, Turin, Italy
| | - Ilaria Depetris
- Medical Oncology, Ospedale Civile Di Ivrea, Ivrea, Turin, Italy
| | - Maria Antonietta Satolli
- Medical Oncology 1 - AOU Città Della Salute E Della Scienza Di Torino; Department of Oncology, University of Turin, Turin, Italy
| |
Collapse
|
39
|
Abstract
Fusion RNAs are a hallmark of some cancers. They result either from chromosomal rearrangements or from splicing mechanisms that are non-chromosomal rearrangements. Chromosomal rearrangements that result in gene fusions are particularly prevalent in sarcomas and hematopoietic malignancies; they are also common in solid tumors. The splicing process can also give rise to more complex RNA patterns in cells. Gene fusions frequently affect tyrosine kinases, chromatin regulators, or transcription factors, and can cause constitutive activation, enhancement of downstream signaling, and tumor development, as major drivers of oncogenesis. In addition, some fusion RNAs have been shown to function as noncoding RNAs and to affect cancer progression. Fusion genes and RNAs will therefore become increasingly important as diagnostic and therapeutic targets for cancer development. Here, we discuss the function, biogenesis, detection, clinical relevance, and therapeutic implications of oncogenic fusion genes and RNAs in cancer development. Further understanding the molecular mechanisms that regulate how fusion RNAs form in cancers is critical to the development of therapeutic strategies against tumorigenesis.
Collapse
Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Cancer Genomics and Precision Medicine, Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido 078-8510, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
40
|
Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| |
Collapse
|
41
|
De Luca C, Pepe F, Iaccarino A, Pisapia P, Righi L, Listì A, Greco L, Gragnano G, Campione S, De Dominicis G, Pagni F, Sgariglia R, Nacchio M, Tufano R, Conticelli F, Vigliar E, Bellevicine C, Cortinovis DL, Novello S, Molina-Vila MA, Rosell R, Troncone G, Malapelle U. RNA-Based Assay for Next-Generation Sequencing of Clinically Relevant Gene Fusions in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13010139. [PMID: 33406752 PMCID: PMC7796105 DOI: 10.3390/cancers13010139] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/02/2021] [Indexed: 02/07/2023] Open
Abstract
Gene fusions represent novel predictive biomarkers for advanced non-small cell lung cancer (NSCLC). In this study, we validated a narrow NGS gene panel able to cover therapeutically-relevant gene fusions and splicing events in advanced-stage NSCLC patients. To this aim, we first assessed minimal complementary DNA (cDNA) input and the limit of detection (LoD) in different cell lines. Then, to evaluate the feasibility of applying our panel to routine clinical samples, we retrospectively selected archived lung adenocarcinoma histological and cytological (cell blocks) samples. Overall, our SiRe RNA fusion panel was able to detect all fusions and a splicing event harbored in a RNA pool diluted up to 2 ng/µL. It also successfully analyzed 46 (95.8%) out of 48 samples. Among these, 43 (93.5%) out of 46 samples reproduced the same results as those obtained with conventional techniques. Intriguingly, the three discordant results were confirmed by a CE-IVD automated real-time polymerase chain reaction (RT-PCR) analysis (Easy PGX platform, Diatech Pharmacogenetics, Jesi, Italy). Based on these findings, we conclude that our new SiRe RNA fusion panel is a valid and robust tool for the detection of clinically relevant gene fusions and splicing events in advanced NSCLC.
Collapse
Affiliation(s)
- Caterina De Luca
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Luisella Righi
- Department of Oncology, San Luigi University Hospital, University of Turin, 10043 Orbassano, Italy; (L.R.); (A.L.)
| | - Angela Listì
- Department of Oncology, San Luigi University Hospital, University of Turin, 10043 Orbassano, Italy; (L.R.); (A.L.)
| | - Lorenza Greco
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Severo Campione
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | - Gianfranco De Dominicis
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | - Fabio Pagni
- Department of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy; (F.P.); (D.L.C.)
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Rossella Tufano
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80131 Naples, Italy;
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Diego Luigi Cortinovis
- Department of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy; (F.P.); (D.L.C.)
| | - Silvia Novello
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | | | - Rafael Rosell
- Cancer Biology and Precision Medicine Program Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital Badalona, 08916 Barcelona, Spain;
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
- Correspondence: ; Fax: +39-(011)-0817-463-679
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| |
Collapse
|
42
|
Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
Collapse
Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
| |
Collapse
|
43
|
Ferrari A, Ghelli Luserna Di Rora A, Domizio C, Papayannidis C, Simonetti G, Maria Hernández-Rivas J, Rondoni M, Giglio F, Abruzzese E, Imovilli A, Iacobucci I, Calistri D, Martinelli G. Rearrangements of ATP5L-KMT2A in acute lymphoblastic leukaemia. Br J Haematol 2020; 192:e139-e144. [PMID: 33314053 DOI: 10.1111/bjh.17265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Anna Ferrari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| | - Andrea Ghelli Luserna Di Rora
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| | - Chiara Domizio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy.,Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Cristina Papayannidis
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
| | - Giorgia Simonetti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| | | | - Michela Rondoni
- Hematology Unit & Romagna Transplant Network, Ravenna Hospital, Ravenna, Italy
| | - Fabio Giglio
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| | - Giovanni Martinelli
- Scientific Directorate, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| |
Collapse
|
44
|
Di Dalmazi G, Altieri B, Scholz C, Sbiera S, Luconi M, Waldman J, Kastelan D, Ceccato F, Chiodini I, Arnaldi G, Riester A, Osswald A, Beuschlein F, Sauer S, Fassnacht M, Appenzeller S, Ronchi CL. RNA Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights. J Clin Endocrinol Metab 2020; 105:5900388. [PMID: 32875319 DOI: 10.1210/clinem/dgaa616] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
CONTEXT Pathogenesis of autonomous steroid secretion and adrenocortical tumorigenesis remains partially obscure. OBJECTIVE To investigate the relationship between transcriptome profile and genetic background in a large series of adrenocortical tumors and identify new potential pathogenetic mechanisms. DESIGN Cross-sectional study. SETTING University Hospitals of the European Network for the Study of Adrenal Tumors (ENSAT). PATIENTS We collected snap-frozen tissue from patients with adrenocortical tumors (n = 59) with known genetic background: 26 adenomas with Cushing syndrome (CS- cortisol-producing adenoma [CPA]), 17 adenomas with mild autonomous cortisol secretion (MACS-CPAs), 9 endocrine-inactive adenomas (EIAs), and 7 adrenocortical carcinomas (ACCs). INTERVENTION Ribonucleic acid (RNA) sequencing. MAIN OUTCOME MEASURES Gene expression, long noncoding RNA (lncRNA) expression, and gene fusions. Correlation with genetic background defined by targeted Sanger sequencing, targeted panel- or whole-exome sequencing. RESULTS Transcriptome analysis identified 2 major clusters for adenomas: Cluster 1 (n = 32) mainly consisting of MACS-CPAs with CTNNB1 or without identified driver mutations (46.9% of cases) and 8/9 EIAs; Cluster 2 (n = 18) that comprised CP-CPAs with or without identified driver mutation in 83.3% of cases (including all CS-CPAs with PRKACA mutation). Two CS-CPAs, 1 with CTNNB1 and 1 with GNAS mutation, clustered separately and relatively close to ACC. lncRNA analysis well differentiate adenomas from ACCs. Novel gene fusions were found, including AKAP13-PDE8A in one CS-CPA sample with no driver mutation. CONCLUSIONS MACS-CPAs and EIAs showed a similar transcriptome profile, independently of the genetic background, whereas most CS-CPAs clustered together. Still unrevealed molecular alterations in the cAMP/PKA or Wnt/beta catenin pathways might be involved in the pathogenesis of adrenocortical tumors.
Collapse
Affiliation(s)
- Guido Di Dalmazi
- Endocrinology Unit, Department of Medical and Surgical Sciences, University of Bologna, Italy
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Claus Scholz
- Life and Medical Sciences Institute, University of Bonn, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Michaela Luconi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | | | - Darko Kastelan
- Department of Endocrinology, University Hospital Center Zagreb, Croatia
| | - Filippo Ceccato
- Endocrinology Unit, Department of Medicine DIMED, University-Hospital of Padua, Italy
| | - Iacopo Chiodini
- Istituto Auxologico Italiano, IRCCS, Unit for Bone Metabolism Diseases and Diabetes & Lab of Endocrine and Metabolic Research, Milan, Italy
- University of Milan, Milan, Italy
| | - Giorgio Arnaldi
- Division of Endocrinology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Andrea Osswald
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
- Klinik für Endokrinologie Diabetologie und Klinische Ernährung, Universitäts Spital Zürich, Zürich, Switzerland
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine/Berlin Institute of Health, Berlin, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Silke Appenzeller
- Core Unit BioinformaticFsupps, Comprehensive Cancer Center Mainfranken, University of Würzburg, Germany
| | - Cristina L Ronchi
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
- Institute of Metabolism and Systems Research, University of Birmingham, United Kingdom
| |
Collapse
|
45
|
Chunn LM, Nefcy DC, Scouten RW, Tarpey RP, Chauhan G, Lim MS, Elenitoba-Johnson KSJ, Schwartz SA, Kiel MJ. Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation. Front Genet 2020; 11:577152. [PMID: 33281875 PMCID: PMC7691534 DOI: 10.3389/fgene.2020.577152] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Design and interpretation of genome sequencing assays in clinical diagnostics and research labs is complicated by an inability to identify information from the medical literature and related databases quickly, comprehensively and reproducibly. This challenge is compounded by the complexity and heterogeneity of nomenclatures used to describe diseases, genes and genetic variants. Mastermind is a widely-used bioinformatic platform of genomic associations that has indexed more than 7.5 M full-text articles and 2.5 M supplemental datasets. It has automatically identified, disambiguated and annotated >6.1 M genetic variants and identified >50 K disease-gene associations. Here, we describe how Mastermind improves the sensitivity and reproducibility of clinical variant interpretation and produces comprehensive genomic landscapes of genetic variants driving pharmaceutical research. We demonstrate an alarmingly high degree of heterogeneity across commercially available panels for hereditary cancer that is resolved by evidence from Mastermind. We further examined the sensitivity of Mastermind for variant interpretation by examining 108 clinically-encountered variants and comparing the results to alternate methods. Mastermind demonstrated a sensitivity of 98.4% compared to 4.4, 45.6, and 37.4% for alternatives PubMed, Google Scholar, and ClinVar, respectively, and a specificity of 98.5% compared to 45.1, 57.6, and 68.8% as well as an increase in content yield of 22.6-, 2.2-, and 2.6-fold. When curated for clinical significance, Mastermind identified more than 4.9-fold more pathogenic variants than ClinVar for representative genes. For structural variants, we compared Mastermind's ability to sensitively identify evidence for 10 representative disease-causing CNVs versus results identified in PubMed, as well as its ability to identify evidence for fusion events compared to COSMIC. Mastermind demonstrated a 4.0- to 43.9-fold increase in references for specific CNVs compared to PubMed, as well as 5.4-fold more fusion genes when compared with COSMIC's curated database. Additionally, Mastermind produced an 8.0-fold increase in reference citations for fusion events common to Mastermind and outside databases. Taken together, these results demonstrate the utility and superiority of Mastermind in terms of both sensitivity and specificity of automated results for clinical diagnostic variant interpretation for multiple genetic variant types and highlight the potential benefit in informing pharmaceutical research.
Collapse
Affiliation(s)
| | | | | | - Ryan P. Tarpey
- The Johns Hopkins Hospital, Department of Pharmacy, Baltimore, MD, United States
| | | | - Megan S. Lim
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kojo S. J. Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | | | | |
Collapse
|
46
|
Christiansen L, Alanin KS, Phippen CBW, Olsson S, Stougaard P, Hennessy RC. Fungal-Associated Molecules Induce Key Genes Involved in the Biosynthesis of the Antifungal Secondary Metabolites Nunamycin and Nunapeptin in the Biocontrol Strain Pseudomonas fluorescens In5. Appl Environ Microbiol 2020; 86:e01284-20. [PMID: 32826219 DOI: 10.1128/AEM.01284-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens In5 synthesizes the antifungal cyclic lipopeptides (CLPs) nunamycin and nunapeptin, which are similar in structure and genetic organization to the pseudomonas-derived phytotoxins syringomycin and syringopeptin. Regulation of syringomycin and syringopeptin is dependent on the two-component global regulatory system GacS-GacA and the SalA, SyrF, and SyrG transcription factors, which activate syringomycin synthesis in response to plant signal molecules. Previously, we demonstrated that a specific transcription factor, NunF, positively regulates the synthesis of nunamycin and nunapeptin in P. fluorescens In5 and that the nunF gene is upregulated by fungal-associated molecules. This study focused on further unravelling the complex regulation governing CLP synthesis in P. fluorescens In5. Promoter fusions were used to show that the specific activator NunF is dependent on the global regulator of secondary metabolism GacA and is regulated by fungal-associated molecules and low temperatures. In contrast, GacA is stimulated by plant signal molecules leading to the hypothesis that P. fluorescens is a hyphosphere-associated bacterium carrying transcription factor genes that respond to signals indicating the presence of fungi and oomycetes. Based on these findings, we present a model for how synthesis of nunamycin and nunapeptin is regulated by fungal- and oomycete-associated molecules.IMPORTANCE Cyclic lipopeptide (CLP) synthesis gene clusters in pseudomonads display a high degree of synteny, and the structures of the peptides synthesized are very similar. Accordingly, the genomic island encoding the synthesis of syringomycin and syringopeptin in P. syringae pv. syringae closely resembles that of P. fluorescens In5, which contains genes coding for synthesis of the antifungal and anti-oomycete peptides nunamycin and nunapeptin, respectively. However, the regulation of syringomycin and syringopeptin synthesis is different from that of nunamycin and nunapeptin synthesis. While CLP synthesis in the plant pathogen P. syringae pv. syringae is induced by plant signal molecules, such compounds do not significantly influence synthesis of nunamycin and nunapeptin in P. fluorescens In5. Instead, fungal-associated molecules positively regulate antifungal peptide synthesis in P. fluorescens In5, while the synthesis of the global regulator GacA in P. fluorescens In5 is positively regulated by plant signal molecules but not fungal-associated molecules.
Collapse
|
47
|
Chua SM, Fraser JA. Surveying purine biosynthesis across the domains of life unveils promising drug targets in pathogens. Immunol Cell Biol 2020; 98:819-831. [PMID: 32748425 DOI: 10.1111/imcb.12389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Purines play an integral role in cellular processes such as energy metabolism, cell signaling and encoding the genetic makeup of all living organisms-ensuring that the purine metabolic pathway is maintained across all domains of life. To gain a deeper understanding of purine biosynthesis via the de novo biosynthetic pathway, the genes encoding purine metabolic enzymes from 35 archaean, 69 bacterial and 99 eukaryotic species were investigated. While the classic elements of the canonical purine metabolic pathway were utilized in all domains, a subset of familiar biochemical roles was found to be performed by unrelated proteins in some members of the Archaea and Bacteria. In the Bacteria, a major differentiating feature of de novo purine biosynthesis is the increasing prevalence of gene fusions, where two or more purine biosynthesis enzymes that perform consecutive biochemical functions in the pathway are encoded by a single gene. All species in the Eukaryota exhibited the most common fusions seen in the Bacteria, in addition to new gene fusions to potentially increase metabolic flux. This complexity is taken further in humans, where a reversible biomolecular assembly of enzymes known as the purinosome has been identified, allowing short-term regulation in response to metabolic cues while expanding on the benefits that can come from gene fusion. By surveying purine metabolism across all domains of life, we have identified important features of the purine biosynthetic pathway that can potentially be exploited as prospective drug targets.
Collapse
Affiliation(s)
- Sheena Mh Chua
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
48
|
Brahmi M, Franceschi T, Treilleux I, Pissaloux D, Ray-Coquard I, Dufresne A, Vanacker H, Carbonnaux M, Meeus P, Sunyach MP, Bouhamama A, Karanian M, Meurgey A, Blay JY, Tirode F. Molecular Classification of Endometrial Stromal Sarcomas Using RNA Sequencing Defines Nosological and Prognostic Subgroups with Different Natural History. Cancers (Basel) 2020; 12:cancers12092604. [PMID: 32933053 PMCID: PMC7563240 DOI: 10.3390/cancers12092604] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
A series of 42 patient tumors diagnosed as endometrial stromal sarcoma (ESS) based on the morphology but negative for JAZF1 and/or YWHAE rearrangement in FISH was analyzed by RNA-sequencing. A chromosomal rearrangement was identified in 31 (74%) of the cases and a missense mutation in known oncogenes/tumor suppressor genes in 11 (26%). Cluster analyses on the expression profiles from this series together with a control cohort composed of five samples of low grade ESS harboring a JAZF1-SUZ12 fusion, one high grade ESS harboring a BCOR-ITD, two uterine tumors resembling ovarian sex cord tumors, two samples each of uterine leiomyoma and leiomyosarcomas and a series of BCOR-rearranged family of tumor (n = 8) indicated that tumors could be gather in three distinct subgroups: one mainly composed of BCOR-rearranged samples that contained seven ESS samples, one mainly composed of JAZF1-fused ESS (n = 15) and the last composed of various molecular subtypes (n = 19). These three subgroups display different gene signatures, different in silico cell cycle scores and very different clinical presentations, natural history and survival (log-rank test, p = 0.004). While YWHAE-NUTM2 fusion genes may be present in both high and low grade ESS, the high-grade presents with additional BCOR or BCORL1 gene mutations. RNAseq brings clinically relevant molecular classification, enabling the reclassification of diseases and the guidance of therapeutic strategy.
Collapse
Affiliation(s)
- Mehdi Brahmi
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
- Correspondence: (M.B.); (F.T.)
| | - Tatiana Franceschi
- Department of Biopathology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (T.F.); (I.T.); (A.M.)
| | - Isabelle Treilleux
- Department of Biopathology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (T.F.); (I.T.); (A.M.)
| | - Daniel Pissaloux
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
- Department of Biopathology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (T.F.); (I.T.); (A.M.)
| | - Isabelle Ray-Coquard
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
| | - Armelle Dufresne
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
| | - Helene Vanacker
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
| | - Melodie Carbonnaux
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
| | - Pierre Meeus
- Department of Surgery, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France;
| | - Marie-Pierre Sunyach
- Department of Radiation Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France;
| | - Amine Bouhamama
- Department of Radiology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France;
| | - Marie Karanian
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
- Department of Biopathology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (T.F.); (I.T.); (A.M.)
| | - Alexandra Meurgey
- Department of Biopathology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (T.F.); (I.T.); (A.M.)
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
| | - Franck Tirode
- Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69008 Lyon, France; (I.R.-C.); (A.D.); (H.V.); (M.C.); (J.-Y.B.)
- Cancer Research Center of Lyon, Centre Léon Bérard, Univ Lyon, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; (D.P.); (M.K.)
- Correspondence: (M.B.); (F.T.)
| |
Collapse
|
49
|
Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:diagnostics10080521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
Collapse
Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
- Correspondence:
| |
Collapse
|
50
|
Hodgson A, Swanson D, Tang S, Dickson BC, Turashvili G. Gene fusions characterize a subset of uterine cellular leiomyomas. Genes Chromosomes Cancer 2020; 59:688-696. [PMID: 32677742 DOI: 10.1002/gcc.22888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/03/2020] [Accepted: 07/14/2020] [Indexed: 01/12/2023] Open
Abstract
Uterine leiomyomas are the most common benign tumor of the female genital tract. Previous studies have shown that conventional leiomyomas often harbor-specific alterations including rearrangements involving HMGA2. Cellular leiomyomas are a variant of uterine leiomyoma that are less well-studied from a genomic point of view. Morphologically and immunohistochemically, cellular leiomyomas may be confused with low-grade endometrial stromal neoplasms, a group of tumors which frequently harbor a number of recurrent gene fusions. Ancillary molecular testing may be used to investigate tumors where low-grade endometrial stromal neoplasms enter into the differential diagnosis. At our institution, we identified a uterine cellular leiomyoma harboring a HMGA2-TRAF3IP2 fusion. After a retrospective review 11 additional tumors were identified. All included cases were reviewed and evaluated for immunohistochemical expression of smooth muscle actin, desmin, h-caldesmon, CD10, estrogen receptor, and progesterone receptor. RNA sequencing using the TruSight RNA Fusion Panel was performed on formalin-fixed paraffin-embedded tissue samples. In addition to the index case, two other cases harbored fusions: HMGA2-NAA11 and TPCN2-YAP1, of which the latter is novel and was confirmed with reverse transcriptase-polymerase chain reaction. In conclusion, a subset of cellular leiomyomas harbor rearrangements involving HMGA2, suggesting molecular kinship with conventional uterine leiomyomas. In addition, the prevalence of the novel TPCN2-YAP1 gene fusion in cellular leiomyomas requires further study. The fusions reported here, when identified, may be useful when the diagnosis of cellular leiomyoma is in question.
Collapse
Affiliation(s)
- Anjelica Hodgson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Shangguo Tang
- Department of Pathology, McMaster University Medical Centre, Hamilton, Ontario, Canada
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|