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Saeed-Vafa D, Chatzopoulos K, Hernandez-Prera J, Cano P, Saller JJ, Hallanger Johnson JE, McIver B, Boyle TA. RET splice site variants in medullary thyroid carcinoma. Front Genet 2024; 15:1377158. [PMID: 38566816 PMCID: PMC10985236 DOI: 10.3389/fgene.2024.1377158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Medullary thyroid carcinoma (MTC) is an aggressive cancer that is often caused by driver mutations in RET. Splice site variants (SSV) reflect changes in mRNA processing, which may alter protein function. RET SSVs have been described in thyroid tumors in general but have not been extensively studied in MTC. Methods: The prevalence of RET SSVs was evaluated in 3,624 cases with next generation sequence reports, including 25 MTCs. Fisher exact analysis was performed to compare RET SSV frequency in cancers with/without a diagnosis of MTC. Results: All 25 MTCs had at least one of the two most common RET SSVs versus 0.3% of 3,599 cancers with other diagnoses (p < 0.00001). The 11 cancers with non-MTC diagnoses that had the common RET SSVs were 4 neuroendocrine cancers, 4 non-small cell lung carcinomas, 2 non-MTC thyroid cancers, and 1 melanoma. All 25 MTCs analyzed had at least one of the two most common RET SSVs, including 4 with no identified mutational driver. Discussion: The identification of RET SSVs in all MTCs, but rarely in other cancer types, demonstrates that these RET SSVs distinguish MTCs from other cancer types. Future studies are needed to investigate whether these RET SSVs play a pathogenic role in MTC.
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Hegde SG, Devi S, Sivadas A, Shubha AM, Thomas A, Mukhopadhyay A, Kurpad AV. Maternal Vitamin A Status as a Risk Factor of Hirschsprung Disease in the Child. Clin Transl Gastroenterol 2023; 14:e00619. [PMID: 37490568 PMCID: PMC10522106 DOI: 10.14309/ctg.0000000000000619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/14/2023] [Indexed: 07/27/2023] Open
Abstract
INTRODUCTION The gene-environment interaction of the REarranged during Transfection ( RET ) gene with vitamin A in the etiopathogenesis of Hirschsprung disease (HSCR) has been suggested in rodents. The aim of this study was to evaluate vitamin A status in mothers of children with HSCR and to assess its association with pathogenic variants of the RET gene in affected children. METHODS This was a case-control study of stable isotope-based vitamin A measurement stores of mothers of children diagnosed with HSCR (within 8 months from birth, n = 7) and age-matched mothers of normal children (n = 6). Next-generation sequencing of RET exons, along with their upstream promoter region, was performed in the 7 HSCR proband-parent triads to evaluate pathogenic variants. RESULTS Maternal vitamin A stores in the HSCR group was almost 50% that of those in controls, tending toward significance (0.50 ± 0.17 vs 0.89 ± 0.51 μmol/g respectively, P = 0.079). Two novel pathogenic de novo mutations were identified in 2 cases, and a rare single-nucleotide deletion was detected in the 3.5-kb RET upstream region, in a heterozygous state, in all 7 proband-parent triads. Low-penetrance RET haplotypes associated with HSCR were detected in 5 cases. DISCUSSION Mothers with children with HSCR had lower vitamin A liver stores than mothers with normal children, and the children who were affected had HSCR despite having no established pathogenic RET variants. Lower maternal vitamin A status may increase the penetrance of genetic mutations in RET , and vitamin-A mediated gene-environment interactions may underpin some of the etiology of HSCR.
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Affiliation(s)
- Shalini G. Hegde
- Department of Paediatric Surgery, St. John's Medical College Hospital, Bangalore, India
| | - Sarita Devi
- Division of Nutrition, St. John's Research Institute, Bangalore, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, Bangalore, India
| | | | - Annamma Thomas
- Department of Obstetrics and Gynaecology, St. John's Medical College Hospital, Bangalore, India
| | | | - Anura V. Kurpad
- Department of Physiology, St. John's Medical College Hospital, Bangalore, India
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Cerrizuela S, Vega-Lopez GA, Méndez-Maldonado K, Velasco I, Aybar MJ. The crucial role of model systems in understanding the complexity of cell signaling in human neurocristopathies. WIREs Mech Dis 2022; 14:e1537. [PMID: 35023327 DOI: 10.1002/wsbm.1537] [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: 03/30/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/07/2022]
Abstract
Animal models are useful to study the molecular, cellular, and morphogenetic mechanisms underlying normal and pathological development. Cell-based study models have emerged as an alternative approach to study many aspects of human embryonic development and disease. The neural crest (NC) is a transient, multipotent, and migratory embryonic cell population that generates a diverse group of cell types that arises during vertebrate development. The abnormal formation or development of the NC results in neurocristopathies (NCPs), which are characterized by a broad spectrum of functional and morphological alterations. The impaired molecular mechanisms that give rise to these multiphenotypic diseases are not entirely clear yet. This fact, added to the high incidence of these disorders in the newborn population, has led to the development of systematic approaches for their understanding. In this article, we have systematically reviewed the ways in which experimentation with different animal and cell model systems has improved our knowledge of NCPs, and how these advances might contribute to the development of better diagnostic and therapeutic tools for the treatment of these pathologies. This article is categorized under: Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Stem Cells and Development Congenital Diseases > Molecular and Cellular Physiology Neurological Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Santiago Cerrizuela
- Division of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina
| | - Guillermo A Vega-Lopez
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Karla Méndez-Maldonado
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Departamento de Fisiología y Farmacología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Iván Velasco
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Reprogramación Celular del Instituto de Fisiología Celular, UNAM en el Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Ciudad de México, Mexico
| | - Manuel J Aybar
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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Upadhya A, Yadav KS, Misra A. Targeted drug therapy in non-small cell lung cancer: Clinical significance and possible solutions-Part I. Expert Opin Drug Deliv 2020; 18:73-102. [PMID: 32954834 DOI: 10.1080/17425247.2021.1825377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Non-small cell lung cancer (NSCLC) comprises of 84% of all lung cancer cases. The treatment options for NSCLC at advanced stages are chemotherapy and radiotherapy. Chemotherapy involves conventional nonspecific chemotherapeutics, and targeted-protein/receptor-specific small molecule inhibitors. Biologically targeted therapies such as an antibody-based immunotherapy have been approved in combination with conventional therapeutics. Approved targeted chemotherapy is directed against the kinase domains of mutated cellular receptors such as epidermal growth factor receptor (EGFR), anaplastic lymphoma kinases (ALK), neurotrophic receptor kinases (NTRK) and against downstream signaling molecules such as BRAF (v-raf murine sarcoma viral oncogene homolog B1). Approved biologically targeted therapy involves the use of anti-angiogenesis antibodies and antibodies against immune checkpoints. AREAS COVERED The rationale for the employment of targeted therapeutics and the resistance that may develop to therapy are discussed. Novel targeted therapeutics in clinical trials are also included. EXPERT OPINION Molecular and histological profiling of a given tumor specimen to determine the aberrant onco-driver is a must before deciding a targeted therapeutic regimen for the patient. Periodic monitoring of the patients response to a given therapeutic regimen is also mandatory so that any semblance of resistance to therapy can be deciphered and the regimen may be accordingly altered.
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Affiliation(s)
- Archana Upadhya
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS , Mumbai, Maharashtra, India
| | - Khushwant S Yadav
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS , Mumbai, Maharashtra, India
| | - Ambikanandan Misra
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS , Mumbai, Maharashtra, India
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Ilieva M, Nielsen J, Korshunova I, Gotfryd K, Bock E, Pankratova S, Michel TM. Artemin and an Artemin-Derived Peptide, Artefin, Induce Neuronal Survival, and Differentiation Through Ret and NCAM. Front Mol Neurosci 2019; 12:47. [PMID: 30853893 PMCID: PMC6396024 DOI: 10.3389/fnmol.2019.00047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 02/07/2019] [Indexed: 12/17/2022] Open
Abstract
Artemin (ARTN) is a neurotrophic factor from the GDNF family ligands (GFLs) that is involved in development of the nervous system and neuronal differentiation and survival. ARTN signals through a complex receptor system consisting of the RET receptor tyrosine kinase and a glycosylphosphatidylinositol-anchored co-receptor GFL receptor α, GFRα3. We found that ARTN binds directly to neural cell adhesion molecule (NCAM) and that ARTN-induced neuritogenesis requires NCAM expression and activation of NCAM-associated signaling partners, thus corroborating that NCAM is an alternative receptor for ARTN. We designed a small peptide, artefin, that could interact with GFRα3 and demonstrated that this peptide agonist induces RET phosphorylation and mimics the biological functions of ARTN – neuroprotection and neurite outgrowth. Moreover, artefin mimicked the binding of ARTN to NCAM and required NCAM expression and activation for its neurite elongation effect, thereby suggesting that artefin represents a binding site for NCAM within ARTN. We showed that biological effects of ARTN and artefin can be inhibited by abrogation of both NCAM and RET, suggesting a more complex signaling mechanism that previously thought. As NCAM plays a significant role in neurodevelopment, regeneration, and synaptic plasticity we suggest that ARTN and its mimetics are promising candidates for treatment of neurological disorders and warrant further investigations.
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Affiliation(s)
- Mirolyuba Ilieva
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark.,Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark.,Brain Research - Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Janne Nielsen
- Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Irina Korshunova
- Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Kamil Gotfryd
- Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Bock
- Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Stanislava Pankratova
- Laboratory of Neural Plasticity, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark.,Research Laboratory for Stereology and Neuroscience, Bispebjerg-Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tanja Maria Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark.,Brain Research - Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data. G3-GENES GENOMES GENETICS 2018; 8:2923-2940. [PMID: 30021829 PMCID: PMC6118309 DOI: 10.1534/g3.118.200373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative splicing leverages genomic content by allowing the synthesis of multiple transcripts and, by implication, protein isoforms, from a single gene. However, estimating the abundance of transcripts produced in a given tissue from short sequencing reads is difficult and can result in both the construction of transcripts that do not exist, and the failure to identify true transcripts. An alternative approach is to catalog the events that make up isoforms (splice junctions and exons). We present here the Event Analysis (EA) approach, where we project transcripts onto the genome and identify overlapping/unique regions and junctions. In addition, all possible logical junctions are assembled into a catalog. Transcripts are filtered before quantitation based on simple measures: the proportion of the events detected, and the coverage. We find that mapping to a junction catalog is more efficient at detecting novel junctions than mapping in a splice aware manner. We identify 99.8% of true transcripts while iReckon identifies 82% of the true transcripts and creates more transcripts not included in the simulation than were initially used in the simulation. Using PacBio Iso-seq data from a mouse neural progenitor cell model, EA detects 60% of the novel junctions that are combinations of existing exons while only 43% are detected by STAR. EA further detects ∼5,000 annotated junctions missed by STAR. Filtering transcripts based on the proportion of the transcript detected and the number of reads on average supporting that transcript captures 95% of the PacBio transcriptome. Filtering the reference transcriptome before quantitation, results in is a more stable estimate of isoform abundance, with improved correlation between replicates. This was particularly evident when EA is applied to an RNA-seq study of type 1 diabetes (T1D), where the coefficient of variation among subjects (n = 81) in the transcript abundance estimates was substantially reduced compared to the estimation using the full reference. EA focuses on individual transcriptional events. These events can be quantitate and analyzed directly or used to identify the probable set of expressed transcripts. Simple rules based on detected events and coverage used in filtering result in a dramatic improvement in isoform estimation without the use of ancillary data (e.g., ChIP, long reads) that may not be available for many studies.
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Wang J, Li Q, Kong Y, Zhou F, Li J, Li W, Wang K, Wu T, Guan Y, Xie J, Wen T. Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice. Front Aging Neurosci 2018; 9:393. [PMID: 29311893 PMCID: PMC5735351 DOI: 10.3389/fnagi.2017.00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
Aging progression is a process that an individual encounters as they become older, and usually results from a series of normal physiological changes over time. The hippocampus, which contributes to the loss of spatial and episodic memory and learning in older people, is closely related to the detrimental effects of aging at the morphological and molecular levels. However, age-related genetic changes in hippocampal molecular mechanisms are not yet well-established. To provide additional insight into the aging process, differentially-expressed genes of 3- versus 24- and 29-month old mice were re-analyzed. The results revealed that a large number of immune and inflammatory response-related genes were up-regulated in the aged hippocampus, and membrane receptor-associated genes were down-regulated. The down-regulation of transmembrane receptors may indicate the weaker perception of environmental exposure in older people, since many transmembrane proteins participate in signal transduction. In addition, molecular interaction analysis of the up-regulated immune genes indicated that the hub gene, Ywhae, may play essential roles in immune and inflammatory responses during aging progression, as well as during hippocampal development. Our biological experiments confirmed the conserved roles of Ywhae and its partners between human and mouse. Furthermore, comparison of microarray data between advanced-age mice treated with human umbilical cord blood plasma protein and the phosphate-buffered saline control showed that the genes that contribute to the revitalization of advanced-age mice are different from the genes induced by aging. These results implied that the revitalization of advanced-age mice is not a simple reverse process of normal aging progression. Our data assigned novel roles of genes during aging progression and provided further theoretic evidence for future studies exploring the underlying mechanisms of aging and anti-aging-related disease therapy.
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Affiliation(s)
- Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Qian Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yanyan Kong
- Position Emission Computed Tomography Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangfang Zhou
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jie Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Weihao Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Kai Wang
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Wu
- Shanghai Stem Cell Group, Shanghai, China
| | - Yihui Guan
- Position Emission Computed Tomography Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Tieqiao Wen
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
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Vitale G, Gaudenzi G, Circelli L, Manzoni MF, Bassi A, Fioritti N, Faggiano A, Colao A. Animal models of medullary thyroid cancer: state of the art and view to the future. Endocr Relat Cancer 2017; 24:R1-R12. [PMID: 27799362 DOI: 10.1530/erc-16-0399] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 12/16/2022]
Abstract
Medullary thyroid carcinoma is a neuroendocrine tumour originating from parafollicular C cells accounting for 5-10% of thyroid cancers. Increased understanding of disease-specific molecular targets of therapy has led to the regulatory approval of two drugs (vandetanib and cabozantinib) for the treatment of medullary thyroid carcinoma. These drugs increase progression-free survival; however, they are often poorly tolerated and most treatment responses are transient. Animal models are indispensable tools for investigating the pathogenesis, mechanisms for tumour invasion and metastasis and new therapeutic approaches for cancer. Unfortunately, only few models are available for medullary thyroid carcinoma. This review provides an overview of the state of the art of animal models in medullary thyroid carcinoma and highlights future developments in this field, with the aim of addressing salient features and clinical relevance.
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Affiliation(s)
- Giovanni Vitale
- Department of Clinical Sciences and Community Health (DISCCO)University of Milan, Milan, Italy
- Laboratory of Endocrine and Metabolic ResearchIstituto Auxologico Italiano IRCCS, Milan, Italy
| | - Germano Gaudenzi
- Department of Clinical Sciences and Community Health (DISCCO)University of Milan, Milan, Italy
| | - Luisa Circelli
- Department of Experimental OncologyLaboratory of Molecular Biology and Viral Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, 'Fondazione Pascale' - IRCCS, Naples, Italy
| | - Marco F Manzoni
- Department of Endocrinology and Internal MedicineEndocrine Tumors Unit, San Raffaele Hospital Vita-Salute San Raffaele University, Milan, Italy
| | - Andrea Bassi
- Department of PhysicsPolitecnico di Milano, Milan, Italy
| | | | - Antongiulio Faggiano
- Thyroid and Parathyroid Surgery UnitIstituto Nazionale per lo Studio e la Cura dei Tumori 'Fondazione G. Pascale' - IRCCS, Naples, Italy
| | - Annamaria Colao
- Department of Clinical Medicine and SurgerySection of Endocrinology, 'Federico II' University of Naples, Naples, Italy
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