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Tali G, Payne AE, Hudson TJ, da Silva SD, Pusztaszeri M, Tamilia M, Forest VI. The Difference in Clinical Behavior of Gene Fusions Involving RET/PTC Fusions and THADA/IGF2BP3 Fusions in Thyroid Nodules. Cancers (Basel) 2023; 15:3394. [PMID: 37444504 DOI: 10.3390/cancers15133394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Molecular testing has been used as an adjunct to morphological evaluation in the workup of thyroid nodules. This study investigated the impact of two gene fusions, RET/PTC and THADA/IGF2BP3, that have been described as oncogenic events in thyroid neoplasms. METHODS We performed a retrospective, single-centered study at a McGill University teaching hospital in Montreal, Canada, from January 2016 to August 2021. We included patients who underwent surgery for thyroid nodules that pre-operatively underwent molecular testing showing either RET/PTC or THADA/IGF2BP3 gene fusion. RESULTS This study included 697 consecutive operated thyroid nodules assessed using molecular testing, of which five had the RET/PTC fusion and seven had the THADA/IGF2BP3 fusion. Of the five nodules in the RET/PTC group, 100% were malignant and presented as Bethesda V/VI. Eighty percent (4/5) were found to have lymph node metastasis. Twenty percent (1/5) had extrathyroidal extensions. Sixty percent (3/5) were a diffuse sclerosing variant of papillary thyroid carcinoma, and the rest were the classical variant. Of the seven THADA/IGF2BP3 nodules, all presented as Bethesda III/IV and 71.4% (5/7) were malignant based on the final pathology analysis, and 28.6% (2/7) were NIFTP. All the THADA/IGF2BP3 fusion malignancies were a follicular variant of papillary thyroid carcinoma. None had lymph node metastasis or displayed extrathyroidal extensions. CONCLUSIONS RET/PTC nodules presented as Bethesda V/VI and potentially had more aggressive features, whereas THADA/IGF2BP3 nodules presented as Bethesda III/IV and had more indolent behavior. This understanding may allow clinicians to develop more targeted treatment plans, such as the extent of surgery and adjuvant radioactive iodine treatment.
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Affiliation(s)
- George Tali
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Alexandra E Payne
- Health Science Program, Marianopolis College, Westmount, QC H3Y 1X9, Canada
| | - Thomas J Hudson
- Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, QC H3A 0G4, Canada
| | - Sabrina Daniela da Silva
- Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, QC H3A 0G4, Canada
| | - Marc Pusztaszeri
- Department of Pathology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Michael Tamilia
- Division of Endocrinology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Véronique-Isabelle Forest
- Department of Otolaryngology-Head and Neck Surgery, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
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Roberts JW, Lubin DJ, Shi Q, Viswanathan K. Cytomorphologic features of thyroid nodules harboring thyroid adenoma‐associated fusion: A single institutional review of 11 cases. Diagn Cytopathol 2022; 50:327-334. [DOI: 10.1002/dc.24958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 11/10/2022]
Affiliation(s)
- James W. Roberts
- Department of Pathology and Laboratory Medicine Emory University Hospital Midtown Atlanta Georgia USA
| | - Daniel J. Lubin
- Department of Pathology and Laboratory Medicine Emory University Hospital Midtown Atlanta Georgia USA
| | - Qiuying Shi
- Department of Pathology and Laboratory Medicine Emory University Hospital Midtown Atlanta Georgia USA
| | - Kartik Viswanathan
- Department of Pathology and Laboratory Medicine Emory University Hospital Midtown Atlanta Georgia USA
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Abstract
Background Gene fusions have been studied extensively, as frequent drivers of tumorigenesis as well as potential therapeutic targets. In many well-known cases, breakpoints occur at two intragenic positions, leading to in-frame gene-gene fusions that generate chimeric mRNAs. However, fusions often occur with intergenic breakpoints, and the role of such fusions has not been carefully examined. Results We analyze whole-genome sequencing data from 268 patients to catalog gene-intergenic and intergenic-intergenic fusions and characterize their impact. First, we discover that, in contrast to the common assumption, chimeric oncogenic transcripts—such as those involving ETV4, ERG, RSPO3, and PIK3CA—can be generated by gene-intergenic fusions through splicing of the intervening region. Second, we find that over-expression of an upstream or downstream gene by a fusion-mediated repositioning of a regulatory sequence is much more common than previously suspected, with enhancers sometimes located megabases away. We detect a number of recurrent fusions, such as those involving ANO3, RGS9, FUT5, CHI3L1, OR1D4, and LIPG in breast; IGF2 in colon; ETV1 in prostate; and IGF2BP3 and SIX2 in thyroid cancers. Conclusion Our findings elucidate the potential oncogenic function of intergenic fusions and highlight the wide-ranging consequences of structural rearrangements in cancer genomes.
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Combinatorial Electrophoresis and Mass Spectrometry-Based Proteomics in Breast Milk for Breast Cancer Biomarker Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:451-467. [PMID: 31347064 DOI: 10.1007/978-3-030-15950-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Innovations in approaches for early detection and individual risk assessment of different cancers, including breast cancer (BC), are needed to reduce cancer morbidity and associated mortality. The assessment of potential cancer biomarkers in accessible bodily fluids provides a novel approach to identify the risk and/or onset of cancer. Biomarkers are biomolecules, such as proteins, that are indicative of an abnormality or a disease. Human milk is vastly underutilized biospecimen that offers the opportunity to investigate potential protein BC-biomarkers in young, reproductively active women. As a first step, we have examined the entire protein pattern in human milk samples from breastfeeding mothers with cancer, who were diagnosed either before or after milk donation, and from women without cancer, using mass spectrometry (MS)-based proteomics.
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Aslebagh R, Channaveerappa D, Arcaro KF, Darie CC. Proteomics analysis of human breast milk to assess breast cancer risk. Electrophoresis 2018; 39:653-665. [PMID: 29193311 DOI: 10.1002/elps.201700123] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/19/2022]
Abstract
Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from eight women provided five paired-groups (cancer versus control) for analysis of dysregulatedproteins: two within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and three across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the five comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research. Data are available via ProteomeXchange with identifier PXD007066.
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Affiliation(s)
- Roshanak Aslebagh
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Devika Channaveerappa
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
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Prasad RB, Lessmark A, Almgren P, Kovacs G, Hansson O, Oskolkov N, Vitai M, Ladenvall C, Kovacs P, Fadista J, Lachmann M, Zhou Y, Sonestedt E, Poon W, Wollheim CB, Orho-Melander M, Stumvoll M, Tuomi T, Pääbo S, Koranyi L, Groop L. Excess maternal transmission of variants in the THADA gene to offspring with type 2 diabetes. Diabetologia 2016; 59:1702-13. [PMID: 27155871 DOI: 10.1007/s00125-016-3973-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/01/2016] [Indexed: 02/04/2023]
Abstract
AIMS/HYPOTHESIS Genome-wide association studies (GWAS) have identified more than 65 genetic loci associated with risk of type 2 diabetes. However, the contribution of distorted parental transmission of alleles to risk of type 2 diabetes has been mostly unexplored. Our goal was therefore to search for parent-of-origin effects (POE) among type 2 diabetes loci in families. METHODS Families from the Botnia study (n = 4,211, 1,083 families) were genotyped for 72 single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes and assessed for POE on type 2 diabetes. The family-based Hungarian Transdanubian Biobank (HTB) (n = 1,463, >135 families) was used to replicate SNPs showing POE. Association of type 2 diabetes loci within families was also tested. RESULTS Three loci showed nominal POE, including the previously reported variants in KCNQ1, for type 2 diabetes in families from Botnia (rs2237895: p POE = 0.037), which can be considered positive controls. The strongest POE was seen for rs7578597 SNP in the THADA gene, showing excess transmission of the maternal risk allele T to diabetic offspring (Botnia: p POE = 0.01; HTB p POE = 0.045). These data are consistent with previous evidence of allelic imbalance for expression in islets, suggesting that the THADA gene can be imprinted in a POE-specific fashion. Five CpG sites, including those flanking rs7578597, showed differential methylation between diabetic and non-diabetic donor islets. CONCLUSIONS/INTERPRETATION Taken together, the data emphasise the need for genetic studies to consider from which parent an offspring has inherited a susceptibility allele.
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Affiliation(s)
- Rashmi B Prasad
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden.
| | - Anna Lessmark
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Peter Almgren
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | | | - Ola Hansson
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Nikolay Oskolkov
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Marta Vitai
- Heart Center Foundation, DRC, Balatonfured, Hungary
| | - Claes Ladenvall
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Joao Fadista
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | | | - Yuedan Zhou
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Emily Sonestedt
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Wenny Poon
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Claes B Wollheim
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
- Department of Cell Physiology and Metabolism, University Medical Center, Geneva, Switzerland
| | - Marju Orho-Melander
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Tiinamaija Tuomi
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden.
- Finnish Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland.
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Nikiforov YE, Carty SE, Chiosea SI, Coyne C, Duvvuri U, Ferris RL, Gooding WE, Hodak SP, LeBeau SO, Ohori NP, Seethala RR, Tublin ME, Yip L, Nikiforova MN. Highly accurate diagnosis of cancer in thyroid nodules with follicular neoplasm/suspicious for a follicular neoplasm cytology by ThyroSeq v2 next-generation sequencing assay. Cancer 2014; 120:3627-34. [PMID: 25209362 PMCID: PMC7737376 DOI: 10.1002/cncr.29038] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND Fine-needle aspiration (FNA) cytology is a common approach to evaluating thyroid nodules, although 20% to 30% of FNAs have indeterminate cytology, which hampers the appropriate management of these patients. Follicular (or oncocytic) neoplasm/suspicious for a follicular (or oncocytic) neoplasm (FN/SFN) is a common indeterminate diagnosis with a cancer risk of approximately 15% to 30%. In this study, the authors tested whether the most complete next-generation sequencing (NGS) panel of genetic markers could significantly improve cancer diagnosis in these nodules. METHODS The evaluation of 143 consecutive FNA samples with a cytologic diagnosis of FN/SFN from patients with known surgical outcomes included 91 retrospective samples and 52 prospective samples. Analyses were performed on a proprietary sequencer using the targeted ThyroSeq v2 NGS panel, which simultaneously tests for point mutations in 13 genes and for 42 types of gene fusions that occur in thyroid cancer. The expression of 8 genes was used to assess the cellular composition of FNA samples. RESULTS In the entire cohort, histologic analysis revealed 104 benign nodules and 39 malignant nodules. The most common point mutations involved the neuroblastoma RAS viral oncogene homolog (NRAS), followed by the Kirsten rat sarcoma viral oncogene homolog (KRAS), the telomerase reverse transcriptase (TERT) gene, and the thyroid-stimulating hormone receptor (TSHR) gene. The identified fusions involved the thyroid adenoma associated (THADA) gene; the peroxisome proliferator-activated receptor γ (PPARG) gene; and the neurotrophic tyrosine kinase, receptor, type 3 (NTRK3) gene. Performance characteristics were similar in the retrospective and prospective groups. Among all FN/SFN nodules, preoperative ThyroSeq v2 performed with 90% sensitivity (95% confidence interval [CI], 80%-99%), 93% specificity (95% CI, 88%-98%), a positive predictive value of 83% (95% CI, 72%-95%), a negative predictive value of 96% (95% CI, 92%-100%), and 92% accuracy (95% CI, 88%-97%). CONCLUSIONS The current results indicate that comprehensive genotyping of thyroid nodules using a broad NGS panel provides a highly accurate diagnosis for nodules with FN/SFN cytology and should facilitate the optimal management of these patients.
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Affiliation(s)
- Yuri E. Nikiforov
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sally E. Carty
- Division of Endocrine Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Simon I. Chiosea
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christopher Coyne
- Division of Endocrinology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Umamaheswar Duvvuri
- Department of Otolaryngology, Head Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert L. Ferris
- Department of Otolaryngology, Head Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - William E. Gooding
- Biostatistics Facility, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Steven P. Hodak
- Division of Endocrinology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shane O. LeBeau
- Division of Endocrinology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - N. Paul Ohori
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Raja R. Seethala
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mitchell E. Tublin
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Linwah Yip
- Division of Endocrine Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
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