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Katoh M, Katoh M. Precision medicine for human cancers with Notch signaling dysregulation (Review). Int J Mol Med 2020; 45:279-297. [PMID: 31894255 PMCID: PMC6984804 DOI: 10.3892/ijmm.2019.4418] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
NOTCH1, NOTCH2, NOTCH3 and NOTCH4 are transmembrane receptors that transduce juxtacrine signals of the delta‑like canonical Notch ligand (DLL)1, DLL3, DLL4, jagged canonical Notch ligand (JAG)1 and JAG2. Canonical Notch signaling activates the transcription of BMI1 proto‑oncogene polycomb ring finger, cyclin D1, CD44, cyclin dependent kinase inhibitor 1A, hes family bHLH transcription factor 1, hes related family bHLH transcription factor with YRPW motif 1, MYC, NOTCH3, RE1 silencing transcription factor and transcription factor 7 in a cellular context‑dependent manner, while non‑canonical Notch signaling activates NF‑κB and Rac family small GTPase 1. Notch signaling is aberrantly activated in breast cancer, non‑small‑cell lung cancer and hematological malignancies, such as T‑cell acute lymphoblastic leukemia and diffuse large B‑cell lymphoma. However, Notch signaling is inactivated in small‑cell lung cancer and squamous cell carcinomas. Loss‑of‑function NOTCH1 mutations are early events during esophageal tumorigenesis, whereas gain‑of‑function NOTCH1 mutations are late events during T‑cell leukemogenesis and B‑cell lymphomagenesis. Notch signaling cascades crosstalk with fibroblast growth factor and WNT signaling cascades in the tumor microenvironment to maintain cancer stem cells and remodel the tumor microenvironment. The Notch signaling network exerts oncogenic and tumor‑suppressive effects in a cancer stage‑ or (sub)type‑dependent manner. Small‑molecule γ‑secretase inhibitors (AL101, MRK‑560, nirogacestat and others) and antibody‑based biologics targeting Notch ligands or receptors [ABT‑165, AMG 119, rovalpituzumab tesirine (Rova‑T) and others] have been developed as investigational drugs. The DLL3‑targeting antibody‑drug conjugate (ADC) Rova‑T, and DLL3‑targeting chimeric antigen receptor‑modified T cells (CAR‑Ts), AMG 119, are promising anti‑cancer therapeutics, as are other ADCs or CAR‑Ts targeting tumor necrosis factor receptor superfamily member 17, CD19, CD22, CD30, CD79B, CD205, Claudin 18.2, fibroblast growth factor receptor (FGFR)2, FGFR3, receptor‑type tyrosine‑protein kinase FLT3, HER2, hepatocyte growth factor receptor, NECTIN4, inactive tyrosine‑protein kinase 7, inactive tyrosine‑protein kinase transmembrane receptor ROR1 and tumor‑associated calcium signal transducer 2. ADCs and CAR‑Ts could alter the therapeutic framework for refractory cancers, especially diffuse‑type gastric cancer, ovarian cancer and pancreatic cancer with peritoneal dissemination. Phase III clinical trials of Rova‑T for patients with small‑cell lung cancer and a phase III clinical trial of nirogacestat for patients with desmoid tumors are ongoing. Integration of human intelligence, cognitive computing and explainable artificial intelligence is necessary to construct a Notch‑related knowledge‑base and optimize Notch‑targeted therapy for patients with cancer.
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Affiliation(s)
| | - Masaru Katoh
- Department of Omics Network, National Cancer Center, Tokyo 104-0045, Japan
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102
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Di Nardo L, Pellegrini C, Di Stefani A, Del Regno L, Sollena P, Piccerillo A, Longo C, Garbe C, Fargnoli MC, Peris K. Molecular genetics of cutaneous squamous cell carcinoma: perspective for treatment strategies. J Eur Acad Dermatol Venereol 2020; 34:932-941. [PMID: 31747091 DOI: 10.1111/jdv.16098] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022]
Abstract
Cutaneous squamous cell carcinoma (cSCC) represents 20% of all skin cancers. Although primary cSCCs can be successfully treated with surgery, a subset of highly aggressive lesions may progress to advanced disease, representing a public healthcare problem with significant cancer-related morbidity and mortality. A complex network of genes (TP53, CDKN2A, NOTCH1 and NOTCH2, EGFR and TERT) and molecular pathways (RAS/RAF/MEK/ERK and PI3K/AKT/mTOR) have been shown to play an important role in the pathogenesis of cSCC. The epigenetic regulation of TP53 and CDKN2A is an attractive therapeutic target for the treatment of cSCC, as well as NOTCH-activating agents capable to restore its tumour-suppressor function. EGFR inhibitors including both monoclonal antibodies (cetuximab and panitumumab) and tyrosine kinase inhibitors (erlotinib, gefitinib and dasatinib) have been used in clinical trials for the treatment of advanced cSCC, achieving only partial clinical benefit. Recently, an immune-modulatory drug (cemiplimab) has been introduced for the treatment of advanced cSCC with good clinical results and a favourable safety profile, while other PD1/PD-L1 inhibitors, either as monotherapy or in combination with targeted therapies, are currently under investigation. This review focuses on molecular findings involved in the pathogenesis of cSCC and their implications for the future development of new treatment strategies. In addition, current and ongoing treatments on targeted therapies and/or immunotherapy are illustrated.
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Affiliation(s)
- L Di Nardo
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - C Pellegrini
- Department of Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - A Di Stefani
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - L Del Regno
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - P Sollena
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - A Piccerillo
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
| | - C Longo
- Centro Oncologico ad Alta Tecnologia Diagnostica, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy
| | - C Garbe
- Centre for Dermatooncology, Department of Dermatology, Eberhard-Karls University, Tuebingen, Germany
| | - M C Fargnoli
- Department of Dermatology, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - K Peris
- Institute of Dermatology, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome, Italy
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103
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Yamamoto S. Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila. Dev Growth Differ 2020; 62:15-34. [PMID: 31943162 DOI: 10.1111/dgd.12640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022]
Abstract
Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.,Department of Neuroscience, BCM, Houston, TX, USA.,Program in Developmental Biology, BCM, Houston, TX, USA.,Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
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Molecular Biology of Basal and Squamous Cell Carcinomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1268:171-191. [PMID: 32918219 DOI: 10.1007/978-3-030-46227-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The prevalent keratinocyte-derived neoplasms of the skin are basal cell carcinoma and squamous cell carcinoma. Both so-called non-melanoma skin cancers comprise the most common cancers in humans by far. Common risk factors for both tumor entities include sun exposure, DNA repair deficiencies leading to chromosomal instability, or immunosuppression. Yet, fundamental differences in the development of the two different entities have been and are currently unveiled. The constitutive activation of the sonic hedgehog signaling pathway by acquired mutations in the PTCH and SMO genes appears to represent the early basal cell carcinoma developmental determinant. Although other signaling pathways are also affected, small hedgehog inhibitory molecules evolve as the most promising basal cell carcinoma treatment options systemically as well as topically in current clinical trials. For squamous cell carcinoma development, mutations in the p53 gene, especially UV-induced mutations, have been identified as early events. Yet, other signaling pathways including epidermal growth factor receptor, RAS, Fyn, or p16INK4a signaling may play significant roles in squamous cell carcinoma development. The improved understanding of the molecular events leading to different tumor entities by de-differentiation of the same cell type has begun to pave the way for modulating new molecular targets therapeutically with small molecules.
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105
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Urata Y, Takeuchi H. Effects of Notch glycosylation on health and diseases. Dev Growth Differ 2019; 62:35-48. [PMID: 31886522 DOI: 10.1111/dgd.12643] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Notch signaling is an evolutionarily conserved signaling pathway and is essential for cell-fate specification in metazoans. Dysregulation of Notch signaling results in various human diseases, including cardiovascular defects and cancer. In 2000, Fringe, a known regulator of Notch signaling, was discovered as a Notch-modifying glycosyltransferase. Since then, glycosylation-a post-translational modification involving literal sugars-on the Notch extracellular domain has been noted as a critical mechanism for the regulation of Notch signaling. Additionally, the presence of diverse O-glycans decorating Notch receptors has been revealed in the extracellular domain epidermal growth factor-like (EGF) repeats. Here, we concisely summarize the recent studies in the human diseases associated with aberrant Notch glycosylation.
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Affiliation(s)
- Yusuke Urata
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideyuki Takeuchi
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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106
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Hervás-Marín D, Higgins F, Sanmartín O, López-Guerrero JA, Bañó MC, Igual JC, Quilis I, Sandoval J. Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma. PLoS One 2019; 14:e0223341. [PMID: 31860637 PMCID: PMC6924689 DOI: 10.1371/journal.pone.0223341] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/06/2019] [Indexed: 01/23/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. Although most cSCCs have good prognosis, a subgroup of high-risk cSCC has a higher frequency of recurrence and mortality. Therefore, the identification of molecular risk factors associated with this aggressive subtype is of major interest. In this work we carried out a global-scale approach to investigate the DNA-methylation profile in patients at different stages, from premalignant actinic keratosis to low-risk invasive and high-risk non-metastatic and metastatic cSCC. The results showed massive non-sequential changes in DNA-methylome and identified a minimal methylation signature that discriminates between stages. Importantly, a direct comparison of low-risk and high-risk stages revealed epigenetic traits characteristic of high-risk tumours. Finally, a prognostic prediction model in cSCC patients identified a methylation signature able to predict the overall survival of patients. Thus, the analysis of DNA-methylation in cSCC revealed changes during the evolution of the disease through the different stages that can be of great value not only in the diagnosis but also in the prognosis of the disease.
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Affiliation(s)
- David Hervás-Marín
- Department of Biostatistics, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Faatiemah Higgins
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Onofre Sanmartín
- Dermatology Department, Instituto Valenciano de Oncología, Valencia, Spain
- Facultad de Medicina, Universidad Católica de Valencia, Valencia, Spain
| | | | - M. Carmen Bañó
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - J. Carlos Igual
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Inma Quilis
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP), Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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107
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Anekpuritanang T, Pongsapich W, Watcharadilokkul T, Ngaotepprutaram P, Pithuksurachai P, Bunbanjerdsuk S. Notch Intracellular Domain (NICD) Expression and Clinical Manifestations of Second Primary Tumor at Esophagus in Patients with Head and Neck Squamous Cell Carcinoma. Onco Targets Ther 2019; 12:11175-11181. [PMID: 31908484 PMCID: PMC6925551 DOI: 10.2147/ott.s227745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 12/02/2019] [Indexed: 12/01/2022] Open
Abstract
Introduction Second primary tumor (SPT) is a major factor that affects the survival of head and neck squamous cell carcinoma (HNSCC) patients, and the esophagus is a common site. Detection of SPT is essential for optimal HNSCC treatment planning and follow-up. Mutation of the NOTCH1 gene is common in head and neck cancer. However, details relating to Notch signaling and clinical outcomes among different primary tumors are still inconclusive. This study aimed to identify the role of the Notch signaling pathway in HNSCC, and to compare NOTCH1 expression in HNSCC compared between those with and without SPT at esophagus while focusing on the Notch intracellular domain (NICD). Methods Twenty-three cases of esophageal SPT and 47 non-SPT controls that were treated at Siriraj Hospital during 2006–2017 were included. Patient information and clinical outcomes were analyzed. NICD expression demonstrated by immunohistochemistry technique in formalin-fixed paraffin-embedded specimens was studied. Results Mean age of SPT and non-SPT was 55.13 and 62.09 years, respectively, and 94.3% of patients were male. Regarding SPT detection, 82.6% were synchronous and 17.4% were metachronous. There was significantly more active smoking among SPT than among non-SPT (87.0% vs 51.1%, p=0.01). Active alcohol use was also significantly greater among SPT than among non-SPT (87.0% vs 61.7%; p=0.04). Hypopharynx was the most common primary tumor site among SPT. Three-year and 5-year survival among SPT patients was 38.0% and 25.3%, respectively. NICD expression was absent in 52.2% of SPT, and in 53.3% of non-SPT. NICD expression intensity was mostly weak or moderate. Conclusion Active smoking and alcohol use were found to be significantly associated with SPT development. A high percentage of NICD inactivation was noted in HNSCC with no significant difference between groups. The Notch signaling pathway is involved in HNSCC tumorigenesis, but may not be a suitable molecular marker for SPT development.
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Affiliation(s)
- Tauangtham Anekpuritanang
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warut Pongsapich
- Department of Otorhinolaryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tanasarun Watcharadilokkul
- Department of Otorhinolaryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Premyot Ngaotepprutaram
- Department of Otorhinolaryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paveena Pithuksurachai
- Department of Otorhinolaryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sacarin Bunbanjerdsuk
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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108
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De Blasio C, Zonfrilli A, Franchitto M, Mariano G, Cialfi S, Verma N, Checquolo S, Bellavia D, Palermo R, Benelli D, Screpanti I, Talora C. PLK1 targets NOTCH1 during DNA damage and mitotic progression. J Biol Chem 2019; 294:17941-17950. [PMID: 31597699 PMCID: PMC6879332 DOI: 10.1074/jbc.ra119.009881] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/25/2019] [Indexed: 12/13/2022] Open
Abstract
Notch signaling plays a complex role in carcinogenesis, and its signaling pathway has both tumor suppressor and oncogenic components. To identify regulators that might control this dual activity of NOTCH1, we screened a chemical library targeting kinases and identified Polo-like kinase 1 (PLK1) as one of the kinases involved in arsenite-induced NOTCH1 down-modulation. As PLK1 activity drives mitotic entry but also is inhibited after DNA damage, we investigated the PLK1-NOTCH1 interplay in the G2 phase of the cell cycle and in response to DNA damage. Here, we found that PLK1 regulates NOTCH1 expression at G2/M transition. However, when cells in G2 phase are challenged with DNA damage, PLK1 is inhibited to prevent entry into mitosis. Interestingly, we found that the interaction between NOTCH1 and PLK1 is functionally important during the DNA damage response, as we found that whereas PLK1 activity is inhibited, NOTCH1 expression is maintained during DNA damage response. During genotoxic stress, cellular transformation requires that promitotic activity must override DNA damage checkpoint signaling to drive proliferation. Interestingly, we found that arsenite-induced genotoxic stress causes a PLK1-dependent signaling response that antagonizes the involvement of NOTCH1 in the DNA damage checkpoint. Taken together, our data provide evidence that Notch signaling is altered but not abolished in SCC cells. Thus, it is also important to recognize that Notch plasticity might be modulated and could represent a key determinant to switch on/off either the oncogenic or tumor suppressor function of Notch signaling in a single type of tumor.
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Affiliation(s)
- Carlo De Blasio
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Azzurra Zonfrilli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
- Center of Life Nano Science Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Matteo Franchitto
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Germano Mariano
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Samantha Cialfi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Nagendra Verma
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Saula Checquolo
- Department of Medico-Surgical Sciences and Biotechnology, Sapienza University, 04100 Latina, Italy
| | - Diana Bellavia
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Rocco Palermo
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Isabella Screpanti
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Claudio Talora
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
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109
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Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Münzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ. Aspartate/asparagine-β-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern. Nat Commun 2019; 10:4910. [PMID: 31659163 PMCID: PMC6817910 DOI: 10.1038/s41467-019-12711-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/26/2019] [Indexed: 01/18/2023] Open
Abstract
AspH is an endoplasmic reticulum (ER) membrane-anchored 2-oxoglutarate oxygenase whose C-terminal oxygenase and tetratricopeptide repeat (TPR) domains present in the ER lumen. AspH catalyses hydroxylation of asparaginyl- and aspartyl-residues in epidermal growth factor-like domains (EGFDs). Here we report crystal structures of human AspH, with and without substrate, that reveal substantial conformational changes of the oxygenase and TPR domains during substrate binding. Fe(II)-binding by AspH is unusual, employing only two Fe(II)-binding ligands (His679/His725). Most EGFD structures adopt an established fold with a conserved Cys1–3, 2–4, 5–6 disulfide bonding pattern; an unexpected Cys3–4 disulfide bonding pattern is observed in AspH-EGFD substrate complexes, the catalytic relevance of which is supported by studies involving stable cyclic peptide substrate analogues and by effects of Ca(II) ions on activity. The results have implications for EGFD disulfide pattern processing in the ER and will enable medicinal chemistry efforts targeting human 2OG oxygenases. AspH catalyses hydroxylation of asparagine and aspartate residues in epidermal growth factor-like domains (EGFDs). Here, the authors present crystal structures of AspH with and without substrates and show that AspH uses EFGD substrates with a non-canonical disulfide pattern.
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Affiliation(s)
- Inga Pfeffer
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Sacha A Jensen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Grazyna T Kochan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Nadia J Kershaw
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsty S Hewitson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Luke A McNeill
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Holger Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Martin Münzel
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.,NDORMS, Botnar Research Centre, University of Oxford, Old Road, Oxford, OX3 7LD, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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110
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Ma B, Huang Z, Wang Q, Zhang J, Zhou B, Wu J. Integrative analysis of genetic and epigenetic profiling of lung squamous cell carcinoma (LSCC) patients to identify smoking level relevant biomarkers. BioData Min 2019; 12:18. [PMID: 31641374 PMCID: PMC6802182 DOI: 10.1186/s13040-019-0207-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Incidence and mortality of lung cancer have dramatically decreased during the last decades, yet still approximately 160,000 deaths per year occurred in United States. Smoking intensity, duration, starting age, as well as environmental cofactors including air-pollution, showed strong association with major types of lung cancer. Lung squamous cell carcinoma is a subtype of non-small cell lung cancer, which represents 25% of the cases. Thus, exploring the molecular pathogenic mechanisms of lung squamous cell carcinoma plays crucial roles in lung cancer clinical diagnosis and therapy. RESULTS In this study, we performed integrative analyses on 299 comparative datasets of RNA-seq and methylation data, collected from 513 lung squamous cell carcinoma cases in The Cancer Genome Atlas. The data were divided into high and low smoking groups based on smoking intensity (Numbers of packs per year). We identified 1002 significantly up-regulated genes and 534 significantly down-regulated genes, and explored their cellular functions and signaling pathways by bioconductor packages GOseq and KEGG. Global methylation status was analyzed and visualized in circular plot by CIRCOS. RNA-and methylation data were correlatively analyzed, and 24 unique genes were identified, for further investigation of regional CpG sites' interactive patterns by bioconductor package coMET. AIRE, PENK, and SLC6A3 were the top 3 genes in the high and low smoking groups with significant differences. CONCLUSIONS Gene functions and DNA methylation patterns of these 24 genes are important and useful in disclosing the differences of gene expression and methylation profiling caused by different smoking levels.
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Affiliation(s)
- Bidong Ma
- Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People’s Republic of China
| | - Zhiyou Huang
- Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People’s Republic of China
| | - Qian Wang
- Tianjia Genomes Tech CO., LTD., No. 6 Longquan Road, Anhui Chaohu economic develop zone, Hefei, 238014 People’s Republic of China
| | - Jizhou Zhang
- Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People’s Republic of China
| | - Bin Zhou
- Department of Medical Oncology, Zhe Jiang Chinese Medicine University affiliated Chinese Medicine Hospital, Wen Zhou, Zhe Jiang province People’s Republic of China
| | - Jiaohong Wu
- Department of Gynecology and Oncology, Wen Zhou Medical University affiliated People’s Hospital, Wen Zhou, Zhe Jiang province People’s Republic of China
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111
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Lee JH, Shin KM, Lee SY, Hong MJ, Choi JE, Kang HG, Do SK, Lee WK, Lee EB, Seok Y, Jeong JY, Yoo SS, Lee J, Cha SI, Kim CH, Cho S, Jheon S, Kim YC, Oh IJ, Na KJ, Kim MS, Lee JM, Yang HC, Jung CY, Park CK, Lee MK, Kim DK, Park JY. Genetic Variant of Notch Regulator DTX1 Predicts Survival After Lung Cancer Surgery. Ann Surg Oncol 2019; 26:3756-3764. [DOI: 10.1245/s10434-019-07614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Indexed: 08/30/2023]
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112
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Jansen AML, Ghosh P, Dakal TC, Slavin TP, Boland CR, Goel A. Novel candidates in early-onset familial colorectal cancer. Fam Cancer 2019; 19:1-10. [PMID: 31555933 DOI: 10.1007/s10689-019-00145-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022]
Abstract
In 20-30% of patients suspected of a familial colorectal cancer (CRC) syndrome, no underlying genetic cause is detected. Recent advances in whole exome sequencing have generated evidence for new CRC-susceptibility genes including POLE, POLD1 and NTHL1¸ but many patients remain unexplained. Whole exome sequencing was performed on DNA from nine patients from five different families with familial clusters of CRC in which traditional genetic testing failed to yield a diagnosis. Variants were filtered by minor allele frequencies, followed by prioritization based on in silico prediction tools, and the presence in cancer susceptibility genes or genes in cancer-associated pathways. Effects of frameshift variants on protein structure were modeled using I-Tasser. One known pathogenic variant in POLD1 was detected (p.S478N), together with variants in 17 candidate genes not previously associated with CRC. Additional in silico analysis using SIFT, PROVEAN and PolyPhen on the 14 missense variants indicated a possible damaging effect in nine of 14 variants. Modeling of the insertions/deletions showed a damaging effect of two variants in NOTCH2 and CYP1B1. One family was explained by a mutation in a known familial CRC gene. In the remaining four families, the most promising candidates found are a frameshift NOTCH2 and a missense RAB25 variant. This study provides potential novel candidate variants in unexplained familial CRC patients, however, functional validation is imperative to confirm the role of these variants in CRC tumorigenesis. Additionally, while whole exome sequencing enables detection of variants throughout the exome, other causes explaining the familial phenotype such as multiple single nucleotide polymorphisms accumulating to a polygenic risk or epigenetic events, might be missed with this approach.
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Affiliation(s)
- Anne M L Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tikam C Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Thomas P Slavin
- Division of Clinical Cancer Genomics City of Hope, Department of Medical Oncology, National Medical Center, Duarte, CA, USA
| | - C Richard Boland
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA.
- Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91016, USA.
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113
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Jeon SH, Chie EK, Kim YJ, Lee KH, Lee HS, Kim MJ, Im SA, Kim JI, Kim TY. Targeted next-generation DNA sequencing identifies Notch signaling pathway mutation as a predictor of radiation response. Int J Radiat Biol 2019; 95:1640-1647. [PMID: 31525117 DOI: 10.1080/09553002.2019.1665212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Purpose: Identifying the association between somatic mutations and the radiation response of tumor is essential for understanding the mechanisms and practicing personalized radiotherapy. The present study aimed to discover specific genes or pathways that are associated with radiation response using targeted next-generation DNA sequencing.Material and methods: Fifty-five patients with various solid tumors whose specimen were sequenced using institutional panel which includes 148 cancer-related genes and received radiotherapy for a measurable tumor were analyzed. Patients with irradiated tumors in complete or partial remission for more than 6 months were defined as responders. Association between mutations including pathogenic single nucleotide variants and insertions/deletions in the 148 genes and 39 molecular pathways and radiation response was investigated.Results: Analyzing 17 responders and 38 non-responders, biologically effective dose (BED), but not concurrent chemotherapy, was associated with radiation response. No single gene correlated with radiation response. Mutations in Notch signaling pathway were associated with radiosensitivity after correction for multiple comparison (adjusted p = .094). When BED and Notch signaling pathway mutation were tested with logistic regression, both variables were associated with radiation response.Conclusions: Our results suggest that somatic mutations in Notch signaling pathway may be related to sensitivity to radiation, although these results should be validated in a larger and more homogeneous cohort.
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Affiliation(s)
- Seung Hyuck Jeon
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea.,Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Yi-Jun Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun-Seob Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Min Jung Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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114
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Ceritinib-Induced Regression of an Insulin-Like Growth Factor-Driven Neuroepithelial Brain Tumor. Int J Mol Sci 2019; 20:ijms20174267. [PMID: 31480400 PMCID: PMC6747232 DOI: 10.3390/ijms20174267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
The insulin-like growth factor (IGF) pathway plays an important role in several brain tumor entities. However, the lack of inhibitors crossing the blood–brain barrier remains a significant obstacle for clinical translation. Here, we targeted the IGF pathway using ceritinib, an off-target inhibitor of the IGF1 receptor (IGF1R) and insulin receptor (INSR), in a pediatric patient with an unclassified brain tumor and a notch receptor 1 (NOTCH1) germline mutation. Pathway analysis of the tumor revealed activation of the sonic hedgehog (SHH), the wingless and integrated-1 (WNT), the IGF, and the Notch pathway. The proliferation of the patient tumor cells (225ZL) was inhibited by arsenic trioxide (ATO), which is an inhibitor of the SHH pathway, by linsitinib, which is an inhibitor of IGF1R and INSR, and by ceritinib. 225ZL expressed INSR but not IGF1R at the protein level, and ceritinib blocked the phosphorylation of INSR. Our first personalized treatment included ATO, but because of side effects, we switched to ceritinib. After 46 days, we achieved a concentration of 1.70 µM of ceritinib in the plasma, and after 58 days, MRI confirmed that there was a response to the treatment. Ceritinib accumulated in the tumor at a concentration of 2.72 µM. Our data suggest ceritinib as a promising drug for the treatment of IGF-driven brain tumors.
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115
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Lang CMR, Chan CK, Veltri A, Lien WH. Wnt Signaling Pathways in Keratinocyte Carcinomas. Cancers (Basel) 2019; 11:cancers11091216. [PMID: 31438551 PMCID: PMC6769728 DOI: 10.3390/cancers11091216] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
The skin functions as a barrier between the organism and the surrounding environment. Direct exposure to external stimuli and the accumulation of genetic mutations may lead to abnormal cell growth, irreversible tissue damage and potentially favor skin malignancy. Skin homeostasis is coordinated by an intricate signaling network, and its dysregulation has been implicated in the development of skin cancers. Wnt signaling is one such regulatory pathway orchestrating skin development, homeostasis, and stem cell activation. Aberrant regulation of Wnt signaling cascades not only gives rise to tumor initiation, progression and invasion, but also maintains cancer stem cells which contribute to tumor recurrence. In this review, we summarize recent studies highlighting functional evidence of Wnt-related oncology in keratinocyte carcinomas, as well as discussing preclinical and clinical approaches that target oncogenic Wnt signaling to treat cancers. Our review provides valuable insight into the significance of Wnt signaling for future interventions against keratinocyte carcinomas.
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Affiliation(s)
| | - Chim Kei Chan
- de Duve Institute, Université catholique de Louvain, Brussels 1200, Belgium
| | - Anthony Veltri
- de Duve Institute, Université catholique de Louvain, Brussels 1200, Belgium
| | - Wen-Hui Lien
- de Duve Institute, Université catholique de Louvain, Brussels 1200, Belgium.
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116
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Ileana Dumbrava EE, Mills GB, Yap TA. Targeting gamma secretase: has progress moved up a Notch? Ann Oncol 2019; 29:1889-1891. [PMID: 30084907 DOI: 10.1093/annonc/mdy307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- E E Ileana Dumbrava
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston
| | - G B Mills
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston; Department of Cell Developmental & Cancer Biology, OHSU Knight Cancer Institute, Portland; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T A Yap
- Department of Investigational Cancer Therapeutics (Phase I Program), The University of Texas MD Anderson Cancer Center, Houston; Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston; Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
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117
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Knepper TC, Montesion M, Russell JS, Sokol ES, Frampton GM, Miller VA, Albacker LA, McLeod HL, Eroglu Z, Khushalani NI, Sondak VK, Messina JL, Schell MJ, DeCaprio JA, Tsai KY, Brohl AS. The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy. Clin Cancer Res 2019; 25:5961-5971. [PMID: 31399473 DOI: 10.1158/1078-0432.ccr-18-4159] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is a rare, aggressive cutaneous malignancy, which has demonstrated sensitivity to immune checkpoint inhibitor therapy. Here, we perform the largest genomics study in MCC to date to characterize the molecular landscape and evaluate for clinical and molecular correlates to immune checkpoint inhibitor response. EXPERIMENTAL DESIGN Comprehensive molecular profiling was performed on 317 tumors from patients with MCC, including the evaluation of oncogenic mutations, tumor mutational burden (TMB), mutational signatures, and the Merkel cell polyomavirus (MCPyV). For a subset of 57 patients, a retrospective analysis was conducted to evaluate for clinical and molecular correlates to immune checkpoint inhibitor response and disease survival. RESULTS Genomic analyses revealed a bimodal distribution in TMB, with 2 molecularly distinct subgroups. Ninety-four percent (n = 110) of TMB-high specimens exhibited an ultraviolet light (UV) mutational signature. MCPyV genomic DNA sequences were not identified in any TMB-high cases (0/117), but were in 63% (110/175) of TMB-low cases. For 36 evaluable patients treated with checkpoint inhibitors, the overall response rate was 44% and response correlated with survival at time of review (100% vs. 20%, P < 0.001). Response rate was 50% in TMB-high/UV-driven and 41% in TMB-low/MCPyV-positive tumors (P = 0.63). Response rate was significantly correlated with line of therapy: 75% in first-line, 39% in second-line, and 18% in third-line or beyond (P = 0.0066). PD-1, but not PD-L1, expression was associated with immunotherapy response (77% vs. 21%, P = 0.00598, for PD-1 positive and negative, respectively). CONCLUSIONS We provide a comprehensive genomic landscape of MCC and demonstrate clinicogenomic associates of immunotherapy response.
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Affiliation(s)
- Todd C Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | | | | | | | | | | | - Howard L McLeod
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nikhil I Khushalani
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vernon K Sondak
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jane L Messina
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth Y Tsai
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. .,Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Andrew S Brohl
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. .,Sarcoma, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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118
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Allgayer H, Leupold JH, Patil N. Defining the "Metastasome": Perspectives from the genome and molecular landscape in colorectal cancer for metastasis evolution and clinical consequences. Semin Cancer Biol 2019; 60:1-13. [PMID: 31362074 DOI: 10.1016/j.semcancer.2019.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Metastasis still poses the highest challenge for personalized therapy in cancer, partly due to a still incomplete understanding of its molecular evolution. We recently presented the most comprehensive whole-genome study of colorectal metastasis vs. matched primary tumors and suggested novel components of disease progression and metastasis evolution, some of them potentially relevant for targeted therapy. In this review, we try to put these findings into perspective with latest discoveries of colleagues and recent literature, and propose a systematic international team effort to collectively define the "metastasome", a term we introduce to summarize all genomic, epigenomic, transcriptomic, further -omic, molecular and functional characteristics rendering metastases different from primary tumors. Based on recent discoveries, we propose a revised metastasis model for colorectal cancer which is based on a common ancestor clone, early dissemination but flexible early or late stage clonal separation paralleling stromal interactions. Furthermore, we discuss hypotheses on site-specific metastasis, colorectal cancer progression, metastasis-targeted diagnosis and therapy, and metastasis prevention based on latest metastasome data.
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Affiliation(s)
- Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany.
| | - Jörg H Leupold
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
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119
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Hassan S, Purdie KJ, Wang J, Harwood CA, Proby CM, Pourreyron C, Mladkova N, Nagano A, Dhayade S, Athineos D, Caley M, Mannella V, Blyth K, Inman GJ, Leigh IM. A Unique Panel of Patient-Derived Cutaneous Squamous Cell Carcinoma Cell Lines Provides a Preclinical Pathway for Therapeutic Testing. Int J Mol Sci 2019; 20:E3428. [PMID: 31336867 PMCID: PMC6678499 DOI: 10.3390/ijms20143428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/28/2019] [Accepted: 07/04/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cutaneous squamous cell carcinoma (cSCC) incidence continues to rise with increasing morbidity and mortality, with limited treatment options for advanced disease. Future improvements in targeted therapy will rely on advances in genomic/transcriptomic understanding and the use of model systems for basic research. We describe here the panel of 16 primary and metastatic cSCC cell lines developed and characterised over the past three decades in our laboratory in order to provide such a resource for future preclinical research and drug screening. METHODS Primary keratinocytes were isolated from cSCC tumours and metastases, and cell lines were established. These were characterised using short tandem repeat (STR) profiling and genotyped by whole exome sequencing. Multiple in vitro assays were performed to document their morphology, growth characteristics, migration and invasion characteristics, and in vivo xenograft growth. RESULTS STR profiles of the cSCC lines allow the confirmation of their unique identity. Phylogenetic trees derived from exome sequence analysis of the matched primary and metastatic lines provide insight into the genetic basis of disease progression. The results of in vivo and in vitro analyses allow researchers to select suitable cell lines for specific experimentation. CONCLUSIONS There are few well-characterised cSCC lines available for widespread preclinical experimentation and drug screening. The described cSCC cell line panel provides a critical tool for in vitro and in vivo experimentation.
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Affiliation(s)
- Sakinah Hassan
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Karin J Purdie
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Jun Wang
- Barts Cancer Institute, QMUL, London EC1M 6BQ, UK
| | - Catherine A Harwood
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Charlotte M Proby
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Celine Pourreyron
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Nikol Mladkova
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Ai Nagano
- Barts Cancer Institute, QMUL, London EC1M 6BQ, UK
| | - Sandeep Dhayade
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Dimitris Athineos
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Matthew Caley
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Viviana Mannella
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1GH, UK
| | - Irene M Leigh
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK.
- Division of Cancer, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK.
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120
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North JP, Solomon DA, Golovato J, Bloomer M, Benz SC, Cho RJ. Loss of ZNF750 in ocular and cutaneous sebaceous carcinoma. J Cutan Pathol 2019; 46:736-741. [PMID: 31148199 DOI: 10.1111/cup.13516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Sebaceous carcinoma (SeC) is an uncommon malignancy arising from sebaceous glands of the conjunctiva and skin. Recurrent mutations in the ZNF750 were recently identified in ocular SeC. We assessed whether ZNF750 loss is a specific feature of ocular SeC or a general feature of sebaceous tumors. METHODS Immunostaining for ZNF750 expression was performed in 54 benign and malignant sebocytic proliferations. Staining for ZNF750 was scored on a three-tier scale: positive (>75%), partially positive (5%-74%), and negative (<5%). RESULTS ZNF750 expression was negative in 4/11 ocular SeC, and partially positive in 4/11 ocular SeC and 6/13 cutaneous SeC. No extraocular tumors were negative. No loss was found in sebaceous adenoma or sebaceous hyperplasia. In nine previously sequenced ocular SeCs, two lacked detectable somatic mutations in ZNF750, but showed complete loss of staining, indicating non-mutational inactivation of ZNF750. CONCLUSION We show complete loss of the ZNF750 epidermal differentiation regulator in about half of ocular SeC, highlighting the most common genetic defect in this cancer type. Loss of ZNF750 expression is seen even in tumors without truncating mutations and reduced in many of the remaining ocular and cutaneous SeC. In contrast, no ZNF750 loss was detected in benign sebaceous proliferations.
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Affiliation(s)
- Jeffrey P North
- Department of Dermatology, University of California, San Francisco, San Francisco, California.,Department of Pathology, University of California, San Francisco, San Francisco, California
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | | | - Michele Bloomer
- Department of Pathology, University of California, San Francisco, San Francisco, California.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | | | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California
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121
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Downregulation of Notch Signaling in Kras-Induced Gastric Metaplasia. Neoplasia 2019; 21:810-821. [PMID: 31276933 PMCID: PMC6611983 DOI: 10.1016/j.neo.2019.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/28/2019] [Accepted: 06/04/2019] [Indexed: 11/21/2022] Open
Abstract
Activating mutations and amplification of Kras and, more frequently, signatures for Kras activation are noted in stomach cancer. Expression of mutant KrasG12D in the mouse gastric mucosa has been shown to induce hyperplasia and metaplasia. However, the mechanisms by which Kras activation leads to gastric metaplasia are not fully understood. Here we report that KrasLSL-G12D/+;Pdx1-cre, a mouse model known for pancreatic cancer, also mediates KrasG12D expression in the stomach, causing gastric hyperplasia and metaplasia prior to the pathologic changes in the pancreas. These mice exhibit ectopic cell proliferation at the base of gastric glands, whereas wild-type mice contain proliferating cells primarily at the isthmus/neck of the gastric glands. Notch signaling is decreased in the KrasLSL-G12D/+;Pdx1-cre gastric mucosa, as shown by lower levels of cleaved Notch intracellular domains and downregulation of Notch downstream target genes. Expression of a Notch ligand Jagged1 is downregulated at the base of the mutant gland, accompanied by loss of chief cell marker Mist1. We demonstrate that exogenous Jagged1 or overexpression of Notch intracellular domain stimulates Mist1 expression in gastric cancer cell lines, suggesting positive regulation of Mist1 by Notch signaling. Finally, deletion of Jagged1 or Notch3 in KrasLSL-G12D/+;Pdx1-cre mice promoted development of squamous cell carcinoma in the forestomach, albeit short of invasive adenocarcinoma in the glandular stomach. Taken together, these results reveal downregulation of Notch signaling and Mist1 expression during the initiation of Kras-driven gastric tumorigenesis and suggest a tumor-suppressive role for Notch in this context.
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122
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Therapeutic Targeting of Notch Signaling Pathway in Hematological Malignancies. Mediterr J Hematol Infect Dis 2019; 11:e2019037. [PMID: 31308913 PMCID: PMC6613627 DOI: 10.4084/mjhid.2019.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Notch pathway plays a key role in several processes, including stem-cell self-renewal, proliferation, and cell differentiation. Several studies identified recurrent mutations in hematological malignancies making Notch one of the most desirable targets in leukemia and lymphoma. The Notch signaling mediates resistance to therapy and controls cancer stem cells supporting the development of on-target therapeutic strategies to improve patients’ outcome. In this brief review, we outline the therapeutic potential of targeting Notch pathway in T-cell acute jlymphoblastic leukemia, chronic lymphocytic leukemia, and mantle cell lymphoma.
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123
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Li W, Li Y, Zhang H, Li Y, Yuan Y, Gong H, Wei S, Liu H, Chen J. [Study on the Difference of Gene Expression between Central and Peripheral Lung Squamous Cell Carcinoma Based on TCGA Database]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2019; 22:280-288. [PMID: 31109437 PMCID: PMC6533195 DOI: 10.3779/j.issn.1009-3419.2019.05.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
背景与目的 肺癌是一种具有高发病率与高死亡率的恶性肿瘤疾病,最常见的类型为非小细胞肺癌(non-small cell lung cancer, NSCLC),其中肺鳞癌作为NSCLC中的一个亚型,具有特殊的病理学类型及其特定的治疗方法,根据临床表型不同又可分为周围型和中央型。本研究基于中央型和周围型肺鳞癌的临床差异进一步探索其基因水平的差异和其潜在的价值。 方法 从癌症基因组图谱(The Cancer Genome Atlas, TCGA)数据库收集肺鳞癌数据集,下载临床信息资料及基因表达谱资料。整理资料,分析临床数据及相对应的基因信息。 结果 在临床特征分析中发现,中央型肺鳞癌较周围型肺鳞癌更容易发生淋巴结转移(46.2%, 67/145 vs 28.9%, 26/90; P=0.019),而在性别、年龄、肿瘤大小、有无远处转移、TNM分期、表皮生长因子受体(epidermal growth factor receptor, EGFR)突变等方面未见明显差异。在基因表达水平分析中发现,中央型与周围型肺鳞癌具有1, 031个差异表达基因,其中,周围型与中央型相比,629个基因表达水平上调,402个基因表达水平下调。进一步富集分析显示差异表达基因主要体现在6个信号通路中,其中,刺激神经组织的配体-受体相互作用(neuroactive ligand-receptor interaction)通路是差异表达基因主要富集通路,其他差异表达基因主要与脂类代谢和糖代谢有关。相互作用网络分析显示,在表达上调差异基因中,肝细胞核因子1同源体A(hepatocyte nuclear factor 1 homeobox A, HNF1A)和细胞色素P450家族里的A亚家族发现的第四种酶(cytochrome p450 family, Cytochrome P450 3A4, CYP3A4)影响较为广泛,在表达下调差异基因中,人血清白蛋白(Albumin, ALB)与载脂蛋白A1(Apolipoprotein, APOA1)位于该作用网络的关键位置。 结论 中央型和周围型肺鳞癌患者不仅在淋巴结转移发生率上存在临床特征的差异,而且在基因表达水平亦有明显的不同。其中,HNF1A、CYP3A4、ALB、APOA1位于差异基因相互作用网络的关键位置,有可能参与调控二者的差异表型(phenotypic difference)。
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Affiliation(s)
- Weiting Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hongbing Zhang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ying Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yin Yuan
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hao Gong
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Sen Wei
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hongyu Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jun Chen
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
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MicroRNA Dysregulation in Cutaneous Squamous Cell Carcinoma. Int J Mol Sci 2019; 20:ijms20092181. [PMID: 31052530 PMCID: PMC6540078 DOI: 10.3390/ijms20092181] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Cutaneous squamous cell carcinoma (CSCC) is the second most frequent cancer in humans and it can be locally invasive and metastatic to distant sites. MicroRNAs (miRNAs or miRs) are endogenous, small, non-coding RNAs of 19–25 nucleotides in length, that are involved in regulating gene expression at a post-transcriptional level. MicroRNAs have been implicated in diverse biological functions and diseases. In cancer, miRNAs can proceed either as oncogenic miRNAs (onco-miRs) or as tumor suppressor miRNAs (oncosuppressor-miRs), depending on the pathway in which they are involved. Dysregulation of miRNA expression has been shown in most of the tumors evaluated. MiRNA dysregulation is known to be involved in the development of cutaneous squamous cell carcinoma (CSCC). In this review, we focus on the recent evidence about the role of miRNAs in the development of CSCC and in the prognosis of this form of skin cancer.
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125
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Wang X, Wan J, Xu Z, Jiang S, Ji L, Liu Y, Zhai S, Cui R. Identification of competitive endogenous RNAs network in breast cancer. Cancer Med 2019; 8:2392-2403. [PMID: 30932362 PMCID: PMC6536941 DOI: 10.1002/cam4.2099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/08/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MiRNAs can regulate gene expression directly or indirectly, and long noncoding RNAs as competing endogenous RNA (ceRNAs) can bind to miRNAs competitively and affect mRNA expression. The ceRNA network is still unclear in breast cancer. In this study, a ceRNA network was constructed, and new treatment and prognosis targets and biomarkers for breast cancer were explored. METHODS A total of 1 096 cancer tissues and 112 adjacent normal tissues to cancer from the TCGA database were used to screen out significant differentially expressed mRNAs (DEMs), lncRNAs (DELs), and miRNAs (DEMis) to construct a ceRNA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to predict potential functions. Survival analysis was performed to predict which functions were significant for prognosis. RESULTS From the analysis, 2 139 DEMs, 1 059 DELs, and 84 DEMis were obtained. Targeting predictions for DEMis-DELs and DEMis-DEMs can yield 26 DEMs, 90 DELs, and 18 DEMis. We performed GO enrichment analysis, and the results showed that the upregulated DEMs were involved in nucleosomes, extracellular regions, and nucleosome assembly, while the downregulated DEMs were mainly involved in Z disk, muscle contraction, and structural constituents of muscle. KEGG pathway analysis was performed on all DEMs, and the pathways were enriched in retinol metabolism, steroid hormone biosynthesis, and tyrosine metabolism. Through survival analysis of the ceRNA network, we identified four DEMs, two DELs, and two DEMis that were significant for poor prognosis. CONCLUSIONS This study suggested that constructing a ceRNA network and performing survival analysis on the network could screen out new significant treatment and prognosis targets and biomarkers.
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Affiliation(s)
- Xiaojin Wang
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Jiahui Wan
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Zhanxiang Xu
- Department of Cardiovascular MedicineHongqi Hospital Affiliated to Mudanjiang Medical UniversityMudanjiangChina
| | - Shijun Jiang
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Lin Ji
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Yutian Liu
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Shuwen Zhai
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
| | - Rongjun Cui
- Department of Biochemistry and Molecular BiologyMudanjiang Medical UniversityMudanjiangChina
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126
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Xiu MX, Liu YM. The role of oncogenic Notch2 signaling in cancer: a novel therapeutic target. Am J Cancer Res 2019; 9:837-854. [PMID: 31218097 PMCID: PMC6556604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023] Open
Abstract
Deregulated Notch signaling is a key factor thought to facilitate the stem-like proliferation of cancer cells, thereby facilitating disease progression. Four subtypes of Notch receptor have been described to date, with each playing a distinct role in cancer development and progression, therefore warranting a careful and comprehensive examination of the targeting of each receptor subtype in the context of oncogenesis. Clinical efforts to translate the DAPT, which blocks Notch signaling, have been unsuccessful due to a combination of serious gastrointestinal side effects and a lack of complete blocking efficacy. There is therefore a clear need to identify better therapeutic strategies for targeting and manipulating Notch signaling. Notch2 is a Notch receptor that is commonly overexpressed in a range of cancers, and which is linked to a unique oncogenic mechanism. Successful efforts to block Notch2 signaling will depend upon doing so both efficiently and specifically in patients. As such, in the present review we will explore the role of Notch2 signaling in the development and progression of cancer, and we will assess agents and strategies with the potential to effectively disrupt Notch2 signaling and thereby yield novel cancer treatment regimens.
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Affiliation(s)
- Meng-Xi Xiu
- Medical School of Nanchang University Nanchang, Jiangxi, China
| | - Yuan-Meng Liu
- Medical School of Nanchang University Nanchang, Jiangxi, China
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127
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Kacew AJ, Harris EJ, Lorch JH, Haddad RI, Chau NG, Rabinowits G, LeBoeuf NR, Schmults CD, Thakuria M, MacConaill LE, Hanna GJ. Chromosome 3q arm gain linked to immunotherapy response in advanced cutaneous squamous cell carcinoma. Eur J Cancer 2019; 113:1-9. [PMID: 30954880 DOI: 10.1016/j.ejca.2019.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/15/2019] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
Abstract
AIMS The activity that the immune checkpoint inhibitor (ICI) cemiplimab has recently demonstrated has led to a paradigm shift in the management of patients with advanced cutaneous squamous cell carcinoma (cSCC). To identify predictive biomarkers of response to ICIs in advanced cSCC, we studied 33 patients who received ICI therapy at the Dana-Farber/Harvard Cancer Center (DF/HCC) and analysed sequencing data for a subset of these patients. METHODS We collected clinical data using electronic health records and genomic data using the institutional OncoPanel platform of the DF/HCC. We compared tumour genomics with data from previously sequenced cSCC cohorts. RESULTS We observed high tumour mutational burden regardless of smoking status and response to ICI and longer median overall survival among those patients who achieved an ICI response. We compared the genetic data from our cohort with data from other cohorts that included fewer patients with distant metastatic disease. Although our cohort had a similar genetic landscape to those of comparator cohorts, mutations in PIK3C2B were more common in our study. In our cohort, copy number alterations (CNAs) in the 3q chromosomal arm appeared to predict response to ICI therapy. CONCLUSION CNAs in the 21-27 bands of chromosome arm 3q, a region that includes PIK3CA, ETV5 and BCL6, may represent predictors of response to ICI and may be candidates for drug targeting in combination or sequence with ICI agents.
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Affiliation(s)
- Alec J Kacew
- Medical Oncology, Dana-Farber Cancer Institute, USA
| | | | | | | | | | | | - Nicole R LeBoeuf
- Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, USA
| | | | - Manisha Thakuria
- Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, USA
| | - Laura E MacConaill
- Department of Pathology and Center for Cancer Genome Discovery, Dana-Farber/Brigham and Women's Cancer Center, USA
| | - Glenn J Hanna
- Medical Oncology, Dana-Farber Cancer Institute, USA.
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128
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Koike Y, Yozaki M, Kuwatsuka Y, Utani A. Epithelial-mesenchymal transition in Bowen's disease when arising de novo and acquiring invasive capacity. J Dermatol 2018; 45:748-750. [PMID: 29864224 DOI: 10.1111/1346-8138.14290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Yuta Koike
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mariko Yozaki
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yutaka Kuwatsuka
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Atsushi Utani
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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129
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Cancer-associated fibroblasts suppress SOX2-induced dysplasia in a lung squamous cancer coculture. Proc Natl Acad Sci U S A 2018; 115:E11671-E11680. [PMID: 30487219 PMCID: PMC6294935 DOI: 10.1073/pnas.1803718115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tumor−stroma interactions play a critical role in regulating tumorigenesis. However, how these interactions contribute to changes in tissue architecture and cell polarity observed during tumor development is unclear. Here we report a 3D coculture system that recapitulates key phenotypic changes during the progression of lung squamous carcinoma (LUSC) as well as the dynamic interactions between LUSC cells and components of the tumor microenvironment (TME). Our data suggest that two major components of TME, including the extracellular matrix and cancer-associated fibroblasts, could override cell intrinsic oncogenic changes in determining the disease phenotype in the context of LUSC. These findings may have broad implications for LUSC biology as well as the design of future therapies. Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding microenvironment. While oncogenic drivers in lung squamous carcinoma (LUSC) have been described, the role of stroma in modulating tissue architecture, particularly cell polarity, remains unclear. Here, we report the establishment of a 3D coculture system of LUSC epithelial cells with cancer-associated fibroblasts (CAFs) and extracellular matrix that together capture key components of the tumor microenvironment (TME). Single LUSC epithelial cells develop into acinar-like structures with 0.02% efficiency, and addition of CAFs provides proper tumor−stromal interactions within an appropriate 3D architectural context. Using this model, we recapitulate key pathological changes during tumorigenesis, from hyperplasia to dysplasia and eventually invasion, in malignant LUSC spheroids that undergo phenotypic switching in response to cell intrinsic and extrinsic changes. Overexpression of SOX2 is sufficient to mediate the transition from hyperplasia to dysplasia in LUSC spheroids, while the presence of CAFs makes them invasive. Unexpectedly, CAFs suppress the activity of high SOX2 levels, restore hyperplasia, and enhance the formation of acinar-like structures. Taken together, these observations suggest that stromal factors can override cell intrinsic oncogenic changes in determining the disease phenotype, thus providing fundamental evidence for the existence of dynamic reciprocity between the nucleus and the TME of LUSC.
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130
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Sosa Iglesias V, Theys J, Groot AJ, Barbeau LMO, Lemmens A, Yaromina A, Losen M, Houben R, Dubois L, Vooijs M. Synergistic Effects of NOTCH/γ-Secretase Inhibition and Standard of Care Treatment Modalities in Non-small Cell Lung Cancer Cells. Front Oncol 2018; 8:460. [PMID: 30464927 PMCID: PMC6234899 DOI: 10.3389/fonc.2018.00460] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Lung cancer is the leading cause of cancer death worldwide. More effective treatments are needed to increase durable responses and prolong patient survival. Standard of care treatment for patients with non-operable stage III-IV NSCLC is concurrent chemotherapy and radiation. An activated NOTCH signaling pathway is associated with poor outcome and treatment resistance in non-small cell lung cancer (NSCLC). NOTCH/γ-secretase inhibitors have been effective in controlling tumor growth in preclinical models but the therapeutic benefit of these inhibitors as monotherapy in patients has been limited so far. Because NOTCH signaling has been implicated in treatment resistance, we hypothesized that by combining NOTCH inhibitors with chemotherapy and radiotherapy this could result in an increased therapeutic effect. A direct comparison of the effects of NOTCH inhibition when combined with current treatment combinations for NSCLC is lacking. Methods: Using monolayer growth assays, we screened 101 FDA-approved drugs from the Cancer Therapy Evaluation Program alone, or combined with radiation, in the H1299 and H460 NSCLC cell lines to identify potent treatment interactions. Subsequently, using multicellular three-dimensional tumor spheroid assays, we tested a selection of drugs used in clinical practice for NSCLC patients, and combined these with a small molecule inhibitor, currently being tested in clinical trials, of the NOTCH pathway (BMS-906024) alone, or in combination with radiation, and measured specific spheroid growth delay (SSGD). Statistical significance was determined by one-way ANOVA with post-hoc Bonferroni correction, and synergism was assessed using two-way ANOVA. Results: Monolayer assays in H1299 and H460 suggest that 21 vs. 5% were synergistic, and 17 vs. 11% were additive chemoradiation interactions, respectively. In H1299 tumor spheroids, significant SSGD was obtained for cisplatin, etoposide, and crizotinib, which increased significantly after the addition of the NOTCH inhibitor BMS-906024 (but not for paclitaxel and pemetrexed), and especially in triple combination with radiation. Synergistic interactions were observed when BMS-906024 was combined with chemoradiation (cisplatin, paclitaxel, docetaxel, and crizotinib). Similar results were observed for H460 spheroids using paclitaxel or crizotinib in dual combination treatment with NOTCH inhibition and triple with radiation. Conclusions: Our findings point to novel synergistic combinations of NOTCH inhibition and chemoradiation that should be tested in NSCLC in vivo models for their ability to achieve an improved therapeutic ratio.
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Affiliation(s)
- Venus Sosa Iglesias
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jan Theys
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Arjan J Groot
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lydie M O Barbeau
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Alyssa Lemmens
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Ala Yaromina
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Mario Losen
- Department of Psychology and Neuropsychology, MHeNS, Maastricht University Medical Center, Maastricht, Netherlands
| | - Ruud Houben
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands.,MAASTRO Clinic, Maastricht, Netherlands
| | - Ludwig Dubois
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marc Vooijs
- Department of Radiotherapy (MAASTRO), GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands.,MAASTRO Clinic, Maastricht, Netherlands
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Halani SH, Yousefi S, Velazquez Vega J, Rossi MR, Zhao Z, Amrollahi F, Holder CA, Baxter-Stoltzfus A, Eschbacher J, Griffith B, Olson JJ, Jiang T, Yates JR, Eberhart CG, Poisson LM, Cooper LAD, Brat DJ. Multi-faceted computational assessment of risk and progression in oligodendroglioma implicates NOTCH and PI3K pathways. NPJ Precis Oncol 2018; 2:24. [PMID: 30417117 PMCID: PMC6219505 DOI: 10.1038/s41698-018-0067-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 09/18/2018] [Accepted: 09/24/2018] [Indexed: 12/22/2022] Open
Abstract
Oligodendrogliomas are diffusely infiltrative gliomas defined by IDH-mutation and co-deletion of 1p/19q. They have highly variable clinical courses, with survivals ranging from 6 months to over 20 years, but little is known regarding the pathways involved with their progression or optimal markers for stratifying risk. We utilized machine-learning approaches with genomic data from The Cancer Genome Atlas to objectively identify molecular factors associated with clinical outcomes of oligodendroglioma and extended these findings to study signaling pathways implicated in oncogenesis and clinical endpoints associated with glioma progression. Our multi-faceted computational approach uncovered key genetic alterations associated with disease progression and shorter survival in oligodendroglioma and specifically identified Notch pathway inactivation and PI3K pathway activation as the most strongly associated with MRI and pathology findings of advanced disease and poor clinical outcome. Our findings that Notch pathway inactivation and PI3K pathway activation are associated with advanced disease and survival risk will pave the way for clinically relevant markers of disease progression and therapeutic targets to improve clinical outcomes. Furthermore, our approach demonstrates the strength of machine learning and computational methods for identifying genetic events critical to disease progression in the era of big data and precision medicine.
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Affiliation(s)
| | - Safoora Yousefi
- Department of Biomedical Informatics, Emory University, Atlanta, GA USA
| | - Jose Velazquez Vega
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA USA
| | - Michael R. Rossi
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA USA
| | - Zheng Zhao
- Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fatemeh Amrollahi
- Department of Biomedical Informatics, Emory University, Atlanta, GA USA
| | - Chad A. Holder
- Department of Radiology, Emory University, Atlanta, GA USA
| | | | - Jennifer Eschbacher
- Department of Neuropathology, Barrow Neurological Institute, Phoenix, AZ USA
| | - Brent Griffith
- Department of Radiology, Henry Ford Health System, Detroit, MI USA
- Josephine Ford Cancer Institute, Henry Ford Health System, Detroit, MI USA
| | - Jeffrey J. Olson
- Emory University School of Medicine, Atlanta, GA USA
- Department of Neurosurgery, Emory University, Atlanta, GA USA
- Winship Cancer Institute, Emory University, Atlanta, GA USA
| | - Tao Jiang
- Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing, China
| | - Joseph R. Yates
- Divisions of Pathology, Ophthalmology, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Charles G. Eberhart
- Divisions of Pathology, Ophthalmology, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Laila M. Poisson
- Josephine Ford Cancer Institute, Henry Ford Health System, Detroit, MI USA
- Department of Public Health Sciences, Henry Ford Hospital Systems, Detroit, MI USA
| | - Lee A. D. Cooper
- Emory University School of Medicine, Atlanta, GA USA
- Department of Biomedical Informatics, Emory University, Atlanta, GA USA
- Winship Cancer Institute, Emory University, Atlanta, GA USA
- Department of Biomedical Engineering, Emory University/Georgia Institute of Technology, Atlanta, GA USA
| | - Daniel J. Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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Co-Expression Analysis Reveals Mechanisms Underlying the Varied Roles of NOTCH1 in NSCLC. J Thorac Oncol 2018; 14:223-236. [PMID: 30408569 DOI: 10.1016/j.jtho.2018.10.162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 09/23/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Notch receptor family dysregulation can be tumor promoting or suppressing depending on cellular context. Our studies shed light on the mechanistic differences that are responsible for NOTCH1's opposing roles in lung adenocarcinoma and lung squamous cell carcinoma. METHODS We integrated transcriptional patient-derived datasets with gene co-expression analyses to elucidate mechanisms behind NOTCH1 function in subsets of NSCLC. Differential co-expression was examined using hierarchical clustering and principal component analysis. Enrichment analysis was used to examine pathways associated with the underlying transcriptional networks. These pathways were validated in vitro and in vivo. Endogenously epitope-tagged NOTCH1 was used to identify novel interacting proteins. RESULTS NOTCH1 co-expressed genes in lung adenocarcinoma and squamous carcinoma were distinct and associated with either angiogenesis and immune system pathways or cell cycle control and mitosis pathways, respectively. Tissue culture and xenograft studies of lung adenocarcinoma and lung squamous models with NOTCH1 knockdown showed growth differences and opposing effects on these pathways. Differential NOTCH1 interacting proteins were identified as potential mediators of these differences. CONCLUSIONS Recognition of the opposing role of NOTCH1 in lung cancer, downstream pathways, and interacting proteins in each context may help direct the development of rational NOTCH1 pathway-dependent targeted therapies for specific tumor subsets of NSCLC.
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Pandey A, Li-Kroeger D, Sethi MK, Lee TV, Buettner FFR, Bakker H, Jafar-Nejad H. Sensitized genetic backgrounds reveal differential roles for EGF repeat xylosyltransferases in Drosophila Notch signaling. Glycobiology 2018; 28:849-859. [PMID: 30169771 PMCID: PMC6454539 DOI: 10.1093/glycob/cwy080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
In multicellular organisms, glycosylation regulates various developmental signaling pathways including the Notch pathway. One of the O-linked glycans added to epidermal growth factor-like (EGF) repeats in animal proteins including the Notch receptors is the xylose-xylose-glucose-O oligosaccharide. Drosophila glucoside xylosyltransferase (Gxylt) Shams negatively regulates Notch signaling in specific contexts. Since Shams adds the first xylose residue to O-glucose, its loss-of-function phenotype could be due to the loss of the first xylose, the second xylose or both. To examine the contribution of the second xylose residues to Drosophila Notch signaling, we have performed biochemical and genetic analysis on CG11388, which is the Drosophila homolog of human xyloside xylosyltransferase 1 (XXYLT1). Experiments in S2 cells indicated that similar to human XXYLT1, CG11388 can add the second xylose to xylose-glucose-O glycans. Flies lacking both copies of CG11388 (Xxylt) are viable and fertile and do not show gross phenotypes indicative of altered Notch signaling. However, genetic interaction experiments show that in sensitized genetic backgrounds with decreased or increased Notch pathway components, loss of Xxylt promotes Delta-mediated activation of Notch. Unexpectedly, we find that in such sensitized backgrounds, even loss of one copy of the fly Gxylt shams enhances Delta-mediated Notch activation. Taken together, these data indicate that while the first xylose plays a key role in tuning the Delta-mediated Notch signaling in Drosophila, the second xylose has a fine-tuning role only revealed in sensitized genetic backgrounds.
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Affiliation(s)
- Ashutosh Pandey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Li-Kroeger
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Maya K Sethi
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Tom V Lee
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Falk FR Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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134
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Guo S. Cancer driver mutations in endometriosis: Variations on the major theme of fibrogenesis. Reprod Med Biol 2018; 17:369-397. [PMID: 30377392 PMCID: PMC6194252 DOI: 10.1002/rmb2.12221] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/03/2018] [Accepted: 06/24/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND One recent study reports cancer driver mutations in deep endometriosis, but its biological/clinical significance remains unclear. Since the natural history of endometriosis is essentially gradual progression toward fibrosis, it is thus hypothesized that the six driver genes reported to be mutated in endometriosis (the RP set) may play important roles in fibrogenesis but not necessarily malignant transformation. METHODS Extensive PubMed search to see whether RP and another set of driver genes not yet reported (NR) to be mutated in endometriosis have any roles in fibrogenesis. All studies reporting on the role of fibrogenesis of the genes in both RP and NR sets were retrieved and evaluated in this review. RESULTS All six RP genes were involved in various aspects of fibrogenesis as compared with only three NR genes. These nine genes can be anchored in networks linking with their upstream and downstream genes that are known to be aberrantly expressed in endometriosis, piecing together seemingly unrelated findings. CONCLUSIONS Given that somatic driver mutations can and do occur frequently in physiologically normal tissues, it is argued that these mutations in endometriosis are not necessarily synonymous with malignancy or premalignancy, but the result of enormous pressure for fibrogenesis.
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Affiliation(s)
- Sun‐Wei Guo
- Shanghai Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiChina
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135
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Baron M. Combining genetic and biophysical approaches to probe the structure and function relationships of the notch receptor. Mol Membr Biol 2018; 34:33-49. [PMID: 30246579 DOI: 10.1080/09687688.2018.1503742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Notch is a conserved cell signalling receptor regulating many aspects of development and tissue homeostasis. Notch is activated by ligand-induced proteolytic cleavages that release the Notch intracellular domain, which relocates to the nucleus to regulate gene transcription. Proteolytic activation first requires mechanical force to be applied to the Notch extracellular domain through an endocytic pulling mechanism transmitted through the ligand/receptor interface. This exposes the proteolytic cleavage site allowing the signal to be initiated following removal of the Notch extracellular domain. Ligands can also act, when expressed in the same cell, through non-productive cis-interactions to inhibit Notch activity. Furthermore, ligand selectivity and Notch activation are regulated by numerous post-translational modifications of the extracellular domain. Additional non-canonical trans and cis interactions with other regulatory proteins may modulate alternative mechanisms of Notch activation that depend on endocytic trafficking of the full-length receptor and proteolytic release of the intracellular domain from endo-lysosomal surface. Mutations of Notch, located in different regions of the protein, are associated with a spectrum of different loss and gain of function phenotypes and offer the possibility to dissect distinct regulatory interactions and mechanisms, particularly when combined with detailed structural analysis of Notch in complex with various regulatory partners.
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Affiliation(s)
- Martin Baron
- a School of Biological Sciences , University of Manchester , Manchester , UK
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136
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Abstract
Squamous cell carcinomas (SCCs) are among the most prevalent human cancers. SCC comprises a wide range of tumours originated from diverse anatomical locations that share common genetic mutations and expression of squamous differentiation markers. SCCs arise from squamous and non-squamous epithelial tissues. Here, we discuss the different studies in which the cell of origin of SCCs has been uncovered by expressing oncogenes and/or deleting tumour suppressor genes in the different cell lineages that compose these epithelia. We present evidence showing that the squamous differentiation phenotype of the tumour depends on the type of mutated oncogene and the cell of origin, which dictate the competence of the cells to initiate SCC formation, as well as on the aggressiveness and invasive properties of these tumours.
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Affiliation(s)
- Adriana Sánchez-Danés
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels, Belgium
| | - Cédric Blanpain
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles, Brussels, Belgium.
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137
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Harbison RA, Kubik M, Konnick EQ, Zhang Q, Lee SG, Park H, Zhang J, Carlson CS, Chen C, Schwartz SM, Rodriguez CP, Duvvuri U, Méndez E. The mutational landscape of recurrent versus nonrecurrent human papillomavirus-related oropharyngeal cancer. JCI Insight 2018; 3:99327. [PMID: 30046007 DOI: 10.1172/jci.insight.99327] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human papillomavirus-related (HPV-related) oropharyngeal squamous cell carcinomas (OPSCCs) have an excellent response rate to platinum-based chemoradiotherapy. Genomic differences between primary HPV-related OPSCCs that do or do not recur are unknown. Furthermore, it is unclear if HPV-related OPSCCs that recur share a genomic landscape with HPV-negative head and neck cancers (HNCs). METHODS We utilized whole exome sequencing to analyze somatic nucleotide (SNVs) and copy number variants (CNVs) among a unique set of 51 primary HPV-related OPSCCs, including 35 that did not recur and 16 that recurred. We evaluated 12 metachronous recurrent OPSCCs (7 with paired primary OPSCCs) and 33 primary HPV-unrelated oral cavity and OPSCCs. RESULTS KMT2D was the most frequently mutated gene among primary HPV-related OPSCCs (n = 51; 14%) and among metachronous recurrent OPSCCs (n = 12; 42%). Primary HPV-related OPSCCs that recurred shared a genomic landscape with primary HPV-related OPSCCs that did not recur. However, TSC2, BRIP1, NBN, and NFE2L2 mutations occurred in primary OPSCCs that recurred but not in those that did not recur. Moreover, primary HPV-related OPSCCs that recur harbor features of HPV-unrelated HNCs, notably including MAPK, JAK/STAT, and differentiation signaling pathway aberrations. Metachronous recurrent OPSCCs shared a genomic landscape with HPV-unrelated HNCs, including a high frequency of TP53, CASP8, FAT1, HLA-A, AJUBA, and NSD1 genomic alterations. CONCLUSION Overall, primary HPV-related OPSCCs that recur share a genomic landscape with nonrecurrent OPSCCs. Metachronous recurrent OPSCCs share genomic features with HPV-negative HNCs. These data aim to guide future deescalation endeavors and functional experiments. FUNDING This study is supported by the American Cancer Society (RSG TBG-123653), funding support for RAH (T32DC00018, Research Training in Otolaryngology, University of Washington), funds to EM from Seattle Translational Tumor Research (Fred Hutchinson Cancer Research Center), and center funds from the Fred Hutchinson Cancer Research Center to EM. UD is supported by the Department of Veterans Affairs, Biomedical Laboratory Research and Development (BLR&D), grant IO1-oo23456, and funds from the Pittsburgh Foundation and PNC Foundation.
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Affiliation(s)
- R Alex Harbison
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark Kubik
- Veterans Affairs Pittsburgh Health System, Pittsburgh PA
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Qing Zhang
- Genomics & Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Seok-Geun Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Science in Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Heuijoon Park
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jianan Zhang
- Solid Tumor Translational Research/Human Biology and
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephen M Schwartz
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cristina P Rodriguez
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Eduardo Méndez
- Departments of Otolaryngology, University of Washington School of Medicine, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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138
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Sosa Iglesias V, Giuranno L, Dubois LJ, Theys J, Vooijs M. Drug Resistance in Non-Small Cell Lung Cancer: A Potential for NOTCH Targeting? Front Oncol 2018; 8:267. [PMID: 30087852 PMCID: PMC6066509 DOI: 10.3389/fonc.2018.00267] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Drug resistance is a major cause for therapeutic failure in non-small cell lung cancer (NSCLC) leading to tumor recurrence and disease progression. Cell intrinsic mechanisms of resistance include changes in the expression of drug transporters, activation of pro-survival, and anti-apoptotic pathways, as well as non-intrinsic influences of the tumor microenvironment. It has become evident that tumors are composed of a heterogeneous population of cells with different genetic, epigenetic, and phenotypic characteristics that result in diverse responses to therapy, and underlies the emergence of resistant clones. This tumor heterogeneity is driven by subpopulations of tumor cells termed cancer stem cells (CSCs) that have tumor-initiating capabilities, are highly self-renewing, and retain the ability for multi-lineage differentiation. CSCs have been identified in NSCLC and have been associated with chemo- and radiotherapy resistance. Stem cell pathways are frequently deregulated in cancer and are implicated in recurrence after treatment. Here, we focus on the NOTCH signaling pathway, which has a role in stem cell maintenance in non-squamous non-small lung cancer, and we critically assess the potential for targeting the NOTCH pathway to overcome resistance to chemotherapeutic and targeted agents using both preclinical and clinical evidence.
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Affiliation(s)
- Venus Sosa Iglesias
- Department of Radiation Oncology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
| | - Lorena Giuranno
- Department of Radiation Oncology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
| | - Ludwig J Dubois
- Department of Radiation Oncology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
| | - Jan Theys
- Department of Radiation Oncology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
| | - Marc Vooijs
- Department of Radiation Oncology, GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
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139
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Giaimo BD, Borggrefe T. Introduction to Molecular Mechanisms in Notch Signal Transduction and Disease Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:3-30. [DOI: 10.1007/978-3-319-89512-3_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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140
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Harbuzariu A, Oprea-Ilies GM, Gonzalez-Perez RR. The Role of Notch Signaling and Leptin-Notch Crosstalk in Pancreatic Cancer. MEDICINES (BASEL, SWITZERLAND) 2018; 5:medicines5030068. [PMID: 30004402 PMCID: PMC6164868 DOI: 10.3390/medicines5030068] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023]
Abstract
There is accumulating evidence that deregulated Notch signaling affects cancer development, and specifically pancreatic cancer (PC) progression. Notch canonical and non-canonical signaling has diverse impact on PC. Moreover, the actions of RBP-Jk (nuclear partner of activated Notch) independent of Notch signaling pathway seem to affect differently cancer progression. Recent data show that in PC and other cancer types the adipokine leptin can modulate Notch/RBP-Jk signaling, thereby, linking the pandemic obesity with cancer and chemoresistance. The potential pivotal role of leptin on PC, and its connection with Notch signaling and chemoresistance are still not completely understood. In this review, we will describe the most important aspects of Notch-RBP-Jk signaling in PC. Further, we will discuss on studies related to RBP-Jk-independent Notch and Notch-independent RPB-Jk signaling. We will also discuss on the novel crosstalk between leptin and Notch in PC and its implications in chemoresistance. The effects of leptin-Notch/RBP-Jk signaling on cancer cell proliferation, apoptosis, and drug resistance require more investigation. Data from these investigations could help to open unexplored ways to improve PC treatment success that has shown little progress for many years.
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Affiliation(s)
- Adriana Harbuzariu
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA.
| | | | - Ruben R Gonzalez-Perez
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA.
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141
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Kikuchi H, Sakakibara-Konishi J, Furuta M, Kikuchi E, Kikuchi J, Oizumi S, Hida Y, Kaga K, Kinoshita I, Dosaka-Akita H, Nishimura M. Numb has distinct function in lung adenocarcinoma and squamous cell carcinoma. Oncotarget 2018; 9:29379-29391. [PMID: 30034624 PMCID: PMC6047666 DOI: 10.18632/oncotarget.25585] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 05/21/2018] [Indexed: 12/16/2022] Open
Abstract
Some reports suggest that Numb is a potential tumor suppressor. However, its role in non-small cell lung cancer remains unclear. Non-small cell lung cancer comprises two major histological subtypes, adenocarcinoma and squamous cell carcinoma. To investigate the role of Numb in tumorigenesis of lung adenocarcinoma and squamous cell carcinoma, we firstly performed loss-of-function and gain-of-function assays. Moreover, Numb expression was investigated in surgically resected lung adenocarcinoma and squamous cell carcinoma tissues by immunohistochemistry and correlations with prognosis were analyzed. Numb suppressed the proliferation, migration, and invasion of adenocarcinoma cells and inhibited Notch signaling and epithelial-mesenchymal transition in vitro. Numb overexpression also inhibited subcutaneous adenocarcinoma tumor growth. In contrast, Numb promoted the proliferation, migration, and invasion of squamous cell carcinoma cells, but did not induce any consistent changes in Notch signaling. High Numb expression was associated with favorable prognosis in patients with lung adenocarcinoma, but not in those with squamous cell carcinoma. Collectively, our data demonstrate that Numb plays distinct roles in lung adenocarcinoma and squamous cell carcinoma. In lung adenocarcinoma, Numb impairs tumor growth and inhibits the Notch pathway and epithelial-mesenchymal transition, whereas in lung squamous cell carcinoma it may promote proliferation.
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Affiliation(s)
- Hajime Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Jun Sakakibara-Konishi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Megumi Furuta
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Eiki Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junko Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Oizumi
- Department of Respiratory Medicine, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Yasuhiro Hida
- Department of Cardiovascular and Thoracic Surgery, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Kichizo Kaga
- Department of Cardiovascular and Thoracic Surgery, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Ichiro Kinoshita
- Department of Medical Oncology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hirotoshi Dosaka-Akita
- Department of Medical Oncology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masaharu Nishimura
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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142
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Christensen SR. Recent advances in field cancerization and management of multiple cutaneous squamous cell carcinomas. F1000Res 2018; 7. [PMID: 29904586 PMCID: PMC5989149 DOI: 10.12688/f1000research.12837.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
Cutaneous squamous cell carcinoma (SCC) is among the most common cancers in humans, and many patients with SCC will develop multiple tumors within their lifetime. The field cancerization concept, originally proposed over 60 years ago, hypothesized that multiple primary cancers may arise simultaneously and coexist with subclinical precursor lesions within a defined field. Genetic sequencing of SCC and precursor lesions has identified what may be the earliest clonal proliferations in SCC development and confirmed that field cancerization in the skin is mediated by ultraviolet radiation. For patients with multiple SCCs and severe actinic damage, treatment of precursor lesions within a cancerized field can decrease the risk of subsequent cancer development. Sunblock is an effective intervention for field cancerization, even in patients with established disease. There is now direct evidence that field therapy with topical 5-fluorouracil is effective in reducing the incidence of subsequent SCC, and there is indirect evidence suggesting that topical imiquimod, topical ingenol mebutate, and photodynamic therapy are similarly effective. There is limited direct evidence to show that systemic acitretin or nicotinamide can decrease incident SCC in patients with field cancerization. In this review, an approach to the management of patients with multiple SCCs and field cancerization is presented along with the rationale to support field-directed therapy.
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Affiliation(s)
- Sean R Christensen
- Section of Dermatologic Surgery and Cutaneous Oncology, Department of Dermatology, Yale University, New Haven, CT, USA
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143
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Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma. Nat Commun 2018; 9:1894. [PMID: 29760388 PMCID: PMC5951856 DOI: 10.1038/s41467-018-04008-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole-exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominates in 10/32 samples, while nine show microsatellite instability (MSI) profiles. UV-damage SeC exhibited poorly differentiated, infiltrative histopathology compared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Moreover, UV-damage SeC transcriptomes and anatomic distribution closely resemble those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations per Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquires far fewer mutations without a dominant signature, but show frequent truncations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.
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144
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Goriki A, Seiler R, Wyatt AW, Contreras-Sanz A, Bhat A, Matsubara A, Hayashi T, Black PC. Unravelling disparate roles of NOTCH in bladder cancer. Nat Rev Urol 2018; 15:345-357. [DOI: 10.1038/s41585-018-0005-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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145
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McCoach CE, Le AT, Gowan K, Jones K, Schubert L, Doak A, Estrada-Bernal A, Davies KD, Merrick DT, Bunn PA, Purcell WT, Dziadziuszko R, Varella-Garcia M, Aisner DL, Camidge DR, Doebele RC. Resistance Mechanisms to Targeted Therapies in ROS1+ and ALK+ Non-small Cell Lung Cancer. Clin Cancer Res 2018; 24:3334-3347. [PMID: 29636358 DOI: 10.1158/1078-0432.ccr-17-2452] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 02/23/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022]
Abstract
Purpose: Despite initial benefit from tyrosine kinase inhibitors (TKIs), patients with advanced non-small cell lung cancer (NSCLC) harboring ALK (ALK+) and ROS1 (ROS1+) gene fusions ultimately progress. Here, we report on the potential resistance mechanisms in a series of patients with ALK+ and ROS1+ NSCLC progressing on different types and/or lines of ROS1/ALK-targeted therapy.Experimental Design: We used a combination of next-generation sequencing (NGS), multiplex mutation assay, direct DNA sequencing, RT-PCR, and FISH to identify fusion variants/partners and copy-number gain (CNG), kinase domain mutations (KDM), and copy-number variations (CNVs) in other cancer-related genes. We performed testing on 12 ROS1+ and 43 ALK+ patients.Results: One of 12 ROS1+ (8%) and 15 of 43 (35%) ALK + patients harbored KDM. In the ROS1+ cohort, we identified KIT and β-catenin mutations and HER2-mediated bypass signaling as non-ROS1-dominant resistance mechanisms. In the ALK+ cohort, we identified a novel NRG1 gene fusion, a RET fusion, 2 EGFR, and 3 KRAS mutations, as well as mutations in IDH1, RIT1, NOTCH, and NF1 In addition, we identified CNV in multiple proto-oncogenes genes including PDGFRA, KIT, KDR, GNAS, K/HRAS, RET, NTRK1, MAP2K1, and others.Conclusions: We identified a putative TKI resistance mechanism in six of 12 (50%) ROS1 + patients and 37 of 43 (86%) ALK+ patients. Our data suggest that a focus on KDMs will miss most resistance mechanisms; broader gene testing strategies and functional validation is warranted to devise new therapeutic strategies for drug resistance. Clin Cancer Res; 24(14); 3334-47. ©2018 AACR.
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Affiliation(s)
- Caroline E McCoach
- Division of Medical Oncology, UCSF Helen Diller Comprehensive Cancer Center, San Francisco, California.
| | - Anh T Le
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Katherine Gowan
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado, Aurora, Colorado
| | - Kenneth Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado, Aurora, Colorado
| | - Laura Schubert
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Andrea Doak
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Adriana Estrada-Bernal
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Kurtis D Davies
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
| | - Daniel T Merrick
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
| | - Paul A Bunn
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - W Tom Purcell
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Rafal Dziadziuszko
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Marileila Varella-Garcia
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
| | - D Ross Camidge
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Robert C Doebele
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
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146
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Aung KL, El-Khoueiry AB, Gelmon K, Tran B, Bajaj G, He B, Chen T, Zhu L, Poojary S, Basak S, Qi Z, Spreafico A, Fischer BS, Desai J. A multi-arm phase I dose escalating study of an oral NOTCH inhibitor BMS-986115 in patients with advanced solid tumours. Invest New Drugs 2018; 36:1026-1036. [PMID: 29637471 DOI: 10.1007/s10637-018-0597-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/26/2018] [Indexed: 10/17/2022]
Abstract
Background Inhibiting Notch is a promising anti-cancer strategy as it plays a critical role in cancer stem cells maintenance and tumour angiogenesis. BMS-986115 is an orally active, selective inhibitor of gamma-secretase mediated Notch signalling. Method Two dose escalation schedules (Arm-A continuous daily schedule and Arm-B intermittent 2 times weekly schedule) of BMS-986115 were evaluated in advanced solid tumour patients. The primary objective was to establish the safety, tolerability and Maximum Tolerated Dose (MTD) of BMS-986115. Results Thirty six patients (24 in Arm A and 12 in Arm B) were treated. The most frequent treatment related adverse advents were diarrhoea (72%), hypophosphataemia (64%), and nausea (61%). The MTD was 1.5 mg daily in Arm A but not established in Arm B. Four patients in Arm A and 2 in Arm B experienced dose limiting toxicities (grade 3 nausea, diarrhoea, pruritus/urticaria and ileus). BMS-986115 showed dose related increase in exposure within the dose range tested. Target inhibition of Notch pathway related genes was observed. Three patients in Arm A and 2 in Arm B achieved stable disease for more than 6 months. Conclusion The daily oral dosing of BMS-986115 is safe and tolerable with biological activity demonstrated by continuous target engagement and Notch signalling inhibition.
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Affiliation(s)
- Kyaw L Aung
- Drug Development Program, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, M5G 2M9, Canada
| | - Anthony B El-Khoueiry
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 900333, USA
| | - Karen Gelmon
- British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 4E6, Canada
| | - Ben Tran
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Gaurav Bajaj
- Clinical Pharmacology & Pharmacometrics, Bristol-Myers Squibb, Lawrenceville, NJ, 08648, USA
| | - Bing He
- Clinical Pharmacology & Pharmacometrics, Bristol-Myers Squibb, Lawrenceville, NJ, 08648, USA
| | - Tian Chen
- Global Biometric Sciences, Bristol-Myers Squibb, Princeton, NJ, 08540, USA
| | - Lili Zhu
- Global Biometric Sciences, Bristol-Myers Squibb, Princeton, NJ, 08540, USA
| | - Sharath Poojary
- Biocon BMS R&D Centre, Syngene International Ltd, Bangalore, 560 099, India
| | - Shashwati Basak
- Biocon BMS R&D Centre, Syngene International Ltd, Bangalore, 560 099, India
| | - Zhenhao Qi
- Clinical Genomics and Genetics, Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08540, USA
| | - Anna Spreafico
- Drug Development Program, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, M5G 2M9, Canada
| | - Bruce S Fischer
- Oncology Early Clinical Development, Bristol-Myers Squibb, Lawrenceville, NJ, 08648, USA
| | - Jayesh Desai
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital, University of Melbourne, 305 Grattan St, Melbourne, VIC, 3000, Australia.
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147
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Kamps-Hughes N, McUsic A, Kurihara L, Harkins TT, Pal P, Ray C, Ionescu-Zanetti C. ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data. PLoS One 2018; 13:e0195272. [PMID: 29630678 PMCID: PMC5890993 DOI: 10.1371/journal.pone.0195272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
The accurate detection of ultralow allele frequency variants in DNA samples is of interest in both research and medical settings, particularly in liquid biopsies where cancer mutational status is monitored from circulating DNA. Next-generation sequencing (NGS) technologies employing molecular barcoding have shown promise but significant sensitivity and specificity improvements are still needed to detect mutations in a majority of patients before the metastatic stage. To address this we present analytical validation data for ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors), a method for accurate and sensitive detection of ultralow frequency DNA variants in NGS data. ERASE-Seq differs from previous methods by creating a robust statistical framework to utilize technical replicates in conjunction with background error modeling, providing a 10 to 100-fold reduction in false positive rates compared to published molecular barcoding methods. ERASE-Seq was tested using spiked human DNA mixtures with clinically realistic DNA input quantities to detect SNVs and indels between 0.05% and 1% allele frequency, the range commonly found in liquid biopsy samples. Variants were detected with greater than 90% sensitivity and a false positive rate below 0.1 calls per 10,000 possible variants. The approach represents a significant performance improvement compared to molecular barcoding methods and does not require changing molecular reagents.
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Affiliation(s)
- Nick Kamps-Hughes
- Fluxion Biosciences Inc., South San Francisco, California, United States of America
| | - Andrew McUsic
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Laurie Kurihara
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Timothy T Harkins
- Swift Biosciences Inc., Ann Arbor, Michigan, United States of America
| | - Prithwish Pal
- Illumina Inc., San Diego, California, United States of America
| | - Claire Ray
- Illumina Inc., San Diego, California, United States of America
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148
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A phase 2 study of vorinostat in locally advanced, recurrent, or metastatic adenoid cystic carcinoma. Oncotarget 2018; 8:32918-32929. [PMID: 28415633 PMCID: PMC5464838 DOI: 10.18632/oncotarget.16464] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
Purpose Vorinostat is a histone deacetylase inhibitor (HDACi). Based on a confirmed partial response (PR) in an adenoid cystic carcinoma (ACC) patient treated with vorinostat in a prior phase 1 trial, we initiated this phase 2 trial. Methods: Vorinostat was administered orally 400 mg daily, 28 day cycles. The primary objective was to evaluate response rate (RR). Exploratory studies included whole exome sequencing (WES) of selected patients. Results Thirty patients were enrolled. Median age of patients was 53 years (range 21–73). Median number of cycles was 5 (range 1-66). Lymphopenia (n = 5), hypertension (n = 3), oral pain (n = 2), thromboembolic events (n = 2) and fatigue (n = 2) were the only grade 3 adverse events (AEs) that occurred in more than 1 patient. Eleven patients were dose reduced secondary to drug-related AEs. Two patients had a partial response (PR), with response durations of 53 and 7.2 months. One patient had a minor response with a decrease in ascites (for 19 cycles). Stable disease was the best response in 27 patients. Targeted and WES of 8 patients in this trial identified mutations in chromatin remodeling genes highlighting the role of the epigenome in ACC. Conclusion: Vorinostat demonstrated efficacy in patients with ACC supporting the inclusion of HDACi in future studies to treat ACC.
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149
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Meyers JM, Grace M, Uberoi A, Lambert PF, Munger K. Inhibition of TGF-β and NOTCH Signaling by Cutaneous Papillomaviruses. Front Microbiol 2018; 9:389. [PMID: 29568286 PMCID: PMC5852067 DOI: 10.3389/fmicb.2018.00389] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
Infections with cutaneous papillomaviruses have been linked to cutaneous squamous cell carcinomas that arise in patients who suffer from a rare genetic disorder, epidermodysplasia verruciformis, or those who have experienced long-term, systemic immunosuppression following organ transplantation. The E6 proteins of the prototypical cutaneous human papillomavirus (HPV) 5 and HPV8 inhibit TGF-β and NOTCH signaling. The Mus musculus papillomavirus 1, MmuPV1, infects laboratory mouse strains and causes cutaneous skin warts that can progress to squamous cell carcinomas. MmuPV1 E6 shares biological and biochemical activities with HPV8 E6 including the ability to inhibit TGF-β and NOTCH signaling by binding the SMAD2/SMAD3 and MAML1 transcription factors, respectively. Inhibition of TGF-β and NOTCH signaling is linked to delayed differentiation and sustained proliferation of differentiating keratinocytes. Furthermore, the ability of MmuPV1 E6 to bind MAML1 is necessary for wart and cancer formation in experimentally infected mice. Hence, experimental MmuPV1 infection in mice will be a robust and valuable experimental system to dissect key aspects of cutaneous HPV infection, pathogenesis, and carcinogenesis.
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Affiliation(s)
- Jordan M Meyers
- Program in Virology, Harvard Medical School, Boston, MA, United States.,Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Miranda Grace
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Aayushi Uberoi
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Karl Munger
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
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150
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Signoretti S, Aster JC. Metastatic penile carcinoma associated with convergent gain-of-function mutations in NOTCH1. HUMAN PATHOLOGY: CASE REPORTS 2018. [DOI: 10.1016/j.ehpc.2017.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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