1
|
Sirico M, Jacobs F, Molinelli C, Nader-Marta G, Debien V, Dewhurst HF, Palleschi M, Merloni F, Gianni C, De Giorgi U, de Azambuja E. Navigating the complexity of PI3K/AKT pathway in HER-2 negative breast cancer: biomarkers and beyond. Crit Rev Oncol Hematol 2024; 200:104404. [PMID: 38815877 DOI: 10.1016/j.critrevonc.2024.104404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024] Open
Abstract
The results of the SOLAR-1 and CAPItello-291, highlight the benefit of the ɑ-selective phosphoinositide 3-Kinase Pathway inhibitor (PI3Ki) alpelisib and the AKT inhibitor (AKTi) capivasertib in patients with hormone receptor-positive (HR+)/Human Epidermal Growth Factor Receptor 2 (HER2)- negative metastatic breast cancer (mBC) that have PIK3CA/AKT1/PTEN tumour alterations. Although effective, these drugs are associated with significant toxicities, which often limit their use, particularly in frail patients. Following the recent incorporation of these agents into clinical practice, and with many others currently in development, significant challenges have emerged, particularly those regarding biomarkers for patient selection. This review will discuss biomarkers of response and their resistance to PI3K/AKT inhibitors (PI3K/AKTis) in HR+/HER- BC in early and advanced settings to ascertain which populations will most benefit from these drugs. Of the biomarkers that were analysed, such as PIK3CA, AKT, PTEN mutations, insulin levels, 18 F-FDG-PET/TC, only the PIK3CA-mutations (PIK3CA-mut) and the AKT pathway alterations seem to have a predictive value for treatments with alpelisib and capivasertib. However, due to the retrospective and exploratory nature of the study, the data did not provide conclusive results. In addition, the different methods used to detect PIK3CA/AKT1/PTEN alterations underline the fact that the optimal diagnostic companion has yet to be established. We have summarised the clinical data on the approved and discontinued agents targeting this pathway and have assessed the drugs development, successes, and failures. Finally, because of tumour heterogeneity, we emphasise the importance of reassessing the mutational status of PI3KCA in both metastatic tissue and blood at the time of disease progression to better tailor treatment for patients.
Collapse
Affiliation(s)
- M Sirico
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy.
| | - F Jacobs
- Humanitas Clinical and Research Center - IRCCS, Humanitas Cancer Center, via Manzoni 56, 20089 Rozzano, Milan, Italy; Early Phase Trials Unit Institut Bergonié Bordeaux, France
| | - C Molinelli
- Early Phase Trials Unit Institut Bergonié Bordeaux, France; Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova, Italy; Department of Medical Oncology, U.O. Clinical di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - V Debien
- Early Phase Trials Unit Institut Bergonié Bordeaux, France
| | - H Faith Dewhurst
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, United Kingdom
| | - M Palleschi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - F Merloni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - C Gianni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - U De Giorgi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | |
Collapse
|
2
|
Zheng S, He S, Liang Y, Tan Y, Liu Q, Liu T, Lu X. Understanding PI3K/Akt/mTOR signaling in squamous cell carcinoma: mutated PIK3CA as an example. MOLECULAR BIOMEDICINE 2024; 5:13. [PMID: 38616230 PMCID: PMC11016524 DOI: 10.1186/s43556-024-00176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/29/2024] [Indexed: 04/16/2024] Open
Abstract
Compared with those in adenocarcinoma, PIK3CA mutations are more common in squamous cell carcinoma (SCC), which arises from stratified squamous epithelia that are usually exposed to adverse environmental factors. Although hotspot mutations in exons 9 and 20 of PIK3CA, including E542K, E545K, H1047L and H1047R, are frequently encountered in the clinic, their clinicopathological meaning remains to be determined in the context of SCC. Considering that few reviews on PIK3CA mutations in SCC are available in the literature, we undertook this review to shed light on the clinical significance of PIK3CA mutations, mainly regarding the implications and ramifications of PIK3CA mutations in malignant cell behavior, prognosis, relapse or recurrence and chemo- or radioresistance of SCC. It should be noted that only those studies regarding SCC in which PIK3CA was mutated were cherry-picked, which fell within the scope of this review. However, the role of mutated PIK3CA in adenocarcinoma has not been discussed. In addition, mutations occurring in other main members of the PI3K-AKT-mTOR signaling pathway other than PIK3CA were also excluded.
Collapse
Affiliation(s)
- Shutao Zheng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Shuo He
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Yan Liang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Yiyi Tan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Tao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China
| | - Xiaomei Lu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, People's Republic of China.
| |
Collapse
|
3
|
Villodre ES, Nguyen APN, Debeb BG. NDRGs in Breast Cancer: A Review and In Silico Analysis. Cancers (Basel) 2024; 16:1342. [PMID: 38611020 PMCID: PMC11011033 DOI: 10.3390/cancers16071342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The N-myc downstream regulated gene family (NDRGs) includes four members: NDRG1, NDRG2, NDRG3, and NDRG4. These members exhibit 53-65% amino acid identity. The role of NDRGs in tumor growth and metastasis appears to be tumor- and context-dependent. While many studies have reported that these family members have tumor suppressive roles, recent studies have demonstrated that NDRGs, particularly NDRG1 and NDRG2, function as oncogenes, promoting tumor growth and metastasis. Additionally, NDRGs are involved in regulating different signaling pathways and exhibit diverse cellular functions in breast cancers. In this review, we comprehensively outline the oncogenic and tumor suppressor roles of the NDRG family members in breast cancer, examining evidence from in vitro and in vivo breast cancer models as well as tumor tissues from breast cancer patients. We also present analyses of publicly available genomic and transcriptomic data from multiple independent cohorts of breast cancer patients.
Collapse
Affiliation(s)
- Emilly S. Villodre
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (E.S.V.); (A.P.N.N.)
- MD Anderson Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anh P. N. Nguyen
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (E.S.V.); (A.P.N.N.)
- MD Anderson Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bisrat G. Debeb
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (E.S.V.); (A.P.N.N.)
- MD Anderson Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
4
|
Migliaccio I, Paoli M, Risi E, Biagioni C, Biganzoli L, Benelli M, Malorni L. PIK3CA co-occurring mutations and copy-number gain in hormone receptor positive and HER2 negative breast cancer. NPJ Breast Cancer 2022; 8:24. [PMID: 35181669 PMCID: PMC8857304 DOI: 10.1038/s41523-022-00382-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/11/2022] [Indexed: 12/31/2022] Open
Abstract
We aim to elucidate the prognostic value of PIK3CA mutations and copy number (CN) gain (PIK3CA-mut/gain) in hormone receptor-positive and HER2-negative (HR + /HER2−) breast cancer (BC). We analyzed primary HR + /HER2− BC from three publicly available datasets comprising over 2000 samples and assessed the associations with tumoral and clinical characteristics and outcome. Clinical benefit (CB) in alpelisib-treated patients from two studies including 46 patients was analyzed. About 8–10% of HR + /HER2− primary BC had PIK3CA-mut/gain. In two of the datasets analyzed, among patients with PIK3CA mutant tumors, those with mut/gain had significantly worse outcome compared to those with CN neutral (PIK3CA-mut/neut) and PIK3CA-mut/gain remained an independent prognostic factor. CB of alpelisib-treated patients with PIK3CA-mut/gain and PIK3CA-mut/neut tumors was comparable. PIK3CA CN might help clarifying the prognostic and predictive role of PIK3CA mutations. Further studies are warranted.
Collapse
Affiliation(s)
- Ilenia Migliaccio
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy.
| | - Marta Paoli
- Bioinformatics Unit, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| | - Emanuela Risi
- "Sandro Pitigliani" Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy.,"Sandro Pitigliani" Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| | - Laura Biganzoli
- "Sandro Pitigliani" Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| | - Luca Malorni
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy.,"Sandro Pitigliani" Department of Medical Oncology, Hospital of Prato, Azienda USL Toscana Centro, 59100, Prato, Italy
| |
Collapse
|
5
|
Scheidmann MC, Castro-Giner F, Strittmatter K, Krol I, Paasinen-Sohns A, Scherrer R, Donato C, Gkountela S, Szczerba BM, Diamantopoulou Z, Muenst S, Vlajnic T, Kunz L, Vetter M, Rochlitz C, Taylor V, Giachino C, Schroeder T, Platt RJ, Aceto N. An In Vivo CRISPR Screen Identifies Stepwise Genetic Dependencies of Metastatic Progression. Cancer Res 2022; 82:681-694. [PMID: 34916221 PMCID: PMC7612409 DOI: 10.1158/0008-5472.can-21-3908] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Blood-borne metastasis of breast cancer involves a series of tightly regulated sequential steps, including the growth of a primary tumor lesion, intravasation of circulating tumor cells (CTC), and adaptation in various distant metastatic sites. The genes orchestrating each of these steps are poorly understood in physiologically relevant contexts, owing to the rarity of experimental models that faithfully recapitulate the biology, growth kinetics, and tropism of human breast cancer. Here, we conducted an in vivo loss-of-function CRISPR screen in newly derived CTC xenografts, unique in their ability to spontaneously mirror the human disease, and identified specific genetic dependencies for each step of the metastatic process. Validation experiments revealed sensitivities to inhibitors that are already available, such as PLK1 inhibitors, to prevent CTC intravasation. Together, these findings present a new tool to reclassify driver genes involved in the spread of human cancer, providing insights into the biology of metastasis and paving the way to test targeted treatment approaches. SIGNIFICANCE A loss-of-function CRISPR screen in human CTC-derived xenografts identifies genes critical for individual steps of the metastatic cascade, suggesting novel drivers and treatment opportunities for metastatic breast cancers.
Collapse
MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/blood
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- CRISPR-Cas Systems
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Neoplasm Metastasis
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA-Seq/methods
- Survival Analysis
- Xenograft Model Antitumor Assays/methods
- Polo-Like Kinase 1
- Mice
Collapse
Affiliation(s)
- Manuel C. Scheidmann
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karin Strittmatter
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ilona Krol
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Aino Paasinen-Sohns
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ramona Scherrer
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Cinzia Donato
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Sofia Gkountela
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Barbara M. Szczerba
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Zoi Diamantopoulou
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Simone Muenst
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Tatjana Vlajnic
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Leo Kunz
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marcus Vetter
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Claudio Giachino
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
6
|
Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nat Commun 2021; 12:5086. [PMID: 34429404 PMCID: PMC8384880 DOI: 10.1038/s41467-021-25177-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.
Collapse
Affiliation(s)
- Hua Sun
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Song Cao
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - R. Jay Mashl
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Chia-Kuei Mo
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Simone Zaccaria
- grid.16750.350000 0001 2097 5006Department of Computer Science, Princeton University, Princeton, NJ USA ,grid.83440.3b0000000121901201Computational Cancer Genomics Research Group and Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michael C. Wendl
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Mathematics, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University in St. Louis, St. Louis, MO USA
| | - Sherri R. Davies
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Matthew H. Bailey
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Tina M. Primeau
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Jeremy Hoog
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Jacqueline L. Mudd
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Dennis A. Dean
- grid.492568.4Seven Bridges Genomics, Inc., Cambridge, Charlestown, MA USA
| | - Rajesh Patidar
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Li Chen
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Matthew A. Wyczalkowski
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Reyka G. Jayasinghe
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Fernanda Martins Rodrigues
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Nadezhda V. Terekhanova
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Yize Li
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Kian-Huat Lim
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Andrea Wang-Gillam
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Brian A. Van Tine
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Cynthia X. Ma
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Rebecca Aft
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Katherine C. Fuh
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Julie K. Schwarz
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO USA
| | - Jose P. Zevallos
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Otolaryngology, Washington University St. Louis, St. Louis, MO USA
| | - Sidharth V. Puram
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Otolaryngology, Washington University St. Louis, St. Louis, MO USA
| | - John F. Dipersio
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | | | | | - Matthew J. Ellis
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Michael T. Lewis
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Meenhard Herlyn
- grid.251075.40000 0001 1956 6678The Wistar Institute, Philadelphia, PA USA
| | - Bingliang Fang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jack A. Roth
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alana L. Welm
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Bryan E. Welm
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Funda Meric-Bernstam
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Feng Chen
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Ryan C. Fields
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Shunqiang Li
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Ramaswamy Govindan
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - James H. Doroshow
- grid.48336.3a0000 0004 1936 8075Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD USA
| | - Jeffrey A. Moscow
- grid.48336.3a0000 0004 1936 8075Investigational Drug Branch, National Cancer Institute, Bethesda, MD USA
| | - Yvonne A. Evrard
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Jeffrey H. Chuang
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Benjamin J. Raphael
- grid.16750.350000 0001 2097 5006Department of Computer Science, Princeton University, Princeton, NJ USA
| | - Li Ding
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| |
Collapse
|
7
|
Lim YX, Lin H, Chu T, Lim YP. WBP2 promotes BTRC mRNA stability to drive migration and invasion in triple-negative breast cancer via NF-κB activation. Mol Oncol 2021; 16:422-446. [PMID: 34197030 PMCID: PMC8763649 DOI: 10.1002/1878-0261.13048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 01/23/2023] Open
Abstract
WW‐domain‐binding protein 2 (WBP2) is an oncogene that drives breast carcinogenesis through regulating Wnt, estrogen receptor (ER), and Hippo signaling. Recent studies have identified neoteric modes of action of WBP2 other than its widely recognized function as a transcriptional coactivator. Here, we identified a previously unexplored role of WBP2 in inflammatory signaling in breast cancer via an integrated proteogenomic analysis of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA BRCA) dataset. WBP2 was shown to enhance the migration and invasion in triple‐negative breast cancer (TNBC) cells especially under tumor necrosis factor alpha (TNF‐α) stimulation. Molecularly, WBP2 potentiates TNF‐α‐induced nuclear factor kappa B (NF‐κB) transcriptional activity and nuclear localization through aggrandizing ubiquitin‐mediated proteasomal degradation of its upstream inhibitor, NF‐κB inhibitor alpha (NFKBIA; also known as IκBα). We further demonstrate that WBP2 induces mRNA stability of beta‐transducin repeat‐containing E3 ubiquitin protein ligase (BTRC), which targets IκBα for ubiquitination and degradation. Disruption of IκBα rescued the impaired migratory and invasive phenotypes in WBP2‐silenced cells, while loss of BTRC ameliorated WBP2‐driven migration and invasion. Clinically, the WBP2‐BTRC‐IκBα signaling axis correlates with poorer prognosis in breast cancer patients. Our findings reveal a pivotal mechanism of WBP2 in modulating BTRC‐IκBα‐NF‐κB pathway to promote TNBC aggressiveness.
Collapse
Affiliation(s)
- Yvonne Xinyi Lim
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hexian Lin
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tinghine Chu
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University Health System, Singapore City, Singapore
| | - Yoon Pin Lim
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,National University Cancer Institute, Singapore City, Singapore
| |
Collapse
|
8
|
Fuchs J, Cheblal A, Gasser SM. Underappreciated Roles of DNA Polymerase δ in Replication Stress Survival. Trends Genet 2021; 37:476-487. [PMID: 33608117 DOI: 10.1016/j.tig.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/06/2023]
Abstract
Recent structural analysis of Fe-S centers in replication proteins and insights into the structure and function of DNA polymerase δ (DNA Pol δ) subunits have shed light on the key role played by this polymerase at replication forks under stress. The sequencing of cancer genomes reveals multiple point mutations that compromise the activity of POLD1, the DNA Pol δ catalytic subunit, whereas the loci encoding the accessory subunits POLD2 and POLD3 are amplified in a very high proportion of human tumors. Consistently, DNA Pol δ is key for the survival of replication stress and is involved in multiple long-patch repair pathways. Synthetic lethality arises from compromising the function and availability of the noncatalytic subunits of DNA Pol δ under conditions of replication stress, opening the door to novel therapies.
Collapse
Affiliation(s)
- Jeannette Fuchs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland.
| |
Collapse
|
9
|
Zhou Q, Xu M, Wang X, Yu M, Chen X, Lu J, Zhou R, Zhang J, Ling X, Ji J. Deficiency of TBL1XR1 causes asthenozoospermia. Andrologia 2021; 53:e13980. [PMID: 33528066 DOI: 10.1111/and.13980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is an evolutionarily conserved protein related to spermatozoa. To clarify its role and mechanism of action in spermatozoa, qRT-PCR was used to analyse the expression of TBL1XR1 in human spermatozoa and mouse testes. The mice were established as an animal model by injecting the mice testes with small interfering RNA against TBL1XR1 or control siRNA. Our results indicated that deficiency of TBL1XR1 in mice reduced the motility of spermatozoa and disrupted the histone-to-protamine transition. We also found the decreased expression of TBL1XR1 in the spermatozoa of human patients with asthenozoospermia (AZ) compared with that in the spermatozoa of healthy males. Moreover, we carried out chromatin immunoprecipitation analyses and found that genes downstream of TBL1XR1 were related to sperm motility. Thus, TBL1XR1 might be related to sperm motility and might function through its downstream genes. Our data highlight the role of TBL1XR1 involved in spermatozoa and provide new molecular insights into the intricate systems required for male fertility.
Collapse
Affiliation(s)
- Qiao Zhou
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Miaofei Xu
- Cellular and Molecular Pathology Branch, National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xin Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Mingming Yu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaojiao Chen
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jing Lu
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Junqiang Zhang
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiufeng Ling
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Juan Ji
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| |
Collapse
|
10
|
Lv Q, Guan S, Zhu M, Huang H, Wu J, Dai X. FGFR1 Is Associated With Tamoxifen Resistance and Poor Prognosis of ER-Positive Breast Cancers by Suppressing ER Protein Expression. Technol Cancer Res Treat 2021; 20:15330338211004935. [PMID: 33783288 PMCID: PMC8013883 DOI: 10.1177/15330338211004935] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/13/2021] [Accepted: 02/25/2021] [Indexed: 01/03/2023] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) is widely recognized as a key player in mammary carcinogenesis and associated with the prognosis and therapeutic response of breast cancers. With the aim of investigating the correlation between FGFR1 expression and estrogen receptor (ER) and exploring the effect of FGFR1 on endocrine therapy response and ER+ breast cancer prognosis, we examined the FGFR1 protein expression among 184 ER-positive breast cancers by the immunohistochemistry (IHC) method, analyzed the association between FGFR1 expression and disease characters using the Pearson's chi-square test, and assessed the prognostic role of FGFR1 among breast cancers using Cox regression and Kaplan-Meier analyses. Moreover, in vitro assays were conducted to confirm the correlation between FGFR1 and ER expression and investigate the effect of FGFR1 on tamoxifen (TAM) sensitivity in ER+ breast cancer. The results showed that ER expression was negatively correlated with FGFR1 expression (P = 0.011, r = -0.221). Moreover, FGFR1 expression was one of the prognostic factors of ER-positive breast cancer (OR = 1.974, 95% CI = 1.043-3.633), and high FGFR1 expression was correlated with decreased breast cancer overall survival. In addition, knocking down FGFR1 inhibited cell proliferation and enhanced TAM sensitivity in TAM-resistant cells. In conclusion, we found that there was a significant negative correlation between FGFR1 and ER levels in ER+ breast cancers, high FGFR1 protein expression was associated with poor breast cancer prognosis, down-regulating FGFR1 could elevate ER expression and is associated with enhanced TAM sensitivity in ER+ breast cancers.
Collapse
Affiliation(s)
- Qing Lv
- Department of Breast Surgery, the Affiliated Hospital of Jiangnan University, Wuxi, People’s Republic of China
| | - Shiming Guan
- Department of Internal Medicine, Huadong Sanatorium, Wuxi, People’s Republic of China
| | - Mingjie Zhu
- Department of Breast Surgery, the Affiliated Hospital of Jiangnan University, Wuxi, People’s Republic of China
| | - Hu Huang
- Department of Breast Surgery, the Affiliated Hospital of Jiangnan University, Wuxi, People’s Republic of China
| | - Junqiang Wu
- Department of Breast Surgery, the Affiliated Hospital of Jiangnan University, Wuxi, People’s Republic of China
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, People’s Republic of China
| |
Collapse
|
11
|
A Self-organizing Deep Auto-Encoder approach for Classification of Complex Diseases using SNP Genomics Data. Appl Soft Comput 2020. [DOI: 10.1016/j.asoc.2020.106718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
12
|
Zheng W, Wang X, Hu J, Bai B, Zhu H. Diverse molecular functions of aspartate β‑hydroxylase in cancer (Review). Oncol Rep 2020; 44:2364-2372. [PMID: 33125119 PMCID: PMC7610305 DOI: 10.3892/or.2020.7792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Aspartate/asparagine β-hydroxylase (AspH) is a type II transmembrane protein that catalyzes the post-translational hydroxylation of definite aspartyl and asparaginyl residues in epidermal growth factor-like domains of substrates. In the last few decades, accumulating evidence has indicated that AspH expression is upregulated in numerous types of human malignant cancer and is associated with poor survival and prognosis. The AspH protein aggregates on the surface of tumor cells, which contributes to inducing tumor cell migration, infiltration and metastasis. However, small-molecule inhibitors targeting hydroxylase activity can markedly block these processes, both in vitro and in vivo. Immunization of tumor-bearing mice with a phage vaccine fused with the AspH protein can substantially delay tumor growth and progression. Additionally, AspH antigen-specific CD4+ and CD8+ T cells were identified in the spleen of tumor-bearing mice. Therefore, these agents may be used as novel strategies for cancer treatment. The present review summarizes the current progress on the underlying mechanisms of AspH expression in cancer development.
Collapse
Affiliation(s)
- Wenqian Zheng
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Xiaowei Wang
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Jinhui Hu
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Bingjun Bai
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Hongbo Zhu
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| |
Collapse
|
13
|
pour AF, Pietrzak M, Sucheston-Campbell LE, Karaesmen E, Dalton LA, Rempała GA. High dimensional model representation of log likelihood ratio: binary classification with SNP data. BMC Med Genomics 2020; 13:133. [PMID: 32957998 PMCID: PMC7504683 DOI: 10.1186/s12920-020-00774-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Developing binary classification rules based on SNP observations has been a major challenge for many modern bioinformatics applications, e.g., predicting risk of future disease events in complex conditions such as cancer. Small-sample, high-dimensional nature of SNP data, weak effect of each SNP on the outcome, and highly non-linear SNP interactions are several key factors complicating the analysis. Additionally, SNPs take a finite number of values which may be best understood as ordinal or categorical variables, but are treated as continuous ones by many algorithms. METHODS We use the theory of high dimensional model representation (HDMR) to build appropriate low dimensional glass-box models, allowing us to account for the effects of feature interactions. We compute the second order HDMR expansion of the log-likelihood ratio to account for the effects of single SNPs and their pairwise interactions. We propose a regression based approach, called linear approximation for block second order HDMR expansion of categorical observations (LABS-HDMR-CO), to approximate the HDMR coefficients. We show how HDMR can be used to detect pairwise SNP interactions, and propose the fixed pattern test (FPT) to identify statistically significant pairwise interactions. RESULTS We apply LABS-HDMR-CO and FPT to synthetically generated HAPGEN2 data as well as to two GWAS cancer datasets. In these examples LABS-HDMR-CO enjoys superior accuracy compared with several algorithms used for SNP classification, while also taking pairwise interactions into account. FPT declares very few significant interactions in the small sample GWAS datasets when bounding false discovery rate (FDR) by 5%, due to the large number of tests performed. On the other hand, LABS-HDMR-CO utilizes a large number of SNP pairs to improve its prediction accuracy. In the larger HAPGEN2 dataset FTP declares a larger portion of SNP pairs used by LABS-HDMR-CO as significant. CONCLUSION LABS-HDMR-CO and FPT are interesting methods to design prediction rules and detect pairwise feature interactions for SNP data. Reliably detecting pairwise SNP interactions and taking advantage of potential interactions to improve prediction accuracy are two different objectives addressed by these methods. While the large number of potential SNP interactions may result in low power of detection, potentially interacting SNP pairs, of which many might be false alarms, can still be used to improve prediction accuracy.
Collapse
Affiliation(s)
- Ali Foroughi pour
- Department of Electrical and Computer Engineering, The Ohio State University, 2015 Neil Ave, Columbus, 43210 OH USA
- Department of Mathematics, The Ohio State University, 231 West 18th Ave, Columbus, 43210 OH USA
| | - Maciej Pietrzak
- Mathematical Biosciences Institute, 1735 Neil Ave, Columbus, 43210 OH USA
- Department of Biomedical Informatics, The Ohio State University, 1585 Neil Ave, Columbus, 43210 OH USA
| | | | - Ezgi Karaesmen
- College of Pharmacy, The Ohio State University, 500 West 12th Ave, Columbus, 43210 OH USA
| | - Lori A. Dalton
- Department of Electrical and Computer Engineering, The Ohio State University, 2015 Neil Ave, Columbus, 43210 OH USA
| | - Grzegorz A. Rempała
- Mathematical Biosciences Institute, 1735 Neil Ave, Columbus, 43210 OH USA
- College of Public Health, The Ohio State University, 1841 Neil Ave, Columbus, 43210 OH USA
| |
Collapse
|
14
|
Kanwal M, Smahel M, Olsen M, Smahelova J, Tachezy R. Aspartate β-hydroxylase as a target for cancer therapy. J Exp Clin Cancer Res 2020; 39:163. [PMID: 32811566 PMCID: PMC7433162 DOI: 10.1186/s13046-020-01669-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/06/2020] [Indexed: 12/24/2022] Open
Abstract
As metastasis is a major cause of death in cancer patients, new anti-metastatic strategies are needed to improve cancer therapy outcomes. Numerous pathways have been shown to contribute to migration and invasion of malignant tumors. Aspartate β-hydroxylase (ASPH) is a key player in the malignant transformation of solid tumors by enhancing cell proliferation, migration, and invasion. ASPH also promotes tumor growth by stimulation of angiogenesis and immunosuppression. These effects are mainly achieved via the activation of Notch and SRC signaling pathways. ASPH expression is upregulated by growth factors and hypoxia in different human tumors and its inactivation may have broad clinical impact. Therefore, small molecule inhibitors of ASPH enzymatic activity have been developed and their anti-metastatic effect confirmed in preclinical mouse models. ASPH can also be targeted by monoclonal antibodies and has also been used as a tumor-associated antigen to induce both cluster of differentiation (CD) 8+ and CD4+ T cells in mice. The PAN-301-1 vaccine against ASPH has already been tested in a phase 1 clinical trial in patients with prostate cancer. In summary, ASPH is a promising target for anti-tumor and anti-metastatic therapy based on inactivation of catalytic activity and/or immunotherapy.
Collapse
Affiliation(s)
- Madiha Kanwal
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michal Smahel
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
| | - Mark Olsen
- Department of Pharmaceutical Sciences, College of Pharmacy - Glendale, Midwestern University, Glendale, AZ, USA
- Crenae Therapeutics, Phoenix, AZ, USA
| | - Jana Smahelova
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| |
Collapse
|
15
|
Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton SE, Bhargava R, Lal A, Prasanth SG, Prasanth KV. LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells. RNA (NEW YORK, N.Y.) 2020; 26:175-185. [PMID: 31690584 PMCID: PMC6961546 DOI: 10.1261/rna.073254.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 05/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.
Collapse
Affiliation(s)
- Aamira Tariq
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad 45550, Pakistan
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Neha Chetlangia
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Sarah E Holton
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute of Advanced Science and Technology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
16
|
Hinz N, Jücker M. Distinct functions of AKT isoforms in breast cancer: a comprehensive review. Cell Commun Signal 2019; 17:154. [PMID: 31752925 PMCID: PMC6873690 DOI: 10.1186/s12964-019-0450-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AKT, also known as protein kinase B, is a key element of the PI3K/AKT signaling pathway. Moreover, AKT regulates the hallmarks of cancer, e.g. tumor growth, survival and invasiveness of tumor cells. After AKT was discovered in the early 1990s, further studies revealed that there are three different AKT isoforms, namely AKT1, AKT2 and AKT3. Despite their high similarity of 80%, the distinct AKT isoforms exert non-redundant, partly even opposing effects under physiological and pathological conditions. Breast cancer as the most common cancer entity in women, frequently shows alterations of the PI3K/AKT signaling. MAIN CONTENT A plethora of studies addressed the impact of AKT isoforms on tumor growth, metastasis and angiogenesis of breast cancer as well as on therapy response and overall survival in patients. Therefore, this review aimed to give a comprehensive overview about the isoform-specific effects of AKT in breast cancer and to summarize known downstream and upstream mechanisms. Taking account of conflicting findings among the studies, the majority of the studies reported a tumor initiating role of AKT1, whereas AKT2 is mainly responsible for tumor progression and metastasis. In detail, AKT1 increases cell proliferation through cell cycle proteins like p21, p27 and cyclin D1 and impairs apoptosis e.g. via p53. On the downside AKT1 decreases migration of breast cancer cells, for instance by regulating TSC2, palladin and EMT-proteins. However, AKT2 promotes migration and invasion most notably through regulation of β-integrins, EMT-proteins and F-actin. Whilst AKT3 is associated with a negative ER-status, findings about the role of AKT3 in regulation of the key properties of breast cancer are sparse. Accordingly, AKT1 is mutated and AKT2 is amplified in some cases of breast cancer and AKT isoforms are associated with overall survival and therapy response in an isoform-specific manner. CONCLUSIONS Although there are several discussed hypotheses how isoform specificity is achieved, the mechanisms behind the isoform-specific effects remain mostly unrevealed. As a consequence, further effort is necessary to achieve deeper insights into an isoform-specific AKT signaling in breast cancer and the mechanism behind it.
Collapse
Affiliation(s)
- Nico Hinz
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| |
Collapse
|
17
|
Campone M, Bachelot T, Penault-Llorca F, Pallis A, Agrapart V, Pierrat MJ, Poirot C, Dubois F, Xuereb L, Bossard CJ, Guigal-Stephan N, Lockhart B, Andre F. A phase Ib dose allocation study of oral administration of lucitanib given in combination with fulvestrant in patients with estrogen receptor-positive and FGFR1-amplified or non-amplified metastatic breast cancer. Cancer Chemother Pharmacol 2019; 83:743-753. [DOI: 10.1007/s00280-018-03765-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/27/2018] [Indexed: 11/25/2022]
|
18
|
A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability. PLoS Genet 2018; 14:e1007802. [PMID: 30496290 PMCID: PMC6289468 DOI: 10.1371/journal.pgen.1007802] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 12/11/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression. Breast cancer is the most common cancer in women worldwide. The molecular mechanisms underlying the disease have been extensively studied, leading to dramatic improvements in diagnostic and prognostic approaches. Despite the overall improvements in survival rate, numerous cases of death by breast cancer are still reported per year, alerting us about the potential gap of knowledge in cancer molecular biology era. The emerging advances in new generation sequencing techniques have revealed that the majority of genome is transcribed into non-protein coding RNAs or ncRNAs, including thousands of long ncRNAs (lncRNAs) of unknown function. Natural antisense RNAs (NATs) constitute a group of lncRNAs that are transcribed in the opposite direction to a sense protein-coding or non-coding gene with partial or complete complementarity. In this manuscript, we investigate the role of NATs in breast cancer progression, focusing on the role of PDCD4-AS1, a NAT expressed from the established tumor suppressor PDCD4 gene locus. We observe that both PDCD4-AS1 and PDCD4 display concordant expression in breast cancer cell lines and patients. In mammary epithelial cells, PDCD4-AS1 promotes the stability of PDCD4 mRNA. PDCD4-AS1 by forming RNA duplex with PDCD4 RNA prevents the interaction between PDCD4 RNA and RNA decay factors in the nucleus.
Collapse
|
19
|
Lemattre C, Thevenon J, Duffourd Y, Nambot S, Haquet E, Vuadelle B, Genevieve D, Sarda P, Bruel AL, Kuentz P, Wells CF, Faivre L, Willems M. TBL1XR1 mutations in Pierpont syndrome are not restricted to the recurrent p.Tyr446Cys mutation. Am J Med Genet A 2018; 176:2813-2818. [PMID: 30365874 DOI: 10.1002/ajmg.a.40510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/02/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023]
Abstract
Pierpont syndrome is a rare and sporadic syndrome, including developmental delay, facial characteristics, and abnormal extremities. Recently, a recurrent de novo TBL1XR1 variant (c.1337A > G; p.Tyr446Cys) has been identified in eight patients by whole-exome sequencing. A dominant-negative effect of this mutation is strongly suspected, since patients with TBL1XR1 deletion and other variants predicting loss of function do not share the same phenotype. We report two patients with typical Pierpont-like syndrome features. Exome sequencing allowed identifying a de novo heterozygous missense TBL1XR1 variant in both patients, different from those already reported: p.Cys325Tyr and p.Tyr446His. The localization of these mutations and clinical features of Pierpont-like syndrome suggest that their functional consequences are comparable with the recurrent mutation previously described, and provided additional data to understand molecular mechanisms of TBL1XR1 anomalies.
Collapse
Affiliation(s)
- C Lemattre
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - J Thevenon
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU, Grenoble, France
| | - Y Duffourd
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France.,Orphanomix, SATT Grand Est, Dijon, France.,UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs et FHU TRANSLAD, Hôpital d'enfants, CHU, Dijon, France
| | - S Nambot
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France
| | - E Haquet
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | | | - D Genevieve
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - P Sarda
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - A L Bruel
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France
| | - P Kuentz
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France.,Laboratoire de Biologie Moléculaire, CHRU Saint-Jacques, Besançon, France
| | - C F Wells
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - L Faivre
- Equipe GAD, UMR1231, Université de Bourgogne Franche Comté, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs et FHU TRANSLAD, Hôpital d'enfants, CHU, Dijon, France
| | - M Willems
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| |
Collapse
|
20
|
Si J, Si Y, Zhang B, Lan G, Wei J, Huang B, Deng Z, Xiong W, Zhang Q. Up-regulation of the IRX2 gene predicts poor prognosis in nasopharyngeal carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:4073-4082. [PMID: 31949798 PMCID: PMC6962795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 06/10/2023]
Abstract
Aberrant expression of the IRX2 gene contributes to the oncogenesis and progression of various cancers. In this study, we analyzed the clinical significance and the prognostic value of mRNA expression level of the IRX2 gene in nasopharyngeal carcinoma (NPC) patients, with the goal to find a novel prognostic biomarker for NPC. Tissue samples were collected prior to treatment from 71 NPC patients for the detection of mRNA expression level of a total of 31503 genes, with high throughput screening of the mRNA expression profile. The Kaplan-Meier curves and log-rank test were used for univariate analyses to determine if the mRNA expression level of IRX2 and other 31502 genes, as well as clinical characteristics were of prognostic value for overall survival (OS), distant metastasis-free survival (DMFS) and disease-free survival (DFS). Regularized Cox regression was performed to test the contribution of prognostic factors to OS, DMFS, and DFS of NPC patients. The Cox proportional hazard model was used to test the independence of prognostic effect of IRX2 and other clinical features. The receiver operator characteristic curve was drawn and the area under the curve (AUC) was calculated to evaluate the predictive power of IRX2 gene. Univariate analyses showed a higher mRNA expression level of the IRX2 gene correlated with shorter OS (P = 0.001), DMFS (P = 0.003), and DFS (P = 0.007). Regularized Cox regression and Cox proportional hazard model analyses further showed that ahigher mRNA expression level of the IRX2 gene in the primary NPC was an independent prognostic factor for OS (Coxnet beta = 0.03, Cox proportion hazard model P = 0.038), DMFS (Coxnet beta = 0.018, Cox proportion hazard model P = 0.01) and DFS (Coxnet beta = 0.008, Cox proportion hazard model P = 0.029). The AUC showed that the mRNA expression level of the IRX2 gene is a significant predictor for predicting the OS (AUC value = 0.7105) and DMFS (AUC value = 0.7027) of NPC patients. Our results demonstrated that the IRX2 gene may be a novel independent unfavorable prognostic factor for NPC patients.
Collapse
Affiliation(s)
- Jinyuan Si
- Department of Otolaryngology-Head and Neck Surgery, Xuan Wu Hospital, Capital Medical UniversityBeijing, PR China
| | - Yongfeng Si
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Benjian Zhang
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Guiping Lan
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Jiazhang Wei
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Bo Huang
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Zhuoxia Deng
- Institue of Nasopharyngeal Carcinoma, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Weiming Xiong
- Department of Otorhinolaryngology Head and Neck Oncology, The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning, PR China
| | - Qiuhang Zhang
- Department of Otolaryngology-Head and Neck Surgery, Xuan Wu Hospital, Capital Medical UniversityBeijing, PR China
| |
Collapse
|
21
|
Khandia R, Pattnaik B, Rajukumar K, Pateriya A, Bhatia S, Murugkar H, Prakash A, Pradhan HK, Dhama K, Munjal A, Joshi SK. Anti-proliferative role of recombinant lethal toxin of Bacillus anthracis on primary mammary ductal carcinoma cells revealing its therapeutic potential. Oncotarget 2018; 8:35835-35847. [PMID: 28415766 PMCID: PMC5482621 DOI: 10.18632/oncotarget.16214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/07/2017] [Indexed: 12/11/2022] Open
Abstract
Bacillus anthracis secretes three secretary proteins; lethal factor (LF), protective antigen (PA) and edema factor (EF). The LF has ability to check proliferation of mammary tumors, chiefly depending on mitogen activated protein kinase (MAPK) signaling pathway. Evaluation of therapeutic potential of recombinant LF (rLF), recombinant PA (rPA) and lethal toxin (rLF + rPA = LeTx) on the primary mammary ductal carcinoma cells revealed significant (p < 0.01) reduction in proliferation of tumor cells with mean inhibition indices of 28.0 ± 1.37% and 19.6 ± 1.47% respectively. However, treatment with rPA alone had no significant anti-proliferative effect as evident by low mean inhibition index of 3.4 ± 3.87%. The higher inhibition index observed for rLF alone as compared to LeTx is contrary to the existing knowledge on LF, which explains the requirement of PA dependent endocytosis for its enzymatic activity. Therefore, the plausible existence of PA independent mode of action of LF including direct receptor mediated endocytosis or modulation of signal transduction cascade via unknown means is hypothesized. In silico protein docking analysis of other cellular receptors for any plausibility to play the role of receptor for LF revealed c-Met receptor showing strongest affinity for LF (H bond = 19; Free energy = −773.96), followed by nerve growth factor receptor (NGFR) and human epidermal growth factor receptor (HER)-1. The study summarizes the use of rLF or LeTx as therapeutic molecule against primary mammary ductal carcinoma cells and also the c-Met as potential alternative receptor for LF to mediate and modulate PA independent signal transduction.
Collapse
Affiliation(s)
- Rekha Khandia
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India.,Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Bramhadev Pattnaik
- Project Directorate on Foot and Mouth Disease, Mukteswar, Uttarakhand, India
| | | | - Atul Pateriya
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - Sandeep Bhatia
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - Harshad Murugkar
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - Anil Prakash
- Department of Microbiology, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Hare Krishna Pradhan
- Ex-Avian Influenza National Consultant, Indian Office of WHO Consultant, Bhartiya Kala Kendra, New Delhi, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly Uttar Pradesh, India
| | - Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Sunil K Joshi
- Cellular Immunology Laboratory, Frank Reidy Research Center of Bioelectrics, College of Health Sciences, Old Dominion University Norfolk, VA USA
| |
Collapse
|
22
|
Rizzolo P, Navazio AS, Silvestri V, Valentini V, Zelli V, Zanna I, Masala G, Bianchi S, Scarnò M, Tommasi S, Palli D, Ottini L. Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers. Oncotarget 2018; 7:74097-74106. [PMID: 27765917 PMCID: PMC5342038 DOI: 10.18632/oncotarget.12272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022] Open
Abstract
Male breast cancer (MBC) is a rare disease. Due to its rarity, MBC research and clinical approach are mostly based upon data derived from its largely known female counterpart. We aimed at investigating whether MBC cases harbor somatic alterations of genes known as prognostic biomarkers and molecular therapeutic targets in female breast cancer. We examined 103 MBC cases, all characterized for germ-line BRCA1/2 mutations, for somatic alterations in PIK3CA, EGFR, ESR1 and CCND1 genes. Pathogenic mutations of PIK3CA were detected in 2% of MBCs. No pathogenic mutations were identified in ESR1 and EGFR. Gene copy number variations (CNVs) analysis showed amplification of PIK3CA in 8.1%, EGFR in 6.8% and CCND1 in 16% of MBCs, whereas deletion of ESR1 was detected in 15% of MBCs. Somatic mutations and gene amplification were found only in BRCA1/2 mutation negative MBCs. Significant associations emerged between EGFR amplification and large tumor size (T4), ER-negative and HER2-positive status, between CCND1 amplification and HER2-positive and MIB1-positive status, and between ESR1 deletion and ER-negative status. Our results show that amplification of targetable oncogenes is frequent in BRCA1/2 mutation negative MBCs and may identify MBC subsets characterized by aggressive phenotype that may benefit from potential targeted therapeutic approaches.
Collapse
Affiliation(s)
- Piera Rizzolo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Sara Navazio
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Veronica Zelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Ines Zanna
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Giovanna Masala
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Simonetta Bianchi
- Division of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Marco Scarnò
- CINECA (Inter University Consortium for Super Computing), Rome, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
23
|
Sahni JM, Keri RA. Targeting bromodomain and extraterminal proteins in breast cancer. Pharmacol Res 2018; 129:156-176. [PMID: 29154989 PMCID: PMC5828951 DOI: 10.1016/j.phrs.2017.11.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022]
Abstract
Breast cancer is a collection of distinct tumor subtypes that are driven by unique gene expression profiles. These transcriptomes are controlled by various epigenetic marks that dictate which genes are expressed and suppressed. During carcinogenesis, extensive restructuring of the epigenome occurs, including aberrant acetylation, alteration of methylation patterns, and accumulation of epigenetic readers at oncogenes. As epigenetic alterations are reversible, epigenome-modulating drugs could provide a mechanism to silence numerous oncogenes simultaneously. Here, we review the impact of inhibitors of the Bromodomain and Extraterminal (BET) family of epigenetic readers in breast cancer. These agents, including the prototypical BET inhibitor JQ1, have been shown to suppress a variety of oncogenic pathways while inducing minimal, if any, toxicity in models of several subtypes of breast cancer. BET inhibitors also synergize with multiple approved anti-cancer drugs, providing a greater response in breast cancer cell lines and mouse models than either single agent. The combined findings of the studies discussed here provide an excellent rationale for the continued investigation of the utility of BET inhibitors in breast cancer.
Collapse
Affiliation(s)
- Jennifer M Sahni
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Ruth A Keri
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, United States; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States; Department of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH 44106, United States.
| |
Collapse
|
24
|
Cheng J, Fu S, Wei C, Tania M, Khan MA, Imani S, Zhou B, Chen H, Xiao X, Wu J, Fu J. Evaluation of PIK3CA mutations as a biomarker in Chinese breast carcinomas from Western China. Cancer Biomark 2018; 19:85-92. [PMID: 28269754 DOI: 10.3233/cbm-160380] [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] [Indexed: 12/19/2022]
Abstract
BACKGROUND PIK3CA gene encodes the p110 α catalytic subunit of the oncoprotein phosphatidylinositol 3-kinase (PI3 K) which regulates many biological processes such as cell proliferation, differentiation, migration and survival through the activation of various signaling pathways. OBJECTIVE In this study, we have investigated the possible somatic mutations in PIK3CA gene in invasive ductal breast carcinomas of Chinese women from Western China. METHODS Genomic DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) tissue samples. The hotspot mutations in PIK3CA gene of exon 9 and exon 20 were studied by pyrosequencing. RESULTS The sequencing identified two hotspot mutations in exon 20 of one cancer samples at p. H1047L (c. 3140A > T) and eight cancer sample at p. H1047R (c. 3140A > G). No mutation in exon 9 of PIK3CA gene was found in these breast cancer tissue samples. PIK3CA mutations showed surprising clinicopathological features in breast cancer patients, as incidence of lymph node invasiveness is increased in the patients with PIK3CA mutation. In addition, all the patients showed tumor size bigger than 3 cm in diameter. It is important that for early detection and early treatment for BC in developing countries or areas like Western China, and for people to provide popularization education using scientific knowledge in cancer fields. CONCLUSIONS This study identified PIK3CA mutations in breast carcinoma patients of Western China that will enable a more rapid molecular diagnosis, and provide a stronger rationale evidence for development of precision therapeutic approaches as well as promising therapeutic targets for breast cancer treatment or patient management.
Collapse
Affiliation(s)
- Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China.,Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Shangyi Fu
- Honors College, University of Houston, Houston, TX 77204, USA.,Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China.,Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Mousumi Tania
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - Saber Imani
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hanchun Chen
- Department of Biochemistry, School of Life Sciencesand the State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410013, China
| | - Xiuli Xiao
- Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jingbo Wu
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China.,Judicial Authentication Center, Southwest Medical University, Luzhou, Sichuan 646000, China
| |
Collapse
|
25
|
Lan X, Atanassov BS, Li W, Zhang Y, Florens L, Mohan RD, Galardy PJ, Washburn MP, Workman JL, Dent SYR. USP44 Is an Integral Component of N-CoR that Contributes to Gene Repression by Deubiquitinating Histone H2B. Cell Rep 2017; 17:2382-2393. [PMID: 27880911 DOI: 10.1016/j.celrep.2016.10.076] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 11/20/2022] Open
Abstract
Decreased expression of the USP44 deubiquitinase has been associated with global increases in H2Bub1 levels during mouse embryonic stem cell (mESC) differentiation. However, whether USP44 directly deubiquitinates histone H2B or how its activity is targeted to chromatin is not known. We identified USP44 as an integral subunit of the nuclear receptor co-repressor (N-CoR) complex. USP44 within N-CoR deubiquitinates H2B in vitro and in vivo, and ablation of USP44 impairs the repressive activity of the N-CoR complex. Chromatin immunoprecipitation (ChIP) experiments confirmed that USP44 recruitment reduces H2Bub1 levels at N-CoR target loci. Furthermore, high expression of USP44 correlates with reduced levels of H2Bub1 in the breast cancer cell line MDA-MB-231. Depletion of either USP44 or TBL1XR1 impairs the invasiveness of MDA-MB-231 cells in vitro and causes an increase of global H2Bub1 levels. Our findings indicate that USP44 contributes to N-CoR functions in regulating gene expression and is required for efficient invasiveness of triple-negative breast cancer cells.
Collapse
Affiliation(s)
- Xianjiang Lan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Epigenetics and Molecular Carcinogenesis, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Boyko S Atanassov
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wenqian Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Epigenetics and Molecular Carcinogenesis, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ryan D Mohan
- University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Paul J Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
26
|
Amin AD, Peters TL, Li L, Rajan SS, Choudhari R, Puvvada SD, Schatz JH. Diffuse large B-cell lymphoma: can genomics improve treatment options for a curable cancer? Cold Spring Harb Mol Case Stud 2017; 3:a001719. [PMID: 28487884 PMCID: PMC5411687 DOI: 10.1101/mcs.a001719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gene-expression profiling and next-generation sequencing have defined diffuse large B-cell lymphoma (DLBCL), the most common lymphoma diagnosis, as a heterogeneous group of subentities. Despite ongoing explosions of data illuminating disparate pathogenic mechanisms, however, the five-drug chemoimmunotherapy combination R-CHOP remains the frontline standard treatment. This has not changed in 15 years, since the anti-CD20 monoclonal antibody rituximab was added to the CHOP backbone, which first entered use in the 1970s. At least a third of patients are not cured by R-CHOP, and relapsed or refractory DLBCL is fatal in ∼90%. Targeted small-molecule inhibitors against distinct molecular pathways activated in different subgroups of DLBCL have so far translated poorly into the clinic, justifying the ongoing reliance on R-CHOP and other long-established chemotherapy-driven combinations. New drugs and improved identification of biomarkers in real time, however, show potential to change the situation eventually, despite some recent setbacks. Here, we review established and putative molecular drivers of DLBCL identified through large-scale genomics, highlighting among other things the care that must be taken when differentiating drivers from passengers, which is influenced by the promiscuity of activation-induced cytidine deaminase. Furthermore, we discuss why, despite having so much genomic data available, it has been difficult to move toward personalized medicine for this umbrella disorder and some steps that may be taken to hasten the process.
Collapse
Affiliation(s)
- Amit Dipak Amin
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Tara L Peters
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Lingxiao Li
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soumya Sundara Rajan
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Ramesh Choudhari
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soham D Puvvada
- Department of Medicine, Division of Hematology-Oncology, University of Arizona Comprehensive Cancer Center, Tucson, Arizona 85719, USA
| | - Jonathan H Schatz
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| |
Collapse
|
27
|
Yang F, Wang Y, Li Q, Cao L, Sun Z, Jin J, Fang H, Zhu A, Li Y, Zhang W, Wang Y, Xie H, Gustafsson JÅ, Wang S, Guan X. Intratumor heterogeneity predicts metastasis of triple-negative breast cancer. Carcinogenesis 2017; 38:900-909. [PMID: 28911002 DOI: 10.1093/carcin/bgx071] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022] Open
Abstract
Even with the identical clinicopathological features, the ability for metastasis is vastly different among triple-negative breast cancer (TNBC) patients. Intratumor heterogeneity (ITH), which is common in breast cancer, may be a key mechanism leading to the tumor progression. In this study, we studied whether a quantitative genetic definition of ITH can predict clinical outcomes in patients with TNBC. We quantified ITH by calculating Shannon index, a measure of diversity in a population, based on Myc, epidermal growth factor receptor/centromeric probe 7 (EGFR/CEP7) and cyclin D1/centromeric probe 11 (CCND1/CEP11) copy number variations (CNVs) in 300 cells at three different locations of a tumor. Among 75 TNBC patients, those who developed metastasis had significantly higher ITH, that is Shannon indices of EGFR/CEP7 and CCND1/CEP11 CNVs. Higher Shannon indices of EGFR/CEP7 and CCND1/CEP11 CNVs were significantly associated with the development of metastasis and were predictive of significantly worse metastasis-free survival (MFS). Regional heterogeneity, defined as the difference in copy numbers of Myc, EGFR or CCND1 at different locations, was found in 52 patients. However, the presence of regional heterogeneity did not correlate with metastasis or MFS. Our findings demonstrate that higher ITH of EGFR/CEP7 and CCND1/CEP11 CNVs is predictive of metastasis and is associated with significantly worse MFS in TNBC patients, suggesting that ITH is a very promising novel prognostic factor in TNBC.
Collapse
Affiliation(s)
- Fang Yang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Yucai Wang
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Quan Li
- Department of Medical Oncology, Jinling Hospital, Southern Medical University, Guangzhou, China
| | - Lulu Cao
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Zijia Sun
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Juan Jin
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Hehui Fang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Aiyu Zhu
- Department of Medical Oncology, Jinling Hospital, Southern Medical University, Guangzhou, China
| | - Yan Li
- Department of Medical Oncology, Jinling Hospital, Southern Medical University, Guangzhou, China
| | - Wenwen Zhang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| | - Yanru Wang
- Department of Medical Oncology, Jinling Hospital, Southern Medical University, Guangzhou, China
| | - Hui Xie
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Jan-Åke Gustafsson
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China
| | - Xiaoxiang Guan
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing 210002, China
| |
Collapse
|
28
|
Meloche J, Lampron MC, Nadeau V, Maltais M, Potus F, Lambert C, Tremblay E, Vitry G, Breuils-Bonnet S, Boucherat O, Charbonneau E, Provencher S, Paulin R, Bonnet S. Implication of Inflammation and Epigenetic Readers in Coronary Artery Remodeling in Patients With Pulmonary Arterial Hypertension. Arterioscler Thromb Vasc Biol 2017; 37:1513-1523. [DOI: 10.1161/atvbaha.117.309156] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/25/2017] [Indexed: 01/08/2023]
Abstract
Objective—
Pulmonary arterial hypertension (PAH) is a vascular disease not restricted to the lungs. Many signaling pathways described in PAH are also of importance in other vascular remodeling diseases, such as coronary artery disease (CAD). Intriguingly, CAD is 4× more prevalent in PAH compared with the global population, suggesting a link between these 2 diseases. Both PAH and CAD are associated with sustained inflammation and smooth muscle cell proliferation/apoptosis imbalance and we demonstrated in PAH that this phenotype is, in part, because of the miR-223/DNA damage/Poly[ADP-ribose] polymerase 1/miR-204 axis activation and subsequent bromodomain protein 4 (BRD4) overexpression. Interestingly, BRD4 is also a trigger for calcification and remodeling processes, both of which are important in CAD. Thus, we hypothesize that BRD4 activation in PAH influences the development of CAD.
Approach and Results—
PAH was associated with significant remodeling of the coronary arteries in both human and experimental models of the disease. As observed in PAH distal pulmonary arteries, coronary arteries of patients with PAH also exhibited increased DNA damage, inflammation, and BRD4 overexpression. In vitro, using human coronary artery smooth muscle cells from PAH, CAD and non-PAH–non-CAD patients, we showed that both PAH and CAD smooth muscle cells exhibited increased proliferation and suppressed apoptosis in a BRD4-dependent manner. In vivo, improvement of PAH by BRD4 inhibitor was associated with a reduction in coronary remodeling and interleukin-6 expression.
Conclusions—
Overall, this study demonstrates that increased BRD4 expression in coronary arteries of patient with PAH contributes to vascular remodeling and comorbidity development.
Collapse
Affiliation(s)
- Jolyane Meloche
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Marie-Claude Lampron
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Valérie Nadeau
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Mélanie Maltais
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - François Potus
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Caroline Lambert
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Eve Tremblay
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Géraldine Vitry
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Sandra Breuils-Bonnet
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Olivier Boucherat
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Eric Charbonneau
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Steeve Provencher
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Roxane Paulin
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| | - Sébastien Bonnet
- From the Pulmonary Hypertension and Vascular Biology Research Group of the Quebec Heart and Lung Institute (J.M., M.-C.L., V.N., M.M., F.P., C.L., E.T., G.V., S.B.-B., O.B., S.P., R.P., S.B.) and the Division of Cardiac Surgery of the Quebec Heart and Lung Institute (E.C.), Laval University, Department of Medicine, Quebec, Canada
| |
Collapse
|
29
|
Ayoubian H, Fröhlich T, Pogodski D, Flatley A, Kremmer E, Schepers A, Feederle R, Arnold GJ, Grässer FA. Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein-Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation. J Gen Virol 2017; 98:2128-2142. [PMID: 28758620 DOI: 10.1099/jgv.0.000870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Epstein-Barr virus is a human herpes virus with oncogenic potential. The virus-encoded nuclear antigen 2 (EBNA2) is a key mediator of viral tumorigenesis. EBNA2 features an arginine-glycine (RG) repeat at amino acids (aa)339-354 that is essential for the transformation of lymphocytes and contains symmetrically (SDMA) and asymmetrically (ADMA) di-methylated arginine residues. The SDMA-modified EBNA2 binds the survival motor neuron protein (SMN), thus mimicking SMD3, a cellular SDMA-containing protein that interacts with SMN. Accordingly, a monoclonal antibody (mAb) specific for the SDMA-modified RG repeat of EBNA2 also binds to SMD3. With the novel mAb 19D4 we now show that EBNA2 contains mono-methylated arginine (MMA) residues within the RG repeat. Using 19D4, we immune-precipitated and analysed by mass spectrometry cellular proteins in EBV-transformed B-cells that feature MMA motifs that are similar to the one in EBNA2. Among the cellular proteins identified, we confirmed by immunoprecipitation and/or Western blot analyses Aly/REF, Coilin, DDX5, FXR1, HNRNPK, LSM4, MRE11, NRIP, nucleolin, PRPF8, RBM26, SMD1 (SNRDP1) and THRAP3 proteins that are either known to contain MMA residues or feature RG repeat sequences that probably serve as methylation substrates. The identified proteins are involved in splicing, tumorigenesis, transcriptional activation, DNA stability and RNA processing or export. Furthermore, we found that several proteins involved in energy metabolism are associated with MMA-modified proteins. Interestingly, the viral EBNA1 protein that features methylated RG repeat motifs also reacted with the antibodies. Our results indicate that the region between aa 34-52 of EBNA1 contains ADMA or SDMA residues, while the region between aa 328-377 mainly contains MMA residues.
Collapse
Affiliation(s)
- Hiresh Ayoubian
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Dagmar Pogodski
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| |
Collapse
|
30
|
Merino VF, Cho S, Liang X, Park S, Jin K, Chen Q, Pan D, Zahnow CA, Rein AR, Sukumar S. Inhibitors of STAT3, β-catenin, and IGF-1R sensitize mouse PIK3CA-mutant breast cancer to PI3K inhibitors. Mol Oncol 2017; 11:552-566. [PMID: 28296140 PMCID: PMC5527464 DOI: 10.1002/1878-0261.12053] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/02/2017] [Accepted: 02/28/2017] [Indexed: 12/15/2022] Open
Abstract
Although mutations in the phosphoinositide 3‐kinase catalytic subunit (PIK3CA) are common in breast cancer, PI3K inhibitors alone have shown modest efficacy. We sought to identify additional pathways altered in PIK3CA‐mutant tumors that might be targeted in combination with PI3K inhibitors. We generated two transgenic mouse models expressing the human PIK3CA‐H1047R‐ and the ‐E545K hotspot‐mutant genes in the mammary gland and evaluated their effects on development and tumor formation. Molecular analysis identified pathways altered in these mutant tumors, which were also targeted in multiple cell lines derived from the PIK3CA tumors. Finally, public databases were analyzed to determine whether novel pathways identified in the mouse tumors were altered in human tumors harboring mutant PIK3CA. Mutant mice showed increased branching and delayed involution of the mammary gland compared to parental FVB/N mice. Mammary tumors arose in 30% of the MMTV‐PIK3CA‐H1047R and in 13% of ‐E545K mice. Compared to MMTV‐Her‐2 transgenic mouse mammary tumors, H1047R tumors showed increased upregulation of Wnt/β‐catenin/Axin2, hepatocyte growth factor (Hgf)/Stat3, insulin‐like growth factor 2 (Igf‐2), and Igf‐1R pathways. Inhibitors of STAT3, β‐catenin, and IGF‐1R sensitized H1047R‐derived mouse tumor cells and PIK3CA‐H1047R overexpressing human HS578T breast cancer cells to the cytotoxic effects of PI3K inhibitors. Analysis of The Cancer Genome Atlas database showed that, unlike primary PIK3CA‐wild‐type and HER‐2+ breast carcinomas, PIK3CA‐mutant tumors display increased expression of AXIN2, HGF, STAT3, IGF‐1, and IGF‐2 mRNA and activation of AKT, IGF1‐MTOR, and WNT canonical signaling pathways. Drugs targeting additional pathways that are altered in PIK3CA‐mutant tumors may improve treatment regimens using PI3K inhibitors alone.
Collapse
Affiliation(s)
- Vanessa F Merino
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Soonweng Cho
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaohui Liang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sunju Park
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kideok Jin
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qian Chen
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Duojia Pan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia A Zahnow
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan R Rein
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD, USA
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
31
|
Sen M, Katragadda S, Ravichandran A, Deshpande G, Parulekar M, Nayanala S, Vittal V, Shen W, Phooi Nee Yong M, Jacob J, Parchuru S, Dhanuskodi K, Eyring K, Agrawal P, Agarwal S, Shanmugam A, Gupta S, Vishwanath D, Kumari K, Hariharan AK, Balaji SA, Liang Q, Robolledo B, Gauribidanur Raghavendrachar V, Oomer Farooque M, Buresh CJ, Ramamoorthy P, Bahadur U, Subramanian K, Hariharan R, Veeramachaneni V, Sankaran S, Gupta V. StrandAdvantage test for early-line and advanced-stage treatment decisions in solid tumors. Cancer Med 2017; 6:883-901. [PMID: 28371134 PMCID: PMC5430095 DOI: 10.1002/cam4.1037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive genetic profiling of tumors using next‐generation sequencing (NGS) is gaining acceptance for guiding treatment decisions in cancer care. We designed a cancer profiling test combining both deep sequencing and immunohistochemistry (IHC) of relevant cancer targets to aid therapy choices in both standard‐of‐care (SOC) and advanced‐stage treatments for solid tumors. The SOC report is provided in a short turnaround time for four tumors, namely lung, breast, colon, and melanoma, followed by an investigational report. For other tumor types, an investigational report is provided. The NGS assay reports single‐nucleotide variants (SNVs), copy number variations (CNVs), and translocations in 152 cancer‐related genes. The tissue‐specific IHC tests include routine and less common markers associated with drugs used in SOC settings. We describe the standardization, validation, and clinical utility of the StrandAdvantage test (SA test) using more than 250 solid tumor formalin‐fixed paraffin‐embedded (FFPE) samples and control cell line samples. The NGS test showed high reproducibility and accuracy of >99%. The test provided relevant clinical information for SOC treatment as well as more information related to investigational options and clinical trials for >95% of advanced‐stage patients. In conclusion, the SA test comprising a robust and accurate NGS assay combined with clinically relevant IHC tests can detect somatic changes of clinical significance for strategic cancer management in all the stages.
Collapse
Affiliation(s)
- Manimala Sen
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Shanmukh Katragadda
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Aarthi Ravichandran
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Gouri Deshpande
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Minothi Parulekar
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Swetha Nayanala
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Vikram Vittal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Weiming Shen
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | | | - Jemima Jacob
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Sravanthi Parchuru
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kalpana Dhanuskodi
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kenneth Eyring
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Pooja Agrawal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Smita Agarwal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Ashwini Shanmugam
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Satish Gupta
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Divya Vishwanath
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kiran Kumari
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Arun K Hariharan
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Sai A Balaji
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Qiaoling Liang
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Belen Robolledo
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | | | | | | | - Preveen Ramamoorthy
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Urvashi Bahadur
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | | | - Ramesh Hariharan
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | | | - Satish Sankaran
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Vaijayanti Gupta
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| |
Collapse
|
32
|
Feng F, Cheng Q, Yang L, Zhang D, Ji S, Zhang Q, Lin Y, Li F, Xiong L, Liu C, Jiang X. Guidance to rational use of pharmaceuticals in gallbladder sarcomatoid carcinoma using patient-derived cancer cells and whole exome sequencing. Oncotarget 2017; 8:5349-5360. [PMID: 28029662 PMCID: PMC5354913 DOI: 10.18632/oncotarget.14146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/22/2016] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Gallbladder sarcomatoid carcinoma is a rare cancer with no clinical standard treatment. With the rapid development of next generation sequencing, it has been able to provide reasonable treatment options for patients based on genetic variations. However, most cancer drugs are not approval for gallbladder sarcomatoid carcinoma indications. The correlation between drug response and a genetic variation needs to be further elucidated. EXPERIMENTAL DESIGN Three patient-derived cells-JXQ-3D-001, JXQ-3D-002, and JXQ-3D-003, were derived from biopsy samples of one gallbladder sarcomatoid carcinoma patient with progression and have been characterized. In order to study the relationship between drug sensitivity and gene alteration, genetic mutations of three patient-derived cells were discovered by whole exome sequencing, and drug screening has been performed based on the gene alterations and related signaling pathways that are associated with drug targets. RESULTS It has been found that there are differences in biological characteristics such as morphology, cell proliferation, cell migration and colony formation activity among these three patient-derived cells although they are derived from the same patient. Their sensitivities to the chemotherapy drugs-Fluorouracil, Doxorubicin, and Cisplatin are distinct. Moreover, none of common chemotherapy drugs could inhibit the proliferations of all three patient-derived cells. Comprehensive analysis of their whole exome sequencing demonstrated that tumor-associated genes TP53, AKT2, FGFR3, FGF10, SDHA, and PI3KCA were mutated or amplified. Part of these alterations are actionable. By screening a set of compounds that are associated with the genetic alteration, it has been found that GDC-0941 and PF-04691502 for PI3K-AKT-mTOR pathway inhibitors could dramatically decrease the proliferation of three patient-derived cells. Importantly, expression of phosphorylated AKT and phosphorylated S6 were markedly decreased after treatments with PI3K-AKT-mTOR pathway inhibitors GDC-0941 (0.5 μM) and PF-04691502 (0.1 μM) in all three patient-derived cells. These data suggested that inhibition of the PI3K-AKT-mTOR pathway that was activated by PIK3CA amplification in all three patient-derived cells could reduce the cell proliferation. CONCLUSIONS A patient-derived cell model combined with whole exome sequencing is a powerful tool to elucidate relationship between drug sensitivities and genetic alternations. In these gallbladder sarcomatoid carcinoma patient-derived cells, it is found that PIK3CA amplification could be used as a biomarker to indicate PI3K-AKT-mTOR pathway activation. Block of the pathway may benefit the gallbladder sarcomatoid carcinoma patient with this alternation in hypothesis. The real efficacy needs to be confirmed in vivo or in a clinical trial.
Collapse
Affiliation(s)
- Feiling Feng
- Department of Biliary I, Third Affiliated Hospital of PLA Second Military Medical University, Shanghai, China
| | - Qingbao Cheng
- Department of Biliary I, Third Affiliated Hospital of PLA Second Military Medical University, Shanghai, China
| | - Liang Yang
- Department of Biliary I, Third Affiliated Hospital of PLA Second Military Medical University, Shanghai, China
| | - Dadong Zhang
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
- Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Shunlong Ji
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
| | - Qiangzu Zhang
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
| | - Yihui Lin
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
| | - Fugen Li
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
| | - Lei Xiong
- Division of Translational Medicine, 3D Medicines Corporation, Shanghai, China
| | - Chen Liu
- Department of Biliary I, Third Affiliated Hospital of PLA Second Military Medical University, Shanghai, China
| | - Xiaoqing Jiang
- Department of Biliary I, Third Affiliated Hospital of PLA Second Military Medical University, Shanghai, China
| |
Collapse
|
33
|
Kaur S, Elkahloun AG, Singh SP, Chen QR, Meerzaman DM, Song T, Manu N, Wu W, Mannan P, Garfield SH, Roberts DD. A function-blocking CD47 antibody suppresses stem cell and EGF signaling in triple-negative breast cancer. Oncotarget 2017; 7:10133-52. [PMID: 26840086 PMCID: PMC4891109 DOI: 10.18632/oncotarget.7100] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 12/18/2022] Open
Abstract
CD47 is a signaling receptor for thrombospondin-1 and the counter-receptor for signal-regulatory protein-α (SIRPα). By inducing inhibitory SIRPα signaling, elevated CD47 expression by some cancers prevents macrophage phagocytosis. The anti-human CD47 antibody B6H12 inhibits tumor growth in several xenograft models, presumably by preventing SIRPα engagement. However, CD47 signaling in nontransformed and some malignant cells regulates self-renewal, suggesting that CD47 antibodies may therapeutically target cancer stem cells (CSCs). Treatment of MDA-MB-231 breast CSCs with B6H12 decreased proliferation and asymmetric cell division. Similar effects were observed in T47D CSCs but not in MCF7 breast carcinoma or MCF10A breast epithelial cells. Gene expression analysis in breast CSCs treated with B6H12 showed decreased expression of epidermal growth factor receptor (EGFR) and the stem cell transcription factor KLF4. EGFR and KLF4 mRNAs are known targets of microRNA-7, and B6H12 treatment correspondingly enhanced microRNA-7 expression in breast CSCs. B6H12 treatment also acutely inhibited EGF-induced EGFR tyrosine phosphorylation. Expression of B6H12-responsive genes correlated with CD47 mRNA expression in human breast cancers, suggesting that the CD47 signaling pathways identified in breast CSCs are functional in vivo. These data reveal a novel SIRPα-independent mechanism by which therapeutic CD47 antibodies could control tumor growth by autonomously forcing differentiation of CSC.
Collapse
Affiliation(s)
- Sukhbir Kaur
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abdel G Elkahloun
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Satya P Singh
- Inflammation Biology Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daoud M Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timothy Song
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nidhi Manu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiwei Wu
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Poonam Mannan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susan H Garfield
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David D Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
34
|
Shi H, Zhang W, Zhi Q, Jiang M. Lapatinib resistance in HER2+ cancers: latest findings and new concepts on molecular mechanisms. Tumour Biol 2016; 37:10.1007/s13277-016-5467-2. [PMID: 27726101 DOI: 10.1007/s13277-016-5467-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022] Open
Abstract
In the era of new and mostly effective molecular targeted therapies, human epidermal growth factor receptor 2 positive (HER2+) cancers are still intractable diseases. Lapatinib, a dual epidermal growth factor receptor (EGFR) and HER2 tyrosine kinase inhibitor, has greatly improved breast cancer prognosis in recent years after the initial introduction of trastuzumab (Herceptin). However, clinical evidence indicates the existence of both primary unresponsiveness and secondary lapatinib resistance, which leads to the failure of this agent in HER2+ cancer patients. It remains a major clinical challenge to target the oncogenic pathways with drugs having low resistance. Multiple pathways are involved in the occurrence of lapatinib resistance, including the pathways of receptor tyrosine kinase, non-receptor tyrosine kinase, autophagy, apoptosis, microRNA, cancer stem cell, tumor metabolism, cell cycle, and heat shock protein. Moreover, understanding the relationship among these mechanisms may contribute to future tumor combination therapies. Therefore, it is of urgent necessity to elucidate the precise mechanisms of lapatinib resistance and improve the therapeutic use of this agent in clinic. The present review, in the hope of providing further scientific support for molecular targeted therapies in HER2+ cancers, discusses about the latest findings and new concepts on molecular mechanisms underlying lapatinib resistance.
Collapse
Affiliation(s)
- Huiping Shi
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China
| | - Weili Zhang
- Department of Gastroenterology, Xiangcheng People's Hospital, Suzhou, Jiangsu Province, 215131, China
| | - Qiaoming Zhi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China.
| | - Min Jiang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China.
| |
Collapse
|
35
|
Zhou Q, Wang X, Yu Z, Wu X, Chen X, Li J, Zhu Z, Liu B, Su L. Transducin (β)-like 1 X-linked receptor 1 promotes gastric cancer progression via the ERK1/2 pathway. Oncogene 2016; 36:1873-1886. [PMID: 27694893 PMCID: PMC5378934 DOI: 10.1038/onc.2016.352] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is one of the most common types of cancer worldwide, and it involves extensive local tumour invasion, metastasis and poor prognosis. Understanding the mechanisms regulating the progression of GC is necessary for the development of effective therapeutic strategies. Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is an important regulator controlling gene activation and repression, which has been thought to be involved in tumorigenesis. However, the role of TBL1XR1 in human GC remains largely unknown. Here, we find that TBL1XR1 is aberrantly expressed in human GC tissues, and TBL1XR1 levels are highly correlated with local tumour invasion, late tumor, lymph node, metastasis (TNM) stage and poor prognosis. Knockdown of TBL1XR1 by shRNA inhibits GC cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT) in vitro, as well as tumorigenesis and peritoneal metastasis in vivo, whereas overexpression of TBL1XR1 produces the opposite effects. These effects are mediated by activation of the ERK1/2 signalling pathway, and inhibition of this pathway with a specific ERK1/2 inhibitor (U0126) significantly impairs the tumour-promoting effects induced by TBL1XR1. Moreover, TBL1XR1 mediated ERK1/2 activation is dependent on the β-catenin/MMP7/EGFR signalling pathway. In conclusion, TBL1XR1 contributes to GC tumorigenesis and progression through the activation of the β-catenin/MMP7/EGFR/ERK signalling pathway and may act as a new therapeutic target for GC.
Collapse
Affiliation(s)
- Q Zhou
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - X Wang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Z Yu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - X Wu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - X Chen
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - J Li
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Z Zhu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - B Liu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - L Su
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| |
Collapse
|
36
|
Rudolph M, Anzeneder T, Schulz A, Beckmann G, Byrne AT, Jeffers M, Pena C, Politz O, Köchert K, Vonk R, Reischl J. AKT1 (E17K) mutation profiling in breast cancer: prevalence, concurrent oncogenic alterations, and blood-based detection. BMC Cancer 2016; 16:622. [PMID: 27515171 PMCID: PMC4982009 DOI: 10.1186/s12885-016-2626-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Background The single hotspot mutation AKT1 [G49A:E17K] has been described in several cancers, with the highest incidence observed in breast cancer. However, its precise role in disease etiology remains unknown. Methods We analyzed more than 600 breast cancer tumor samples and circulating tumor DNA for AKT1E17K and alterations in other cancer-associated genes using Beads, Emulsions, Amplification, and Magnetics digital polymerase chain reaction technology and targeted exome sequencing. Results Overall AKT1E17K mutation prevalence was 6.3 % and not correlated with age or menopausal stage. AKT1E17K mutation frequency tended to be lower in patients with grade 3 disease (1.9 %) compared with those with grade 1 (11.1 %) or grade 2 (6 %) disease. In two cohorts of patients with advanced metastatic disease, 98.0 % (n = 50) and 97.1 % (n = 35) concordance was obtained between tissue and blood samples for the AKT1E17K mutation, and mutation capture rates of 66.7 % (2/3) and 85.7 % (6/7) in blood versus tissue samples were observed. Although AKT1-mutant tumor specimens were often found to harbor concurrent alterations in other driver genes, a subset of specimens harboring AKT1E17K as the only known driver alteration was also identified. Initial follow-up survival data suggest that AKT1E17K could be associated with increased mortality. These findings warrant additional long-term follow-up. Conclusions The data suggest that AKT1E17K is the most likely disease driver in certain breast cancer patients. Blood-based mutation detection is achievable in advanced-stage disease. These findings underpin the need for a further enhanced-precision medicine paradigm in the treatment of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2626-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marion Rudolph
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany.
| | | | - Anke Schulz
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Georg Beckmann
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,At the time of manuscript preparation, the author was on a Science Foundation Ireland-funded industry secondment, Bayer HealthCare Pharmaceuticals, Whippany, NJ, USA
| | | | - Carol Pena
- Bayer HealthCare Pharmaceuticals, Whippany, NJ, USA
| | - Oliver Politz
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Karl Köchert
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Richardus Vonk
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Joachim Reischl
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany.,AstraZeneca R&D, Personalized Healthcare and Biomarkers, Gothenburg, Sweden
| |
Collapse
|
37
|
Tomiguchi M, Yamamoto Y, Yamamoto-Ibusuki M, Goto-Yamaguchi L, Fujiki Y, Fujiwara S, Sueta A, Hayashi M, Takeshita T, Inao T, Iwase H. Fibroblast growth factor receptor-1 protein expression is associated with prognosis in estrogen receptor-positive/human epidermal growth factor receptor-2-negative primary breast cancer. Cancer Sci 2016; 107:491-8. [PMID: 26801869 PMCID: PMC4832856 DOI: 10.1111/cas.12897] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023] Open
Abstract
Recently, research into the development of new targeted therapies has focused on specific genetic alterations to create advanced, more personalized treatment. One of the target genes, fibroblast growth factor receptor‐1 (FGFR1), has been reported to be amplified in estrogen receptor (ER)‐positive subtype breast cancer, and is considered one possible mechanism of endocrine resistance through cross‐talk between ER and growth factor receptor signaling. We performed a comprehensive analysis of FGFR1 at the levels of gene copy number, transcript and protein expression, and examined the relationships between FGFR1 status and clinicopathological parameters, including prognosis in 307 ER‐positive/HER2‐negative primary breast cancer patients treated with standard care at our institute. Most notably, a high level of FGFR1 protein expression was observed in 85 patients (27.7%), and was positively associated with invasive tumor size (P = 0.039). Furthermore, univariate analysis revealed that high FGFR1 protein expression was significantly correlated with poor relapse‐free survival rate (P = 0.0019, HR: 2.63, 95% confidence interval: 1.17–5.98), and showed a tendency towards an increase in recurrent events if the observation period extended beyond the 5 years of the standard endocrine treatment term. FGFR1 gain/amplification was found in 43 (14.0%) patients, which was only associated with higher nuclear grade (P = 0.010). No correlation was found between FGFR1 mRNA expression levels and any clinicopathological factors. Overall, the level of FGFR1 protein expression may be a biomarker of ER‐positive/HER2‐negative primary breast cancer with possible resistance to standard treatment, and may be a useful tool to identify more specific patients who would benefit from FGFR‐1 targeted therapy.
Collapse
Affiliation(s)
- Mai Tomiguchi
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Kumamoto, Japan
| | - Lisa Goto-Yamaguchi
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Fujiki
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Saori Fujiwara
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mitsuhiro Hayashi
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takashi Takeshita
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Touko Inao
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
38
|
Roszik J, Wu CJ, Siroy AE, Lazar AJ, Davies MA, Woodman SE, Kwong LN. Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression. Sci Rep 2016; 6:19649. [PMID: 26787600 PMCID: PMC4726397 DOI: 10.1038/srep19649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023] Open
Abstract
Somatic copy number alterations (SCNAs) affecting oncogenic drivers have a firmly established role in promoting cancer. However, no agreed-upon standard exists for calling locus-specific amplifications and deletions in each patient sample. Here, we report the correlative analysis of copy number amplitude and length with gene expression across 6,109 samples from The Cancer Genome Atlas (TCGA) dataset across 16 cancer types. Using specificity, sensitivity, and precision-based scores, we assigned optimized amplitude and length cutoffs for nine recurrent SCNAs affecting known oncogenic drivers, using mRNA expression as a functional readout. These cutoffs captured the majority of SCNA-driven, highly-expression-altered samples. The majority of oncogenes required only amplitude cutoffs, as high amplitude samples were almost invariably focal; however, CDKN2A and PTEN uniquely required both amplitude and length cutoffs as primary predictors. For PTEN, these extended to downstream AKT activation. In contrast, SCNA genes located peri-telomerically or in fragile sites showed poor expression-copy number correlations. Overall, our analyses identify optimized amplitude and length cutoffs as efficient predictors of gene expression changes for specific oncogenic SCNAs, yet warn against one-size-fits-all interpretations across all loci. Our results have implications for cancer data analyses and the clinic, where copy number and mutation data are increasingly used to personalize cancer therapy.
Collapse
Affiliation(s)
- Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Alan E Siroy
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| |
Collapse
|
39
|
Heinen CA, Jongejan A, Watson PJ, Redeker B, Boelen A, Boudzovitch-Surovtseva O, Forzano F, Hordijk R, Kelley R, Olney AH, Pierpont ME, Schaefer GB, Stewart F, van Trotsenburg ASP, Fliers E, Schwabe JWR, Hennekam RC. A specific mutation in TBL1XR1 causes Pierpont syndrome. J Med Genet 2016; 53:330-7. [PMID: 26769062 PMCID: PMC4853543 DOI: 10.1136/jmedgenet-2015-103233] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/14/2015] [Indexed: 12/30/2022]
Abstract
Background The combination of developmental delay, facial characteristics, hearing loss and abnormal fat distribution in the distal limbs is known as Pierpont syndrome. The aim of the present study was to detect and study the cause of Pierpont syndrome. Methods We used whole-exome sequencing to analyse four unrelated individuals with Pierpont syndrome, and Sanger sequencing in two other unrelated affected individuals. Expression of mRNA of the wild-type candidate gene was analysed in human postmortem brain specimens, adipose tissue, muscle and liver. Expression of RNA in lymphocytes in patients and controls was additionally analysed. The variant protein was expressed in, and purified from, HEK293 cells to assess its effect on protein folding and function. Results We identified a single heterozygous missense variant, c.1337A>C (p.Tyr446Cys), in transducin β-like 1 X-linked receptor 1 (TBL1XR1) as disease-causing in all patients. TBL1XR1 mRNA expression was demonstrated in pituitary, hypothalamus, white and brown adipose tissue, muscle and liver. mRNA expression is lower in lymphocytes of two patients compared with the four controls. The mutant TBL1XR1 protein assembled correctly into the nuclear receptor corepressor (NCoR)/ silencing mediator for retinoid and thyroid receptors (SMRT) complex, suggesting a dominant-negative mechanism. This contrasts with loss-of-function germline TBL1XR1 deletions and other TBL1XR1 mutations that have been implicated in autism. However, autism is not present in individuals with Pierpont syndrome. Conclusions This study identifies a specific TBL1XR1 mutation as the cause of Pierpont syndrome. Deletions and other mutations in TBL1XR1 can cause autism. The marked differences between Pierpont patients with the p.Tyr446Cys mutation and individuals with other mutations and whole gene deletions indicate a specific, but as yet unknown, disease mechanism of the TBL1XR1 p.Tyr446Cys mutation.
Collapse
Affiliation(s)
- Charlotte A Heinen
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands Department of Paediatric Endocrinology, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter J Watson
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester, UK
| | - Bert Redeker
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita Boelen
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Olga Boudzovitch-Surovtseva
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Roel Hordijk
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Richard Kelley
- Division of Metabolism, Kennedy Krieger Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ann H Olney
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Centre, Omaha, Nebraska, USA
| | - Mary Ella Pierpont
- Division of Genetics, Children's Hospitals and Clinics of Minnesota, University of Minnesota, Minneapolis, Minnesota, USA
| | - G Bradley Schaefer
- Division of Medical Genetics, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Fiona Stewart
- Division of Medical Genetics, Belfast City Hospital, Belfast, Ireland
| | - A S Paul van Trotsenburg
- Department of Paediatric Endocrinology, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Fliers
- Department of Endocrinology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - John W R Schwabe
- Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Leicester, UK
| | - Raoul C Hennekam
- Department of Paediatrics, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
40
|
Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells. BMC Cancer 2015; 15:896. [PMID: 26560478 PMCID: PMC4642646 DOI: 10.1186/s12885-015-1907-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background Disseminated tumor cells (DTCs) can be detected using ultrasensitive immunocytochemical assays and their presence in the bone marrow can predict the subsequent occurrence of overt metastasis formation and metastatic relapse. Using expression profiling on early stage primary breast tumors, low IRX2 expression was previously shown to be associated with the presence of DTCs in the bone marrow, suggesting a possible role of IRX2 in the early steps of metastasis formation. The purpose of this study is to gain insights into the significance of IRX2 protein function in the progression of breast cancer. Methods To assess the physiological relevance of IRX2 in breast cancer, we evaluated IRX2 expression in a large breast cancer cohort (n = 1992). Additionally, constitutive IRX2 over expression was established in BT-549 and Hs578T breast cancer cell lines. Subsequently we analyzed whether IRX2 overexpression effects chemokine secretion and cellular motility of these cells. Results Low IRX2 mRNA expression was found to correlate with high tumor grade, positive lymph node status, negative hormone receptor status, and basal type of primary breast tumors. Also in cell lines low IRX2 expression was associated with mainly basal breast cancer cell lines. The functional studies show that overexpression of the IRX2 transcription factor in basal cell lines suppressed secretion of the pro-metastatic chemokines and inhibited cellular motility but did not influence cell proliferation. Conclusion Our results imply that the IRX2 transcription factor might represent a novel metastasis associated protein that acts as a negative regulator of cellular motility and as a repressor of chemokine expression. Loss of IRX2 expression could therefore contribute to early hematogenous dissemination of breast cancer by sustaining chemokine secretion and enabling mobilization of tumor cells. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1907-4) contains supplementary material, which is available to authorized users.
Collapse
|
41
|
Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev 2015. [PMID: 26220994 PMCID: PMC4526735 DOI: 10.1101/gad.267583.115] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NUT midline carcinoma (NMC), a subtype of squamous cell cancer, is one of the most aggressive human solid malignancies known. NMC is driven by the creation of a translocation oncoprotein, BRD4-NUT, which blocks differentiation and drives growth of NMC cells. BRD4-NUT forms distinctive nuclear foci in patient tumors, which we found correlate with ∼100 unprecedented, hyperacetylated expanses of chromatin that reach up to 2 Mb in size. These "megadomains" appear to be the result of aberrant, feed-forward loops of acetylation and binding of acetylated histones that drive transcription of underlying DNA in NMC patient cells and naïve cells induced to express BRD4-NUT. Megadomain locations are typically cell lineage-specific; however, the cMYC and TP63 regions are targeted in all NMCs tested and play functional roles in tumor growth. Megadomains appear to originate from select pre-existing enhancers that progressively broaden but are ultimately delimited by topologically associating domain (TAD) boundaries. Therefore, our findings establish a basis for understanding the powerful role played by large-scale chromatin organization in normal and aberrant lineage-specific gene transcription.
Collapse
Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xin Wang
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adlai R Grayson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter T Hsi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
42
|
Liu T, Zhou W, Cai B, Chu J, Shi G, Teng H, Xu J, Xiao J, Wang Y. IRX2-mediated upregulation of MMP-9 and VEGF in a PI3K/AKT-dependent manner. Mol Med Rep 2015; 12:4346-4351. [PMID: 26062523 DOI: 10.3892/mmr.2015.3915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 04/10/2015] [Indexed: 11/06/2022] Open
Abstract
Osteosarcoma (OS) is the most frequent type of primitive malignant bone tumor with a poor prognosis due to distant metastasis. Our previous studies have demonstrated that IRX2 is overexpressed and is important in cell proliferation and invasion. However, the molecular mechanisms underlying the IRX2‑dependent regulation of OS progression remains to be elucidated. In the present study, the effects of IRX2 on the upregulation of MMP2 and VEGF in OS were determined by western blotting, and the underlying molecular mechanisms were elucidated. These findings provided data suggesting that IRX2 modulates the expression levels of MMP2 and VEGF in an AKT‑dependent manner. The overexpression of IRX2 promoted the activation of PI3K/Akt and increased the proliferation and invasiveness of the OS cell lines as shown by CCK8 and invasion assays. Notably, interruption of the AKT pathway by treatment with LY294002, a specific PI3K inhibitor, attenuated IRX2‑induced cell proliferation and invasive ability, and the upregulation of MMP2 and VEGF. The results of the present study suggested that inhibition of the IRX2‑mediated AKT signaling pathway may be a suitable therapeutic target for the treatment of OS.
Collapse
Affiliation(s)
- Tielong Liu
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Weiwei Zhou
- Department of Radiology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Bing Cai
- Department of Orthopedics, Ningbo Development Zone Center Hospital, Ningbo, Zhejiang 315800, P.R. China
| | - Jianjun Chu
- Department of Orthopedics, First People's Hospital of Hefei, Hefei, Anhui 230061, P.R. China
| | - Guodong Shi
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Honglin Teng
- Department of Orthopedics, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Jian Xu
- Department of Orthopedics, The Workers Hospital of Suqian City, Suqian, Jiangsu 223800, P.R. China
| | - Jianru Xiao
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Yan Wang
- Department of Orthopedics, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| |
Collapse
|
43
|
Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res 2015; 43:e116. [PMID: 26040699 PMCID: PMC4605286 DOI: 10.1093/nar/gkv562] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/15/2015] [Indexed: 12/19/2022] Open
Abstract
We developed an innovative hybrid sequencing approach, IDP-fusion, to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads. We applied IDP-fusion to PacBio data and Illumina data from the MCF-7 breast cancer cells. Compared with the existing tools, IDP-fusion detects fusion genes at higher precision and a very low false positive rate. The results show that IDP-fusion will be useful for unraveling the complexity of multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.
Collapse
Affiliation(s)
- Jason L Weirather
- Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
| | - Pegah Tootoonchi Afshar
- Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA
| | - Tyson A Clark
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Elizabeth Tseng
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Linda S Powers
- Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195-5065, USA
| | - Joseph Zabner
- Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
| | - Jonas Korlach
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Wing Hung Wong
- Department of Statistics and Department of Health Research & Policy, 390 Serra Mall, Stanford University, Stanford, CA 94305, USA
| | - Kin Fai Au
- Department of Internal Medicine, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, USA
| |
Collapse
|
44
|
Using the MCF10A/MCF10CA1a Breast Cancer Progression Cell Line Model to Investigate the Effect of Active, Mutant Forms of EGFR in Breast Cancer Development and Treatment Using Gefitinib. PLoS One 2015; 10:e0125232. [PMID: 25969993 PMCID: PMC4430383 DOI: 10.1371/journal.pone.0125232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/22/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Basal-like and triple negative breast cancer (TNBC) share common molecular features, poor prognosis and a propensity for metastasis to the brain. Amplification of epidermal growth factor receptor (EGFR) occurs in ~50% of basal-like breast cancer, and mutations in the epidermal growth factor receptor (EGFR) have been reported in up to ~ 10% of Asian TNBC patients. In non-small cell lung cancer several different mutations in the EGFR tyrosine kinase domain confer sensitivity to receptor tyrosine kinase inhibitors, but the tumourigenic potential of EGFR mutations in breast cells and their potential for targeted therapy is unknown. MATERIALS AND METHODS Constructs containing wild type, G719S or E746-A750 deletion mutant forms of EGFR were transfected into the MCF10A breast cells and their tumorigenic derivative, MCF10CA1a. The effects of EGFR over-expression and mutation on proliferation, migration, invasion, response to gefitinib, and tumour formation in vivo was investigated. Copy number analysis and whole exome sequencing of the MCF10A and MCF10CA1a cell lines were also performed. RESULTS Mutant EGFR increased MCF10A and MCF10CA1a proliferation and MCF10A gefitinib sensitivity. The EGFR-E746-A750 deletion increased MCF10CA1a cell migration and invasion, and greatly increased MCF10CA1a xenograft tumour formation and growth. Compared to MCF10A cells, MCF10CA1a cells exhibited large regions of gain on chromosomes 3 and 9, deletion on chromosome 7, and mutations in many genes implicated in cancer. CONCLUSIONS Mutant EGFR enhances the oncogenic properties of MCF10A cell line, and increases sensitivity to gefitinib. Although the addition of EGFR E746-A750 renders the MCF10CA1a cells more tumourigenic in vivo it is not accompanied by increased gefitinib sensitivity, perhaps due to additional mutations, including the PIK3CA H1047R mutation, that the MCF10CA1a cell line has acquired. Screening TNBC/basal-like breast cancer for EGFR mutations may prove useful for directing therapy but, as in non-small cell lung cancer, accompanying mutations in PIK3CA may confer gefitinib resistance.
Collapse
|
45
|
Li JY, Daniels G, Wang J, Zhang X. TBL1XR1 in physiological and pathological states. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2015; 3:13-23. [PMID: 26069883 PMCID: PMC4446378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Transducin (beta)-like 1X related protein 1 (TBL1XR1/TBLR1) is an integral subunit of the NCoR (nuclear receptor corepressor) and SMRT (silencing mediator of retinoic acid and thyroid hormone receptors) repressor complexes. It is an evolutionally conserved protein that shares high similarity across all species. TBL1XR1 is essential for transcriptional repression mediated by unliganded nuclear receptors (NRs) and othe regulated transcription factors (TFs). However, it can also act as a transcription activator through the recruitment of the ubiquitin-conjugating/19S proteasome complex that mediates the exchange of corepressors for coactivators. TBL1XR1 is required for the activation of multiple intracellular signaling pathways. TBL1XR1 germline mutations and recurrent mutations are linked to intellectual disability. Upregulation of TBL1XR1 is observed in a variety of solid tumors, which is associated with advanced tumor stage, metastasis and poor prognosis. A variety of genomic alterations, such as translocation, deletion and mutation have been identified in many types of neoplasms. Loss of TBL1XR1 in B-lymphoblastic leukemia disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance. However, the mechanisms of other types of genomic changes in tumorogenesis are still not clear. A pre-clinical study has shown that the disruption of the interaction between TBL1X and β-catenin using a small molecule can inhibit the growth of AML stem and blast cells both in vitro and in vivo. These findings shed light on the therapeutic potentials of targeting TBL1XR1 related proteins in cancer treatment.
Collapse
Affiliation(s)
- Jian Yi Li
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| | - Garrett Daniels
- Department of Pathology, New York University School of MedicineNew York, USA
| | - Jing Wang
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| | - Xinmin Zhang
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of MedicineNew York, USA
| |
Collapse
|
46
|
Nastasie MS, Thissen H, Jans DA, Wagstaff KM. Enhanced tumour cell nuclear targeting in a tumour progression model. BMC Cancer 2015; 15:76. [PMID: 25885577 PMCID: PMC4342815 DOI: 10.1186/s12885-015-1045-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 01/27/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND There is an urgent need for new approaches to deliver bioactive molecules to cancer cells efficiently and specifically. METHODS Here we fuse the cancer cell nuclear targeting module of the Chicken Anaemia Virus Apoptin protein to the core histones H2B and H3 and utilise them in transfection, protein transduction and DNA binding assays. RESULTS We found subsequent nuclear accumulation of these proteins to be 2-3 fold higher in tumour compared to normal cells in transfected isogenic human osteosarcoma and breast tumour progression models. This represents the first demonstration of enhanced nuclear targeting by Apoptin in a tumour progression model, and its functionality in a heterologous protein context. Excitingly, we found that the innate transduction ability of histones could be exploited in combination with the Apoptin nuclear targeting module to effect an overall 13-fold higher delivery of protein to osteosarcoma cancer cell nuclei compared to their isogenic normal counterparts. CONCLUSIONS This is the first report of cancer-cell specificity by a cell penetrating protein, with important implications for the use of protein transduction as a vehicle for gene/drug delivery in the future, and in particular in the development of highly specific and effective anti-cancer agents.
Collapse
Affiliation(s)
- Michael S Nastasie
- Nuclear Signalling Laboratory, Department Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
| | - Helmut Thissen
- CSIRO Molecular and Health Technologies, Bayview Avenue, Clayton, Victoria, 3168, Australia.
| | - David A Jans
- Nuclear Signalling Laboratory, Department Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
| | - Kylie M Wagstaff
- Nuclear Signalling Laboratory, Department Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
| |
Collapse
|
47
|
Rationale for targeting fibroblast growth factor receptor signaling in breast cancer. Breast Cancer Res Treat 2015; 150:1-8. [PMID: 25677745 PMCID: PMC4344551 DOI: 10.1007/s10549-015-3301-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/04/2015] [Indexed: 01/28/2023]
Abstract
Fibroblast growth factor receptor (FGFR) signaling is involved in multiple biological processes, including cell proliferation, survival, differentiation, migration, and apoptosis during embryonic development and adult tissue homeostasis. Given its role in the activation of critical signaling pathways, aberrant FGFR signaling has been implicated in multiple cancer types. A comprehensive search of PubMed and congress abstracts was conducted to identify reports on FGFR pathway components in breast cancer. In breast cancers, FGFR1 and FGFR4 gene amplification and single nucleotide polymorphisms in FGFR2 and FGFR4 have been detected. Commonly, these FGFR aberrations and gene amplifications lead to increased FGFR signaling and have been linked with poor prognosis and resistance to breast cancer treatments. Here, we review the role of FGFR signaling and the impact of FGFR genetic amplifications/aberrations on breast tumors. In addition, we summarize the most recent preclinical and clinical data on FGFR-targeted therapies in breast cancer. Finally, we highlight the ongoing clinical trials of the FGFR-targeted agents dovitinib, AZD4547, lucitanib, BGJ398, and JNJ-42756493, which are selected for patients with FGFR pathway-amplified breast cancer. Aberrant FGFR pathway amplification may drive some breast cancers. Inhibition of FGFR signaling is being explored in the clinic, and data from these trials may refine our ability to select patients who would best respond to these treatments.
Collapse
|
48
|
Liu L, Lin C, Liang W, Wu S, Liu A, Wu J, Zhang X, Ren P, Li M, Song L. TBL1XR1 promotes lymphangiogenesis and lymphatic metastasis in esophageal squamous cell carcinoma. Gut 2015; 64:26-36. [PMID: 24667177 DOI: 10.1136/gutjnl-2013-306388] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) plays an important role in controlling the precisely regulated switch between gene repression and gene activation in transcriptional regulation. We investigated its biological function and clinical significance in esophageal squamous cell carcinoma (ESCC). DESIGN Immunoblotting and immunochemistry were used to determine TBL1XR1 expression in ESCC cell lines, ESCC clinical tissues and 230 clinicopathologically characterised ESCC specimens. The role of TBL1XR1 in lymphangiogenesis and lymphatic metastasis was examined by tube formation, cell invasion and wound-healing assays in vitro, and by a popliteal lymph node metastasis model in vivo. The molecular mechanism by which TBL1XR1 upregulates vascular endothelial growth factor C (VEGF-C) expression was explored using real-time PCR, ELISA, luciferase reporter assay and chromatin immunoprecipitation. RESULTS TBL1XR1 expression was significantly upregulated in ESCC, positively correlated with disease stage and patient survival, and identified as an independent prognostic factor for patient outcome. We found that TBL1XR1 overexpression promoted lymphangiogenesis and lymphatic metastasis in ESCC in vitro and in vivo, whereas TBL1XR1 silencing had the converse effect. We demonstrated that TBL1XR1 induced VEGF-C expression by binding to the VEGF-C promoter. We confirmed the correlation between TBL1XR1 and VEGF-C expression in a large cohort of clinical ESCC samples and through analysis of published datasets in gastric, colorectal and breast cancer. CONCLUSIONS Our results demonstrated that TBL1XR1 induced lymphangiogenesis and lymphatic metastasis in ESCC via upregulation of VEGF-C, and may represent a novel prognostic biomarker and therapeutic target for patients with ESCC.
Collapse
Affiliation(s)
- Liping Liu
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China Guangzhou Research Institute of Respiratory Disease & China State Key Laboratory of Respiratory Disease, Guangzhou, Guangdong, China
| | - Chuyong Lin
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weijiang Liang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shu Wu
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Aibin Liu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jueheng Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xin Zhang
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengli Ren
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mengfeng Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Libing Song
- State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
49
|
Dey N, Leyland-Jones B, De P. MYC-xing it up with PIK3CA mutation and resistance to PI3K inhibitors: summit of two giants in breast cancers. Am J Cancer Res 2014; 5:1-19. [PMID: 25628917 PMCID: PMC4300701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/28/2014] [Indexed: 06/04/2023] Open
Abstract
Approximately 35% of breast cancers exhibit PIK3CA activating mutation. Since PIK3CA hotspot mutation is the most frequently mutated gene in human breast cancers and primarily overlaps in HER2+ as well as ER+ breast cancers, the subset of patients bearing PIK3CA activating mutation does not get fullest benefit from either anti-HER2 or anti-hormonal agents. Literature also suggests that these patients may have chemotherapy resistance. Indeed, multiple clinical trials are currently evaluating the efficacy of over 30 drugs targeting different nodal points in the PI3K-AKT-mTOR pathway in breast and other cancers. However, to date, responses of solid tumors to PI3K pathway inhibitor monotherapy remains modest with an accompanied rapid emergences of drug resistance. MYC elevation represents one of the potential modes of actions by which breast tumors develop resistance to the PI3K pathway-specific targeted therapies. As products of oncogenes, both MYC and PIK3CA are well-established onco-proteins which contribute to breast oncogenesis. However, their similarities out number their dissimilarities in the context of their specific oncogenic cellular signals. In this review we will describe the specific cellular signals initiated following alteration in the MYC gene and PIK3CA gene in breast cancers. We will interrogate how MYC gene alterations influence the action of PI3K pathway targeted drugs in the context of PIK3CA mutation towards the development PI3K inhibitor induced drug-resistance in breast cancers.
Collapse
Affiliation(s)
- Nandini Dey
- Department of Molecular & Experimental Medicine, Avera Research InstituteSioux Falls, SD
- Department of Internal Medicine, SSOM, University of South DakotaSD
| | - Brian Leyland-Jones
- Department of Molecular & Experimental Medicine, Avera Research InstituteSioux Falls, SD
- Department of Internal Medicine, SSOM, University of South DakotaSD
| | - Pradip De
- Department of Molecular & Experimental Medicine, Avera Research InstituteSioux Falls, SD
- Department of Internal Medicine, SSOM, University of South DakotaSD
| |
Collapse
|
50
|
Dubruc E, Balme B, Dijoud F, Disant F, Thomas L, Wang Q, Pissaloux D, de la Fouchardiere A. Mutated and amplifiedNRASin a subset of cutaneous melanocytic lesions with dermal spitzoid morphology: report of two pediatric cases located on the ear. J Cutan Pathol 2014; 41:866-72. [DOI: 10.1111/cup.12389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/16/2014] [Accepted: 07/19/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Estelle Dubruc
- Département de Biopathologie; Centre Léon Bérard; Lyon France
| | - Brigitte Balme
- Département de Pathologie; hôpital Lyon Sud; Lyon France
| | | | | | - Luc Thomas
- Service de Dermatologie Centre Hospitalier Lyon Sud; Pierre Bénite France
- Université Claude Bernard Lyon 1; Lyon France
| | - Qing Wang
- Département de Biopathologie; Centre Léon Bérard; Lyon France
| | | | | |
Collapse
|