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Gopikrishnan M, R HC, R G, Ashour HM, Pintus G, Hammad M, Kashyap MK, C GPD, Zayed H. Therapeutic and diagnostic applications of exosomal circRNAs in breast cancer. Funct Integr Genomics 2023; 23:184. [PMID: 37243750 DOI: 10.1007/s10142-023-01083-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/29/2023] [Imported: 06/18/2023]
Abstract
Circular RNAs (circRNAs) are regulatory elements that are involved in orchestrating gene expression and protein functions and are implicated in various biological processes including cancer. Notably, breast cancer has a significant mortality rate and is one of the most common malignancies in women. CircRNAs have been demonstrated to contribute to the pathogenesis of breast cancer including its initiation, progression, metastasis, and resistance to drugs. By acting as miRNA sponges, circRNAs can indirectly influence gene expression by disrupting miRNA regulation of their target genes, ultimately altering the course of cancer development and progression. Additionally, circRNAs can interact with proteins and modulate their functions including signaling pathways involved in the initiation and development of cancer. Recently, circRNAs can encode peptides that play a role in the pathophysiology of breast cancer and other diseases and their potential as diagnostic biomarkers and therapeutic targets for various cancers including breast cancer. CircRNAs possess biomarkers that differentiate, such as stability, specificity, and sensitivity, and can be detected in several biological specimens such as blood, saliva, and urine. Moreover, circRNAs play an important role in various cellular processes including cell proliferation, differentiation, and apoptosis, all of which are integral factors in the development and progression of cancer. This review synthesizes the functions of circRNAs in breast cancer, scrutinizing their contributions to the onset and evolution of the disease through their interactions with exosomes and cancer-related intracellular pathways. It also delves into the potential use of circRNA as a biomarker and therapeutic target against breast cancer. It discusses various databases and online tools that offer crucial circRNA information and regulatory networks. Lastly, the challenges and prospects of utilizing circRNAs in clinical settings associated with breast cancer are explored.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Hephzibah Cathryn R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Gnanasambandan R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Hossam M Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, Florida, 33701, USA
| | - Gianfranco Pintus
- Department of Biomedical Sciences, University of Sassari, 07100, Sassari, Italy
| | - Mohamed Hammad
- Department of Stem Cell Biology and Regenerative Medicine, City of Hope Beckman Research Institute, Duarte, California, USA
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Manesar (Gurugram), Panchgaon, Haryana (HR), 122413, India
- Clinical Biosamples & Research Services (CBRS), Noida, Uttar Pradesh, 201301, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713, Doha, Qatar.
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Hashemi ZS, Ghavami M, Kashyap MK. Editorial: Exosomes, miRNAs, and lncRNAs in breast cancer: Therapeutic and diagnostic applications. Front Genet 2023; 14:1192866. [PMID: 37229186 PMCID: PMC10203691 DOI: 10.3389/fgene.2023.1192866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] [Imported: 06/18/2023] Open
Affiliation(s)
| | - Mahlegha Ghavami
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Gurugram, Haryana, India
- Clinical Biosamples and Research Services (CBRS), Noida, Uttar Pradesh, India
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Soni A, Bhandari MP, Tripathi GK, Bundela P, Khiriya PK, Khare PS, Kashyap MK, Dey A, Vellingiri B, Sundaramurthy S, Suresh A, Pérez de la Lastra JM. Nano-biotechnology in tumour and cancerous disease: A perspective review. J Cell Mol Med 2023; 27:737-762. [PMID: 36840363 PMCID: PMC10002932 DOI: 10.1111/jcmm.17677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 02/26/2023] [Imported: 06/18/2023] Open
Abstract
In recent years, drug manufacturers and researchers have begun to consider the nanobiotechnology approach to improve the drug delivery system for tumour and cancer diseases. In this article, we review current strategies to improve tumour and cancer drug delivery, which mainly focuses on sustaining biocompatibility, biodistribution, and active targeting. The conventional therapy using cornerstone drugs such as fludarabine, cisplatin etoposide, and paclitaxel has its own challenges especially not being able to discriminate between tumour versus normal cells which eventually led to toxicity and side effects in the patients. In contrast to the conventional approach, nanoparticle-based drug delivery provides target-specific delivery and controlled release of the drug, which provides a better therapeutic window for treatment options by focusing on the eradication of diseased cells via active targeting and sparing normal cells via passive targeting. Additionally, treatment of tumours associated with the brain is hampered by the impermeability of the blood-brain barriers to the drugs, which eventually led to poor survival in the patients. Nanoparticle-based therapy offers superior delivery of drugs to the target by breaching the blood-brain barriers. Herein, we provide an overview of the properties of nanoparticles that are crucial for nanotechnology applications. We address the potential future applications of nanobiotechnology targeting specific or desired areas. In particular, the use of nanomaterials, biostructures, and drug delivery methods for the targeted treatment of tumours and cancer are explored.
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Affiliation(s)
- Ambikesh Soni
- School of Nanotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| | | | - Gagan Kant Tripathi
- School of Nanotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| | - Priyavand Bundela
- School of Nanotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| | | | - Purnima Swarup Khare
- School of Nanotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Haryana, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, West Bengal, Kolkata, India
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Maulana Azad National Institute of Technology, Bathinda, India
| | - Suresh Sundaramurthy
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Madhya Pradesh, Bhopal, India
| | - Arisutha Suresh
- Department of Energy, Maulana Azad National Institute of Technology & M/s Eco Science & Technology, Madhya Pradesh, Bhopal, India
| | - José M Pérez de la Lastra
- Biotecnología de macromoléculas, Instituto de Productos Naturales y Agrobiología, (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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Almaghrbi H, Elkardawy R, Udhaya Kumar S, Kuttikrishnan S, Abunada T, Kashyap MK, Ahmad A, Uddin S, George Priya Doss C, Zayed H. Analysis of signaling cascades from myeloma cells treated with pristimerin. Adv Protein Chem Struct Biol 2023; 134:147-174. [PMID: 36858733 DOI: 10.1016/bs.apcsb.2022.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] [Imported: 06/18/2023]
Abstract
Multiple myeloma (MM) is the 2nd most frequently diagnosed blood cancer after non-Hodgkin's lymphoma. The present study aimed to identify the differentially expressed genes (DEGs) between the control and pristimerin-treated MM cell lines. We examined the GSE14011 microarray dataset and screened DEGs with GEO2R statistical tool using the inbuilt limma package. We used a bioinformatics pipeline to identify the differential networks, signaling cascades, and the survival of the hub genes. We implemented two different enrichment analysis including ClueGO and Metacore™, to get accurate annotation for most significant DEGs. We screened the most significant 408 DEGs from the dataset based on p-values and logFC values. Using protein network analysis, we found the genes UBC, HSP90AB1, HSPH1, HSPA1B, HSPA1L, HSPA6, HSPD1, DNAJB1, HSPE1, DNAJC10, BAG3, and DNAJC7 had higher node degree distribution. In contrast, the functional annotation provided that the DEGs were predominantly enriched in B-cell receptor signaling, unfolded protein response, positive regulation of phagocytosis, HSP70, and HSP40-dependent folding, and ubiquitin-proteasomal proteolysis. Using network algorithms, and comparing enrichment analysis, we found the hub genes enriched were INHBE, UBC, HSPA1A, HSP90AB1, IKBKB, and BAG3. These DEGs were further validated with overall survival and gene expression analysis between the tumor and control groups. Finally, pristimerin effects were validated independently in a cell line model consisting of IM9 and U266 MM cells. Pristimerin induced in vitro cytotoxicity in MM cells in a dose-dependent manner. Pristimerin inhibited NF-κB, induced accumulation of ubiquitinated proteins and inhibited HSP60 in the validation of bioinformatics findings, while pristimerin-induced caspase-3 and PARP cleavage confirmed cell death. Taken together, we found that the identified DEGs were strongly associated with the apoptosis induced in MM cell lines due to pristimerin treatment, and combinatorial therapy derived from pristimerin could act as novel anti-myeloma multifunctional agents.
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Affiliation(s)
- Heba Almaghrbi
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Rehab Elkardawy
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shilpa Kuttikrishnan
- Translational Research Institute & Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Taghreed Abunada
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Gurugram, India
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar.
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Tripathi G, Tripathi A, Johnson J, Kashyap MK. Role of RNA Splicing in Regulation of Cancer Stem Cell. Curr Stem Cell Res Ther 2023; 18:3-6. [PMID: 34875992 DOI: 10.2174/1574888x16666211207103628] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/16/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Affiliation(s)
- Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Joel Johnson
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
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He X, Kashyap MK, Zhao ZJ, Yu J, Shi H. Editorial: Linking cellular metabolism to hematological malignancies. Front Oncol 2022; 12:1077358. [PMID: 36439481 DOI: 10.3389/fonc.2022.1077358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] [Imported: 06/18/2023] Open
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Charles Jacob HK, Signorelli R, Charles Richard JL, Kashuv T, Lavania S, Middleton A, Gomez BA, Ferrantella A, Amirian H, Tao J, Ergonul AB, Boone MM, Hadisurya M, Tao WA, Iliuk A, Kashyap MK, Garcia-Buitrago M, Dawra R, Saluja AK. Identification of novel early pancreatic cancer biomarkers KIF5B and SFRP2 from “first contact” interactions in the tumor microenvironment. J Exp Clin Cancer Res 2022; 41:258. [PMID: 36002889 PMCID: PMC9400270 DOI: 10.1186/s13046-022-02425-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 12/27/2022] [Imported: 06/18/2023] Open
Abstract
Abstract
Background
Pancreatic cancer is one of the most difficult cancers to detect early and most patients die from complications arising due to distant organ metastases. The lack of bona fide early biomarkers is one of the primary reasons for late diagnosis of pancreatic cancer. It is a multifactorial disease and warrants a novel approach to identify early biomarkers.
Methods
In order to characterize the proteome, Extracellular vesicles (EVs) isolated from different in vitro conditions mimicking tumor-microenvironment interactions between pancreatic cancer epithelial and stromal cells were analyzed using high throughput mass spectrometry. The biological activity of the secreted EVome was analyzed by investigating changes in distant organ metastases and associated early changes in the microbiome. Candidate biomarkers (KIF5B, SFRP2, LOXL2, and MMP3) were selected and validated on a mouse-human hybrid Tissue Microarray (TMA) that was specifically generated for this study. Additionally, a human TMA was used to analyze the expression of KIF5B and SFRP2 in progressive stages of pancreatic cancer.
Results
The EVome of co-cultured epithelial and stromal cells is different from individual cells with distinct protein compositions. EVs secreted from stromal and cancer cells cultures could not induce significant changes in Pre-Metastatic Niche (PMN) modulation, which was assessed by changes in the distant organ metastases. However, they did induce significant changes in the early microbiome, as indicated by differences in α and β-diversities. KIF5B and SFRP2 show promise for early detection and investigation in progressive pancreatic cancer. These markers are expressed in all stages of pancreatic cancer such as low grade PanINs, advanced cancer, and in liver and soft tissue metastases.
Conclusions
Proteomic characterization of EVs derived from mimicking conditions of epithelial and stromal cells in the tumor-microenvironment resulted in the identification of several proteins, some for the first time in EVs. These secreted EVs cannot induce changes in distant organ metastases in in vivo models of EV education, but modulate changes in the early murine microbiome. Among all the proteins that were analyzed (MMP3, KIF5B, SFRP2, and LOXL2), KIF5B and SFRP2 show promise as bona fide early pancreatic cancer biomarkers expressed in progressive stages of pancreatic cancer.
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Ali A, Ara A, Kashyap MK. Gut microbiota: Role and Association with Tumorigenesis in Different Malignancies. Mol Biol Rep 2022; 49:8087-8107. [PMID: 35543828 DOI: 10.1007/s11033-022-07357-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/07/2023]
Abstract
The microbiota has been associated with different cancer and may vary from patient to patient. A specific microbial strain can alter the progression of cancer and therapeutic outcome in response to anti-cancer therapy. The variations in microbiota contributed due to the individual microbiome of the microorganism are responsible for diverse clinical outcomes. The expansion of microbiota subpopulation during dysbiosis can lead to toxin production, inducing inflammation and cancer. The microbiota can be a dual-edged sword because it can be tumor-suppressive or oncogenic in the case of the gut. The transition of cancer cells from early to late-stage also impacts the composition of the microbiota, and this alteration could change the behavior of cancer. Multi-omics platforms derived data from an individual's multi-dimensional data (DNA, mRNA, microRNA, protein, metabolite, microbiota, and microbiome), i.e., individualome, to exploit it for personalized tailored treatment for different cancers in a precise manner. A number of studies suggest the importance of microbiota and its add-in suitability to existing treatment options for different malignancies. Furthermore, in vitro, and in vivo studies and cancer clinical trials suggest that probiotics have driven modulation of gut microbiota and other sites discourage the aggressive behavior and progression of different cancers.
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Affiliation(s)
- Altamas Ali
- Department of Biosciences, Jamia Millia Islamia (A central University), Jamia Nagar, 110025, New Delhi, India
| | - Anam Ara
- Department of Biosciences, Jamia Millia Islamia (A central University), Jamia Nagar, 110025, New Delhi, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute/Amity Medical School, Amity University Haryana, Amity Education Valley, Panchgaon (Manesar), Gurugram, HR, 122413, India.
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Udhaya Kumar S, Balasundaram A, Anu Preethi V, Chatterjee S, Kameshwari Gollakota GV, Kashyap MK, George Priya Doss C, Zayed H. Integrative ontology and pathway-based approach identifies distinct molecular signatures in transcriptomes of esophageal squamous cell carcinoma. Adv Protein Chem Struct Biol 2022; 131:177-206. [PMID: 35871890 DOI: 10.1016/bs.apcsb.2022.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] [Imported: 06/18/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) remains a serious concern globally due to many factors that including late diagnosis, lack of an ideal biomarker for diagnosis and prognosis, and high rate of mortality. In this study, we aimed to identify the essential dysregulated genes and molecular signatures associated with the progression and development of ESCC. The dataset with 15 ESCCs and the 15 adjacent normal tissue samples from the surrounding histopathologically tumor-free mucosa was selected. We applied bioinformatics pipelines including various topological parameters from MCODE, CytoNCA, and cytoHubba to prioritize the most significantly associated DEGs with ESCC. We performed functional enrichment annotation for the identified DEGs using DAVID and MetaCore™ GeneGo platforms. Furthermore, we validated the essential core genes in TCGA and GTEx datasets between the normal mucosa and ESCC for their expression levels. These DEGs were primarily enriched in positive regulation of transferase activity, negative regulation of organelle organization, cell cycle mitosis/S-phase transition, spindle organization/assembly, development, and regulation of angiogenesis. Subsequently, the DEGs were associated with the pathways such as oocyte meiosis, cell cycle, and DNA replication. Our study identified the eight-core genes (AURKA, AURKB, MCM2, CDC20, TPX2, PLK1, FOXM1, and MCM7) that are highly expressed among the ESCC, and TCGA dataset. The multigene comparison and principal component analysis resulted in elevated signals for the AURKA, MCM2, CDC20, TPX2, PLK1, and FOXM1. Overall, our study reported GO profiles and molecular signatures that might help researchers to grasp the pathological mechanisms underlying ESCC development and eventually provide novel therapeutic and diagnostic strategies.
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Affiliation(s)
- S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - V Anu Preethi
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - Sayoni Chatterjee
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - G V Kameshwari Gollakota
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Gurugram, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar.
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Kumar D, Kashyap MK, Yu Z, Spaanderman I, Villa R, Kipps TJ, La Clair JJ, Burkart MD, Castro JE. Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B. Aging (Albany NY) 2022; 14:2081-2100. [PMID: 35230971 PMCID: PMC8954975 DOI: 10.18632/aging.203924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alterations in RNA splicing are associated with different malignancies, including leukemia, lymphoma, and solid tumors. The RNA splicing modulators such as FD-895 and pladienolide B have been investigated in different malignancies to target/modulate spliceosome for therapeutic purpose. Different cell lines were screened using an RNA splicing modulator to test in vitro cytotoxicity and the ability to modulate RNA splicing capability via induction of intron retention (using RT-PCR and qPCR). The Cignal Finder Reporter Array evaluated [pathways affected by the splice modulators in HeLa cells. Further, the candidates associated with the pathways were validated at protein level using western blot assay, and gene-gene interaction studies were carried out using GeneMANIA. We show that FD-895 and pladienolide B induces higher apoptosis levels than conventional chemotherapy in different solid tumors. In addition, both agents modulate Wnt signaling pathways and mRNA splicing. Specifically, FD-895 and pladienolide B significantly downregulates Wnt signaling pathway-associated transcripts (GSK3β and LRP5) and both transcript and proteins including LEF1, CCND1, LRP6, and pLRP6 at the transcript, total protein, and protein phosphorylation's levels. These results indicate FD-895 and pladienolide B inhibit Wnt signaling by decreasing LRP6 phosphorylation and modulating mRNA splicing through induction of intron retention in solid tumors.
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Affiliation(s)
- Deepak Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- ThermoFisher Scientific, Carlsbad, CA 92008, USA
| | - Manoj K. Kashyap
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Zhe Yu
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ide Spaanderman
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Hematology-Oncology Division, Mayo Clinic, Phoenix, AZ 85054, USA
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11
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Raina P, Singh SK, Goswami AK, Kashyap MK, Khullar M, Sharma SK, Barwal KC. MN/CA9 gene expression as a potential tumor marker for renal cell carcinoma. Mol Cell Biochem 2022; 477:333-343. [PMID: 34716861 DOI: 10.1007/s11010-021-04279-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/15/2021] [Indexed: 02/07/2023]
Abstract
MN/CA9 is a cell surface glycoprotein and a tumor-associated antigen. It plays a crucial role in the regulation of cell proliferation and oncogenesis. There is no ideal tumor marker currently available for renal cell carcinoma (RCC) with sufficient sensitivity and specificity. Therefore, we studied MN/CA9 gene expression in the tumor tissue, apparently normal kidney tissue, preoperative blood, and urine samples of patients with RCC. We included thirty cases of renal tumors (26 RCC and 4 benign tumors) in the study. We applied an RT-PCR assay for MN/CA9 gene expression to 26 RCC kidney tumor samples and four benign kidney tumor tissue samples. We also evaluated MN/CA9 gene expression in preoperative blood and urine samples of 15 of these cases. Additionally, thirty-five grossly normal renal tissue samples, including 21 from kidneys with RCC, were also evaluated for gene expression. The RT-PCR analysis revealed that twenty-one out of 26 RCC tissue samples showed MN/CA9 gene expression compared to three out of 35 non-malignant renal tissue samples (p < 0.05). Two out of four benign renal tissue samples also expressed this gene. We also observed MN/CA9 gene expression in nine out of 15 blood samples and four out of 15 urine samples. All patients with urinary MN/CA9 gene expression showed expression in blood and tumor tissue samples. We found a correlation in terms of MN/CA9 expression between blood and tumor tissue samples of RCC patients as those who exhibit MN/CA9 expression in blood were also positive at the tumor tissue levels. The difference in MN/CA9 gene expression in tumor tissue, blood, and urine samples in relation to the stage of the disease, nuclear grade, and histological cell-type was not statistically significant. However, all the three patients who had metastatic RCC had MN/CA9 gene expression in their blood. The existence of a tumor-associated antigen such as MN/CA9 may present a possible target for molecular diagnosis and management of RCC.
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Affiliation(s)
- Pamposh Raina
- Department of Urology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, 171001, India
- Department of Urology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - S K Singh
- Department of Urology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - Anil K Goswami
- Department of Urology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - Manoj Kumar Kashyap
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Amity Education Valley, Panchgaon (Manesar), Gurugram, HR, 122413, India
| | - Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - S K Sharma
- Department of Urology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - Kailash Chander Barwal
- Department of Urology, Indira Gandhi Medical College, Shimla, Himachal Pradesh, 171001, India.
- Department of Urology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012, India.
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12
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Chawla U, Kashyap MK, Husain A. Aging and diabetes drive the COVID-19 forwards; unveiling nature and existing therapies for the treatment. Mol Cell Biochem 2021; 476:3911-3922. [PMID: 34169437 PMCID: PMC8224992 DOI: 10.1007/s11010-021-04200-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Human SARS Coronavirus-2 (SARS-CoV-2) has infected more than 170 million people worldwide and resulted in more than 3.5 million deaths so far. The infection causes Coronavirus disease (COVID-19) in people of all age groups, notably diabetic and old age people, at a higher risk of infectivity and fatality. Around 35% of the patients who have died of the disease were diabetic. The infection is associated with weakening immune response, chronic inflammation, and potential direct pancreatic impairment. There seems to be a three-way association of the SARS-CoV-2 infection with diabetes and aging. The COVID-19 infection causes metabolism complications, which may induce diabetes and accelerate aging in healthy individuals. How does diabetes elevate the likelihood of the infection is not clearly understood. we summarize mechanisms of accelerated aging in COVID-19 and diabetes, and the possible correlation of these three diseases. Various drug candidates under different stages of pre-clinical or clinical developments give us hope for the development of COVID-19 therapeutics, but there is no approved drug so far to treat this disease. Here, we explored the potential of anti-diabetic and anti-aging natural compounds for the COVID-19 treatment. We have also reviewed different therapeutic strategies with plant-based natural products that may be used to cure patients infected with SARS-CoV-2 and post-infection syndrome.
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Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry, The University of Arizona, Old Chemistry 226, Tucson, AZ, 85721, USA
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Amity Education Valley Panchgaon, Manesar (Gurugram), Haryana, India
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India.
- Innovation and Incubation Centre for Entrepreneurship, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India.
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13
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Tripathi A, Kashyap A, Tripathi G, Yadav J, Bibban R, Aggarwal N, Thakur K, Chhokar A, Jadli M, Sah AK, Verma Y, Zayed H, Husain A, Bharti AC, Kashyap MK. Tumor reversion: a dream or a reality. Biomark Res 2021; 9:31. [PMID: 33958005 PMCID: PMC8101112 DOI: 10.1186/s40364-021-00280-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Reversion of tumor to a normal differentiated cell once considered a dream is now at the brink of becoming a reality. Different layers of molecules/events such as microRNAs, transcription factors, alternative RNA splicing, post-transcriptional, post-translational modifications, availability of proteomics, genomics editing tools, and chemical biology approaches gave hope to manipulation of cancer cells reversion to a normal cell phenotype as evidences are subtle but definitive. Regardless of the advancement, there is a long way to go, as customized techniques are required to be fine-tuned with precision to attain more insights into tumor reversion. Tumor regression models using available genome-editing methods, followed by in vitro and in vivo proteomics profiling techniques show early evidence. This review summarizes tumor reversion developments, present issues, and unaddressed challenges that remained in the uncharted territory to modulate cellular machinery for tumor reversion towards therapeutic purposes successfully. Ongoing research reaffirms the potential promises of understanding the mechanism of tumor reversion and required refinement that is warranted in vitro and in vivo models of tumor reversion, and the potential translation of these into cancer therapy. Furthermore, therapeutic compounds were reported to induce phenotypic changes in cancer cells into normal cells, which will contribute in understanding the mechanism of tumor reversion. Altogether, the efforts collectively suggest that tumor reversion will likely reveal a new wave of therapeutic discoveries that will significantly impact clinical practice in cancer therapy.
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Affiliation(s)
- Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Joni Yadav
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Rakhi Bibban
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Nikita Aggarwal
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Kulbhushan Thakur
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Arun Chhokar
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Mohit Jadli
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), India
- Department of Pathology and Laboratory Medicine, Medanta-The Medicity, Haryana, Gurugram, India
| | - Yeshvandra Verma
- Department of Toxicology, C C S University, Meerut, UP, 250004, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER), Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Alok Chandra Bharti
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India.
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
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14
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Kumar P, Sah AK, Tripathi G, Kashyap A, Tripathi A, Rao R, Mishra PC, Mallick K, Husain A, Kashyap MK. Role of ACE2 receptor and the landscape of treatment options from convalescent plasma therapy to the drug repurposing in COVID-19. Mol Cell Biochem 2021; 476:553-574. [PMID: 33029696 PMCID: PMC7539757 DOI: 10.1007/s11010-020-03924-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
Since the first case reports in Wuhan, China, the SARS-CoV-2 has caused a pandemic and took lives of > 8,35,000 people globally. This single-stranded RNA virus uses Angiotensin-converting enzyme 2 (ACE2) as a receptor for entry into the host cell. Overexpression of ACE2 is mainly observed in hypertensive, diabetic and heart patients that make them prone to SARS-CoV-2 infection. Mitigations strategies were opted globally by the governments to minimize transmission of SARS-CoV-2 via the implementation of social distancing norms, wearing the facemasks, and spreading awareness using digital platforms. The lack of an approved drug treatment regimen, and non-availability of a vaccine, collectively posed a challenge for mankind to fight against the SARS-CoV-2 pandemic. In this scenario, repurposing of existing drugs and old treatment options like convalescent plasma therapy can be one of the potential alternatives to treat the disease. The drug repurposing provides a selection of drugs based on the scientific rationale and with a shorter cycle of clinical trials, while plasma isolated from COVID-19 recovered patients can be a good source of neutralizing antibody to provide passive immunity. In this review, we provide in-depth analysis on these two approaches currently opted all around the world to treat COVID-19 patients. For this, we used "Boolean Operators" such as AND, OR & NOT to search relevant research articles/reviews from the PUBMED for the repurposed drugs and the convalescent plasma in the COVID-19 treatment. The repurposed drugs like Chloroquine and Hydroxychloroquine, Tenofovir, Remdesivir, Ribavirin, Darunavir, Oseltamivir, Arbidol (Umifenovir), Favipiravir, Anakinra, and Baricitinib are already being used in clinical trials to treat the COVID-19 patients. These drugs have been approved for a different indication and belong to a diverse category such as anti-malarial/anti-parasitic, anti-retroviral/anti-viral, anti-cancer, or against rheumatoid arthritis. Although, the vaccine would be an ideal option for providing active immunity against the SARS-CoV-2, but considering the current situation, drug repurposing and convalescent plasma therapy and repurposed drugs are the most viable option against SARS-CoV-2.
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Affiliation(s)
- Pravindra Kumar
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Rashmi Rao
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Prabhu C Mishra
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Koustav Mallick
- National Liver Disease Biobank, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research, Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research, Bhopal, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India.
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15
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Aggarwal N, Yadav J, Thakur K, Bibban R, Chhokar A, Tripathi T, Bhat A, Singh T, Jadli M, Singh U, Kashyap MK, Bharti AC. Human Papillomavirus Infection in Head and Neck Squamous Cell Carcinomas: Transcriptional Triggers and Changed Disease Patterns. Front Cell Infect Microbiol 2020; 10:537650. [PMID: 33344262 PMCID: PMC7738612 DOI: 10.3389/fcimb.2020.537650] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/02/2020] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous group of cancers. Collectively, HNSCC ranks sixth in incidence rate worldwide. Apart from classical risk factors like tobacco and alcohol, infection of human papillomavirus (HPV) is emerging as a discrete risk factor for HNSCC. HPV-positive HNSCC represent a distinct group of diseases that differ in their clinical presentation. These lesions are well-differentiated, occur at an early age, and have better prognosis. Epidemiological studies have demonstrated a specific increase in the proportions of the HPV-positive HNSCC. HPV-positive and HPV-negative HNSCC lesions display different disease progression and clinical response. For tumorigenic-transformation, HPV essentially requires a permissive cellular environment and host cell factors for induction of viral transcription. As the spectrum of host factors is independent of HPV infection at the time of viral entry, presumably entry of HPV only selects host cells that are permissive to establishment of HPV infection. Growing evidence suggest that HPV plays a more active role in a subset of HNSCC, where they are transcriptionally-active. A variety of factors provide a favorable environment for HPV to become transcriptionally-active. The most notable are the set of transcription factors that have direct binding sites on the viral genome. As HPV does not have its own transcription machinery, it is fully dependent on host transcription factors to complete the life cycle. Here, we review and evaluate the current evidence on level of a subset of host transcription factors that influence viral genome, directly or indirectly, in HNSCC. Since many of these transcription factors can independently promote carcinogenesis, the composition of HPV permissive transcription factors in a tumor can serve as a surrogate marker of a separate molecularly-distinct class of HNSCC lesions including those cases, where HPV could not get a chance to infect but may manifest better prognosis.
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Affiliation(s)
- Nikita Aggarwal
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Joni Yadav
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Kulbhushan Thakur
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Rakhi Bibban
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Arun Chhokar
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Tanya Tripathi
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Anjali Bhat
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Tejveer Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Mohit Jadli
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Ujala Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Manoj K. Kashyap
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Amity Medical School, Stem Cell Institute, Amity University Haryana, Amity Education Valley Panchgaon, Gurugram, India
| | - Alok C. Bharti
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- *Correspondence: Alok C. Bharti,
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16
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Sharma J, Balakrishnan L, Kaushik S, Kashyap MK. Editorial: Multi-Omics Approaches to Study Signaling Pathways. Front Bioeng Biotechnol 2020; 8:829. [PMID: 33014991 PMCID: PMC7499333 DOI: 10.3389/fbioe.2020.00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bengaluru, India
- Manipal Academy of Higher Education, Manipal, India
- *Correspondence: Jyoti Sharma
| | | | - Sandeep Kaushik
- 3B's Research Group, University of Minho, Guimarães, Portugal
| | - Manoj Kumar Kashyap
- Amity Medical School, Amity Stem Cell Institute, Amity University Haryana, Gurugram, India
- Manoj Kumar Kashyap
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17
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Rao R, Husain A, Bharti AC, Kashyap MK. Discovery of a Novel Connecting Link between Renin-Angiotensin System and Cancer in Barrett's Esophagus by Proteomic Screening. Proteomics Clin Appl 2019; 13:e1900006. [PMID: 30891939 DOI: 10.1002/prca.201900006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Indexed: 02/05/2023]
Abstract
The renin-angiotensin system (RAS) plays a central role in the regulation of homeostasis and blood pressure. This involves an important enzyme called angiotensin-converting enzyme that leads to the conversion of angiotensin I into angiotensin II. RAS has been reported to show association with inflammation, and in sporadic studies, with cancer. In particular, angiotensin II has been reported to be prevalent in the hypoxic microenvironment and associated with cancer signaling pathways. In a recent study, Bratlie et al. (Proteomics Clin. Appl. 2019, 4, 1800102) is shown to exploit 2D gel electrophoresis, and mass spectrometry (MS) to identify differentially expressed proteins by comparing low-grade dysplasia in Barrett's Esophagus (BE) following administration of agents that interfere with RAS, that is, enalapril and candesartan, and identified specific modulation of HSP60, PDIA3, and PPA1. Though 2D gel coupled with MS is a commonly-used tool for studying proteomes, it still has limitations in terms of a comprehensive analysis due to lack of absolute quantitation in a high-throughput manner. Despite technical limitations and the small size of the study, preliminary data emerging from the investigation show interference caused by clinically approved RAS inhibitors resulting in alteration of molecular markers associated with tumorigenicity. The authors propose potential factors that may influence the progression of the disease. However, these are conspicuous changes in high-abundance proteins only. Therefore, there is a need to carry out detailed experimental studies either using an in vitro labeling technique (isobaric labeling for relative and absolute quantitation) for tissues or an in vivo labeling technique (stable isotope labeling in animal cell culture) coupled with LC-MS/MS to identify differentially-regulated proteins to delineate the role of RAS in BE.
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Affiliation(s)
- Rashmi Rao
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, 247121, Uttar Pradesh, India
| | - Amjad Husain
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, 247121, Uttar Pradesh, India
| | - Alok C Bharti
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Manoj K Kashyap
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, 247121, Uttar Pradesh, India
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18
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018; 8:12715. [PMID: 30143675 PMCID: PMC6109081 DOI: 10.1038/s41598-018-30579-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India
- Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
- Infosys Technologies Ltd, Bangalore, Karnataka, India
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India.
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India.
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India.
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India.
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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19
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Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget 2018; 9:18422-18434. [PMID: 29719615 PMCID: PMC5915082 DOI: 10.18632/oncotarget.24853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
The vast majority of esophageal cancers in China, India and Iran are esophageal squamous cell carcinomas (ESCC). A timely diagnosis provides surgical removal as the main therapeutic option for patients with ESCC. Currently, there are no targeted therapies available for ESCC. We carried out reverse phase protein array-based protein expression profiling of seven ESCC-derivedcell lines and a non-neoplastic esophageal epithelial cell line (Het-1A) to identify differentially expressed proteins in ESCC. SYK non-receptortyrosine kinase was overexpressed in six out of seven ESCC cell lines that were used in the study. We evaluated the role of SYK in ESCC using the pharmacological inhibitor entospletinib (GS-9973) and siRNA-based knock down studies. Entospletinib is a selective inhibitor of SYK, which is currently being evaluated in phase II clinical trials for hematological malignancies. Using in vivo subcutaneous tumor xenografts in mice, we demonstrate that treatment with entospletinib significantly inhibits tumor growth. Further clinical studies are needed to prove the efficacy of entospletinib as a targeted therapeutic agent for treating ESCC.
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Affiliation(s)
- Mustafa A. Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manoj K. Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, India
| | - Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
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20
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Kashyap MK, Abdel-Rahman O. Expression, regulation and targeting of receptor tyrosine kinases in esophageal squamous cell carcinoma. Mol Cancer 2018; 17:54. [PMID: 29455652 PMCID: PMC5817798 DOI: 10.1186/s12943-018-0790-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer is one of the most common types of cancer, which is a leading cause of cancer-related death worldwide. Based on histological behavior, it is mainly of two types (i) Esophageal squamous cell carcinoma (ESCC), and (ii) esophageal adenocarcinoma (EAD or EAC). In astronomically immense majority of malignancies, receptor tyrosine kinases (RTKs) have been kenned to play a consequential role in cellular proliferation, migration, and metastasis of the cells. The post-translational modifications (PTMs) including phosphorylation of tyrosine (pY) residue of the tyrosine kinase (TK) domain have been exploited for treatment in different malignancies. Lung cancer where pY residues of EGFR have been exploited for treatment purpose in lung adenocarcinoma patients, but we do not have such kind of felicitously studied and catalogued data in ESCC patients. Thus, the goal of this review is to summarize the studies carried out on ESCC to explore the role of RTKs, tyrosine kinase inhibitors, and their pertinence and consequentiality for the treatment of ESCC patients.
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Affiliation(s)
- Manoj Kumar Kashyap
- grid.449790.7School of Life and Allied Health Sciences, Glocal University, Saharanpur, UP 247121 India
- grid.430140.2Department of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh India
| | - Omar Abdel-Rahman
- 0000 0004 0621 1570grid.7269.aClinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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21
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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22
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Kashyap MK, Amaya-Chanaga CI, Kumar D, Simmons B, Huser N, Gu Y, Hallin M, Lindquist K, Yafawi R, Choi MY, Amine AA, Rassenti LZ, Zhang C, Liu SH, Smeal T, Fantin VR, Kipps TJ, Pernasetti F, Castro JE. Targeting the CXCR4 pathway using a novel anti-CXCR4 IgG1 antibody (PF-06747143) in chronic lymphocytic leukemia. J Hematol Oncol 2017; 10:112. [PMID: 28526063 PMCID: PMC5438492 DOI: 10.1186/s13045-017-0435-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The CXCR4-CXCL12 axis plays an important role in the chronic lymphocytic leukemia (CLL)-microenvironment interaction. Overexpression of CXCR4 has been reported in different hematological malignancies including CLL. Binding of the pro-survival chemokine CXCL12 with its cognate receptor CXCR4 induces cell migration. CXCL12/CXCR4 signaling axis promotes cell survival and proliferation and may contribute to the tropism of leukemia cells towards lymphoid tissues and bone marrow. Therefore, we hypothesized that targeting CXCR4 with an IgG1 antibody, PF-06747143, may constitute an effective therapeutic approach for CLL. METHODS Patient-derived primary CLL-B cells were assessed for cytotoxicity in an in vitro model of CLL microenvironment. PF-06747143 was analyzed for cell death induction and for its potential to interfere with the chemokine CXCL12-induced mechanisms, including migration and F-actin polymerization. PF-06747143 in vivo efficacy was determined in a CLL murine xenograft tumor model. RESULTS PF-06747143, a novel-humanized IgG1 CXCR4 antagonist antibody, induced cell death of patient-derived primary CLL-B cells, in presence or absence of stromal cells. Moreover, cell death induction by the antibody was independent of CLL high-risk prognostic markers. The cell death mechanism was dependent on CXCR4 expression, required antibody bivalency, involved reactive oxygen species production, and did not require caspase activation, all characteristics reminiscent of programmed cell death (PCD). PF-06747143 also induced potent B-CLL cytotoxicity via Fc-driven antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity activity (CDC). PF-06747143 had significant combinatorial effect with standard of care (SOC) agents in B-CLL treatment, including rituximab, fludarabine (F-ara-A), ibrutinib, and bendamustine. In a CLL xenograft model, PF-06747143 decreased tumor burden and improved survival as a monotherapy, and in combination with bendamustine. CONCLUSIONS We show evidence that PF-06747143 has biological activity in CLL primary cells, supporting a rationale for evaluation of PF-06747143 for the treatment of CLL patients.
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MESH Headings
- Animals
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/therapeutic use
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- CHO Cells
- Cell Death/drug effects
- Cricetulus
- Female
- Humans
- Immunoglobulin G/immunology
- Immunoglobulin G/therapeutic use
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Mice, Inbred BALB C
- Mice, SCID
- Reactive Oxygen Species/immunology
- Receptors, CXCR4/analysis
- Receptors, CXCR4/antagonists & inhibitors
- Receptors, CXCR4/immunology
- Signal Transduction/drug effects
- T-Lymphocytes/drug effects
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- Manoj K Kashyap
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
| | - Carlos I Amaya-Chanaga
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
| | - Brett Simmons
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
| | - Nanni Huser
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
| | - Yin Gu
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
| | - Max Hallin
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
- Present Address: Mirati Therapeutics, San Diego, CA, USA
| | - Kevin Lindquist
- Oncology Research & Development-Rinat Biotechnology Unit, Pfizer Worldwide Research & Development, South San Francisco, CA, USA
| | - Rolla Yafawi
- Drug Safety Research & Development, Pfizer Worldwide Research & Development, La Jolla, CA, USA
| | - Michael Y Choi
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
- CLL Research Consortium, and Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ale-Ali Amine
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
- CLL Research Consortium, and Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cathy Zhang
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
| | - Shu-Hui Liu
- Oncology Research & Development-Rinat Biotechnology Unit, Pfizer Worldwide Research & Development, South San Francisco, CA, USA
| | - Tod Smeal
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
- Present Address: Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Valeria R Fantin
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA
- Present Address: ORIC Pharmaceuticals, South San Francisco, CA, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA
- CLL Research Consortium, and Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Flavia Pernasetti
- Oncology Research & Development, Pfizer Worldwide Research & Development, 10646 Science Center Drive, San Diego, CA, 92121, USA.
| | - Januario E Castro
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA.
- CLL Research Consortium, and Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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23
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Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Charles Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali G, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U. Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response. Mol Cell Proteomics 2017; 16:891-910. [PMID: 28331001 PMCID: PMC5417828 DOI: 10.1074/mcp.m117.067439] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/24/2017] [Indexed: 02/05/2023] Open
Abstract
Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence 747LREA750, are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations. However, 30-40% of patients with EGFR mutations exhibit primary resistance to these TKIs, underscoring the unmet need of identifying additional biomarkers of treatment response. Here, we sought to characterize the dynamics of tyrosine phosphorylation upon EGFR TKI treatment of mutant EGFR-driven human lung adenocarcinoma cell lines with varying sensitivity to EGFR TKIs, erlotinib and afatinib. We employed stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative mass spectrometry to identify and quantify tyrosine phosphorylated peptides. The proportion of tyrosine phosphorylated sites that had reduced phosphorylation upon erlotinib or afatinib treatment correlated with the degree of TKI-sensitivity. Afatinib, an irreversible EGFR TKI, more effectively inhibited tyrosine phosphorylation of a majority of the substrates. The phosphosites with phosphorylation SILAC ratios that correlated with the TKI-sensitivity of the cell lines include sites on kinases, such as EGFR-Y1197 and MAPK7-Y221, and adaptor proteins, such as SHC1-Y349/350, ERRFI1-Y394, GAB1-Y689, STAT5A-Y694, DLG3-Y705, and DAPP1-Y139, suggesting these are potential biomarkers of TKI sensitivity. DAPP1, is a novel target of mutant EGFR signaling and Y-139 is the major site of DAPP1 tyrosine phosphorylation. We also uncovered several off-target effects of these TKIs, such as MST1R-Y1238/Y1239 and MET-Y1252/1253. This study provides unique insight into the TKI-mediated modulation of mutant EGFR signaling, which can be applied to the development of biomarkers of EGFR TKI response.
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Affiliation(s)
- Xu Zhang
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Tapan Maity
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Manoj K Kashyap
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Mukesh Bansal
- ¶Department of System Biology, Columbia University, New York, New York, 10032
- ‖PsychoGenics Inc., Tarrytown, New York, 10591
| | - Abhilash Venugopalan
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sahib Singh
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Shivangi Awasthi
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | | | | | - Natalya Belkina
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Stephanie Pitts
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Constance M Cultraro
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Shaojian Gao
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Guldal Kirkali
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Romi Biswas
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Raghothama Chaerkady
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
- **Medimmune LLC, Gaithersburg, Maryland, 20878
| | - Andrea Califano
- ¶Department of System Biology, Columbia University, New York, New York, 10032
| | - Akhilesh Pandey
- §Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Udayan Guha
- From the ‡Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892;
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24
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Barile E, Marconi GD, De SK, Baggio C, Gambini L, Salem AF, Kashyap MK, Castro JE, Kipps TJ, Pellecchia M. hBfl-1/hNOXA Interaction Studies Provide New Insights on the Role of Bfl-1 in Cancer Cell Resistance and for the Design of Novel Anticancer Agents. ACS Chem Biol 2017; 12:444-455. [PMID: 28026162 PMCID: PMC5320539 DOI: 10.1021/acschembio.6b00962] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Upregulation of antiapoptotic Bcl-2 proteins in certain tumors confers cancer cell resistance to chemotherapy or radiations. Members of the antiapoptotic Bcl-2 proteins, including Bcl-2, Mcl-1, Bcl-xL, Bcl-w, and Bfl-1, inhibit apoptosis by selectively binding to conserved α-helical regions, named BH3 domains, of pro-apoptotic proteins such as Bim, tBid, Bad, or NOXA. Five antiapoptotic proteins have been identified that interact with various selectivity with BH3 containing pro-apoptotic counterparts. Cancer cells present various and variable levels of these proteins, making the design of effective apoptosis based therapeutics challenging. Recently, BH3 profiling was introduced as a method to classify cancer cells based on their ability to resist apoptosis following exposure to selected BH3 peptides. However, these studies were based on binding affinities measured with model BH3 peptides and Bcl-2-proteins taken from mouse sequences. While the majority of these interactions are conserved between mice and humans, we found surprisingly that human NOXA binds to human Bfl-1 potently and covalently via conserved Cys residues, with over 2 orders of magnitude increased affinity over hMcl-1. Our data suggest that some assumptions of the original BH3 profiling need to be revisited and that perhaps further targeting efforts should be redirected toward Bfl-1, for which no suitable specific inhibitors or pharmacological tools have been reported. In this regard, we also describe the initial design and characterizations of novel covalent BH3-based agents that potently target Bfl-1. These molecules could provide a novel platform on which to design effective Bfl-1 targeting therapeutics.
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Affiliation(s)
- Elisa Barile
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Guya D. Marconi
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Surya K. De
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Luca Gambini
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Ahmed F. Salem
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Manoj K. Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- CLL Research
Consortium, and Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Januario E. Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- CLL Research
Consortium, and Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- CLL Research
Consortium, and Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Maurizio Pellecchia
- Division of Biomedical
Sciences, School of Medicine, University
of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
- Phone: (951)-827-7829. E-mail:
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25
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Kumar D, Kashyap MK, La Clair JJ, Villa R, Spaanderman I, Chien S, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Selectivity in Small Molecule Splicing Modulation. ACS Chem Biol 2016; 11:2716-2723. [PMID: 27499047 DOI: 10.1021/acschembio.6b00399] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dysregulation of RNA splicing is a molecular hallmark of disease, including different and often complex cancers. While gaining recognition as a target for therapeutic discovery, understanding the complex mechanisms guiding RNA splicing remains a challenge for chemical biology. The discovery of small molecule splicing modulators has recently enabled an evaluation of the mechanisms of aberrant splicing. We now report on three unique features within the selectivity of splicing modulators. First, we provide evidence that structural modifications within a splicing modulator can alter the splicing of introns in specific genes differently. These studies indicate that structure activity relationships not only have an effect on splicing activity but also include specificity for specific introns within different genes. Second, we find that these splicing modulators also target the mRNAs encoding components of the spliceosome itself. Remarkably, this effect includes the genes for the SF3B complex, a target of pladienolide B and related splicing modulators. Finally, we report on the first observation of a temporal phenomenon associated with small molecule splicing modulation. Combined, these three observations provide an important new perspective for the exploration of splicing modulation in terms of both future medicinal chemistry programs as well as understanding the key facets underlying its timing.
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Affiliation(s)
- Deepak Kumar
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Manoj K Kashyap
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Ide Spaanderman
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Stephen Chien
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Laura Z Rassenti
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Thomas J Kipps
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Januario E Castro
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
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26
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Abstract
Small-molecule splice modulators have recently been recognized for their clinical potential for diverse cancers. This, combined with their use as tools to study the importance of splice-regulated events and their association with disease, continues to fuel the discovery of new splice modulators. One of the key challenges found in the current class of materials arises from their instability, where rapid metabolic degradation can lead to off-target responses. We now describe the preparation of bench-stable splice modulators by adapting carbohydrate motifs as a central scaffold to provide rapid access to potent splice modulators.
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Affiliation(s)
- Sachin Dhar
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Brian León
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Justin C Hammons
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Zhe Yu
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Manoj K Kashyap
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Januario E Castro
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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27
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Choi MY, Kashyap MK, Kumar D. The chronic lymphocytic leukemia microenvironment: Beyond the B-cell receptor. Best Pract Res Clin Haematol 2016; 29:40-53. [PMID: 27742071 DOI: 10.1016/j.beha.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 07/03/2016] [Accepted: 08/04/2016] [Indexed: 02/07/2023]
Abstract
Malignant B cells accumulate in the peripheral blood, bone marrow, and lymphoid organs of patients with chronic lymphocytic leukemia (CLL). In the tissue compartments, CLL shape a protective microenvironment by coopting normal elements. The efficacy of drugs that target these interactions further underscores their importance in the pathogenesis of CLL. While the B cell receptor (BCR) pathway clearly plays a central role in the CLL microenvironment, there is also rationale to evaluate agents that inhibit other aspects or modulate the immune cells in the microenvironment. Here we review the main cellular components, soluble factors, and signaling pathways of the CLL microenvironment, and highlight recent clinical advances. As the BCR pathway is reviewed elsewhere, we focus on other aspects of the microenvironment.
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Affiliation(s)
- Michael Y Choi
- Moores Cancer Center, UCSD-Moores Cancer Center, La Jolla, 92093-0820, CA, USA.
| | - Manoj Kumar Kashyap
- Moores Cancer Center, UCSD-Moores Cancer Center, La Jolla, 92093-0820, CA, USA.
| | - Deepak Kumar
- Moores Cancer Center, UCSD-Moores Cancer Center, La Jolla, 92093-0820, CA, USA.
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28
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Kashyap MK, Kumar D, Jones H, Amaya-Chanaga CI, Choi MY, Melo-Cardenas J, Ale-Ali A, Kuhne MR, Sabbatini P, Cohen LJ, Shelat SG, Rassenti LZ, Kipps TJ, Cardarelli PM, Castro JE. Ulocuplumab (BMS-936564 / MDX1338): a fully human anti-CXCR4 antibody induces cell death in chronic lymphocytic leukemia mediated through a reactive oxygen species-dependent pathway. Oncotarget 2016; 7:2809-22. [PMID: 26646452 PMCID: PMC4823073 DOI: 10.18632/oncotarget.6465] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 02/07/2023] Open
Abstract
The CXCR4 receptor (Chemokine C-X-C motif receptor 4) is highly expressed in different hematological malignancies including chronic lymphocytic leukemia (CLL). The CXCR4 ligand (CXCL12) stimulates CXCR4 promoting cell survival and proliferation, and may contribute to the tropism of leukemia cells towards lymphoid tissues. Therefore, strategies targeting CXCR4 may constitute an effective therapeutic approach for CLL. To address that question, we studied the effect of Ulocuplumab (BMS-936564), a fully human IgG4 anti-CXCR4 antibody, using a stroma--CLL cells co-culture model. We found that Ulocuplumab (BMS-936564) inhibited CXCL12 mediated CXCR4 activation-migration of CLL cells at nanomolar concentrations. This effect was comparable to AMD3100 (Plerixafor--Mozobil), a small molecule CXCR4 inhibitor. However, Ulocuplumab (BMS-936564) but not AMD3100 induced apoptosis in CLL at nanomolar concentrations in the presence or absence of stromal cell support. This pro-apoptotic effect was independent of CLL high-risk prognostic markers, was associated with production of reactive oxygen species and did not require caspase activation. Overall, these findings are evidence that Ulocuplumab (BMS-936564) has biological activity in CLL, highlight the relevance of the CXCR4-CXCL12 pathway as a therapeutic target in CLL, and provide biological rationale for ongoing clinical trials in CLL and other hematological malignancies.
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Affiliation(s)
| | | | | | | | | | | | | | - Michelle R. Kuhne
- 3 Bristol-Myers Squibb, Department of Cell Biology and Physiology, Redwood City, CA, USA
| | - Peter Sabbatini
- 4 Department of Early Clinical and Translational Research, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Lewis J. Cohen
- 4 Department of Early Clinical and Translational Research, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Suresh G. Shelat
- 4 Department of Early Clinical and Translational Research, Bristol-Myers Squibb, Princeton, NJ, USA
| | | | - Thomas J. Kipps
- 1 UCSD-Moores Cancer Center, La Jolla, CA, USA
- 2 CLL Research Consortium, La Jolla, CA, USA
| | - Pina M. Cardarelli
- 3 Bristol-Myers Squibb, Department of Cell Biology and Physiology, Redwood City, CA, USA
| | - Januario E. Castro
- 1 UCSD-Moores Cancer Center, La Jolla, CA, USA
- 2 CLL Research Consortium, La Jolla, CA, USA
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Kashyap MK. Role of insulin-like growth factor-binding proteins in the pathophysiology and tumorigenesis of gastroesophageal cancers. Tumour Biol 2015; 36:8247-57. [PMID: 26369544 DOI: 10.1007/s13277-015-3972-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/21/2015] [Indexed: 02/07/2023] Open
Abstract
The insulin family of proteins include insulin-like growth factor binding proteins (IGFBPs) that are classified into two groups based on their differential affinities to IGFs: IGF high-affinity binding proteins (IGFBP1-6) and IGF low-affinity IGFBP-related proteins (IGFBP-rP1-10). IGFBPs interact with many proteins, including their canonical ligands insulin-like growth factor 1 (IGF-I) and IGF-II. Together with insulin-like growth factor 1 (IGF1) receptor (IGF1R), IGF2R, and ligands (IGF1 and IGF2), IGFBPs participate in a complex signaling axis called IGF-IGFR-IGFBP. Numerous studies have demonstrated that the IGF-IGFR-IGFBP axis is relevant in gastrointestinal (GI) and other cancers. The presence of different IGFBPs have been reported in gastrointestinal cancers, including esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAD or EAC), and gastric adenocarcinoma (GAD or GAC). A literature-based survey clearly indicates that an urgent need exists for a focused review of the role of IGFBPs in gastrointestinal cancers. The aim of this review is to present the biochemical and molecular characteristics of IGFBPs with an emphasis specifically on the role of these proteins in the pathophysiology and tumorigenesis of gastroesophageal cancers.
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Affiliation(s)
- Manoj K Kashyap
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA.
- Department of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.
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Wu X, Zahari MS, Ma B, Liu R, Renuse S, Sahasrabuddhe NA, Chen L, Chaerkady R, Kim MS, Zhong J, Jelinek C, Barbhuiya MA, Leal-Rojas P, Yang Y, Kashyap MK, Marimuthu A, Ling M, Fackler MJ, Merino V, Zhang Z, Zahnow CA, Gabrielson E, Stearns V, Roa JC, Sukumar S, Gill PS, Pandey A. Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget 2015; 6:29143-60. [PMID: 26356563 PMCID: PMC4745717 DOI: 10.18632/oncotarget.5020] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is the most prevalent cancer in women worldwide. About 15-20% of all breast cancers are triple negative breast cancer (TNBC) and are often highly aggressive when compared to other subtypes of breast cancers. To better characterize the biology that underlies the TNBC phenotype, we profiled the phosphotyrosine proteome of a panel of twenty-six TNBC cell lines using quantitative high resolution Fourier transform mass spectrometry. A heterogeneous pattern of tyrosine kinase activation was observed based on 1,789 tyrosine-phosphorylated peptides identified from 969 proteins. One of the tyrosine kinases, AXL, was found to be activated in a majority of aggressive TNBC cell lines and was accompanied by a higher level of AXL expression. High levels of AXL expression are correlated with a significant decrease in patient survival. Treatment of cells bearing activated AXL with a humanized AXL antibody inhibited cell proliferation and migration in vitro, and tumor growth in mice. Overall, our global phosphoproteomic analysis provided new insights into the heterogeneity in the activation status of tyrosine kinase pathways in TNBCs. Our approach presents an effective means of identifying important novel biomarkers and targets for therapy such as AXL in TNBC.
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Affiliation(s)
- Xinyan Wu
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Muhammad Saddiq Zahari
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Binyun Ma
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Ren Liu
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Santosh Renuse
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Nandini A. Sahasrabuddhe
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Lily Chen
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Raghothama Chaerkady
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Min-Sik Kim
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jun Zhong
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Christine Jelinek
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mustafa A. Barbhuiya
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Pamela Leal-Rojas
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 7 Department of Pathology, Center of Genetic and Immunological Studies (CEGIN) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Yi Yang
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Manoj Kumar Kashyap
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Arivusudar Marimuthu
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 5 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Min Ling
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mary Jo Fackler
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Vanessa Merino
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Zhen Zhang
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Cynthia A. Zahnow
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Edward Gabrielson
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
- 4 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Vered Stearns
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Juan Carlos Roa
- 8 Advanced Center for Chronic Diseases (ACCDiS), Department of Pathology Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Saraswati Sukumar
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Parkash S. Gill
- 6 Department of Medicine, University of Southern California, Los Angeles, USA
| | - Akhilesh Pandey
- 1 Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, USA
- 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- 3 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
- 4 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
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31
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Kashyap MK, Kumar D, Villa R, La Clair JJ, Benner C, Sasik R, Jones H, Ghia EM, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Targeting the spliceosome in chronic lymphocytic leukemia with the macrolides FD-895 and pladienolide-B. Haematologica 2015; 100:945-54. [PMID: 25862704 PMCID: PMC4486229 DOI: 10.3324/haematol.2014.122069] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/02/2015] [Indexed: 02/05/2023] Open
Abstract
RNA splicing plays a fundamental role in human biology. Its relevance in cancer is rapidly emerging as demonstrated by spliceosome mutations that determine the prognosis of patients with hematologic malignancies. We report studies using FD-895 and pladienolide-B in primary leukemia cells derived from patients with chronic lymphocytic leukemia and leukemia-lymphoma cell lines. We found that FD-895 and pladienolide-B induce an early pattern of mRNA intron retention - spliceosome modulation. This process was associated with apoptosis preferentially in cancer cells as compared to normal lymphocytes. The pro-apoptotic activity of these compounds was observed regardless of poor prognostic factors such as Del(17p), TP53 or SF3B1 mutations and was able to overcome the protective effect of culture conditions that resemble the tumor microenvironment. In addition, the activity of these compounds was observed not only in vitro but also in vivo using the A20 lymphoma murine model. Overall, these findings give evidence for the first time that spliceosome modulation is a valid target in chronic lymphocytic leukemia and provide an additional rationale for the development of spliceosome modulators for cancer therapy.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Cell Line, Tumor
- Epoxy Compounds/pharmacology
- Gene Expression
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Macrolides/pharmacology
- Mice
- Mice, Inbred BALB C
- Mutation
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- RNA Splicing/drug effects
- RNA Splicing Factors
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Spliceosomes/drug effects
- Survival Analysis
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Manoj K Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Chris Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Harrison Jones
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Januario E Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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32
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Pawar H, Srikanth SM, Kashyap MK, Sathe G, Chavan S, Singal M, Manju HC, Kumar KVV, Vijayakumar M, Sirdeshmukh R, Pandey A, Prasad TSK, Gowda H, Kumar RV. Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. ScientificWorldJournal 2015; 2015:325721. [PMID: 26788548 PMCID: PMC4691646 DOI: 10.1155/2015/325721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
The development of esophageal squamous cell carcinoma (ESCC) is poorly understood and the major regulatory molecules involved in the process of tumorigenesis have not yet been identified. We had previously employed a quantitative proteomic approach to identify differentially expressed proteins in ESCC tumors. A total of 238 differentially expressed proteins were identified in that study including S100 calcium binding protein A9 (S100A9) as one of the major downregulated proteins. In the present study, we carried out immunohistochemical validation of S100A9 in a large cohort of ESCC patients to determine the expression and subcellular localization of S100A9 in tumors and adjacent normal esophageal epithelia. Downregulation of S100A9 was observed in 67% (n = 192) of 288 different ESCC tumors, with the most dramatic downregulation observed in the poorly differentiated tumors (99/111). Expression of S100A9 was restricted to the prickle and functional layers of normal esophageal mucosa and localized predominantly in the cytoplasm and nucleus whereas virtually no expression was observed in the tumor and stromal cells. This suggests the important role that S100A9 plays in maintaining the differentiated state of epithelium and suggests that its downregulation may be associated with increased susceptibility to tumor formation.
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Affiliation(s)
- Harsh Pawar
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 2Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
- 4Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Srinivas M. Srikanth
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 5Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Manoj Kumar Kashyap
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 7Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 8Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0960, USA
| | - Gajanan Sathe
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sandip Chavan
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Mukul Singal
- 9Government Medical College and Hospital, Sector 32, Chandigarh 160030, India
| | - H. C. Manju
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
| | | | - M. Vijayakumar
- 10Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
| | - Ravi Sirdeshmukh
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- 6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 7Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 11Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 12Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - T. S. Keshava Prasad
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 5Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Harsha Gowda
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- *Harsha Gowda: and
| | - Rekha V. Kumar
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
- *Rekha V. Kumar:
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Abstract
Targeting the spliceosome with small molecule inhibitors provides a new avenue to target cancer by intercepting alternate splicing pathways. Although our understanding of alternate mRNA splicing remains poorly understood, it provides an escape pathway for many cancers resistant to current therapeutics. These findings have encouraged recent academic and industrial efforts to develop natural product spliceosome inhibitors, including FD-895 (1a), pladienolide B (1b), and pladienolide D (1c), into next-generation anticancer drugs. The present study describes the application of semisynthesis and total synthesis to reveal key structure-activity relationships for the spliceosome inhibition by 1a. This information is applied to deliver new analogs with improved stability and potent activity at inhibiting splicing in patient derived cell lines.
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Affiliation(s)
- Reymundo Villa
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Manoj Kumar Kashyap
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA 92093-0820
| | - Deepak Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA 92093-0820
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA 92093-0820
- Department of Medicine, University of California San Diego, La Jolla, California, USA 92093-0820
| | - Januario E. Castro
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA 92093-0820
- Department of Medicine, University of California San Diego, La Jolla, California, USA 92093-0820
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Corresponding Author: Phone +1 858-534-5673.
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Kashyap MK, Pawar HA, Keerthikumar S, Sharma J, Goel R, Mahmood R, Kumar MV, Kumar KVV, Pandey A, Kumar RV, Prasad TSK, Harsha HC. Evaluation of protein expression pattern of stanniocalcin 2, insulin-like growth factor-binding protein 7, inhibin beta A and four and a half LIM domains 1 in esophageal squamous cell carcinoma. Cancer Biomark 2013; 12:1-9. [PMID: 23321464 DOI: 10.3233/cbm-120289] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The pathogenesis of esophageal squamous cell carcinoma (ESCC) involves both genetic and environmental factors. Previously, we have carried out gene and protein expression profiling of ESCC using DNA microarrays and mass spectrometry-based quantitative proteomics, respectively. These studies resulted in identification of several potential biomarkers of ESCC, some with known reports of differential expression in the scientific literature and others that were novel observations from our studies. We report systematic validation of selected markers from our studies on a larger cohort of cancer tissue sections by immunohistochemical labeling of tissue microarrays. We have validated expression of insulin-like growth factor-binding protein 7 (IGFBP7), stanniocalcin 2 (STC2), inhibin beta A (INHBA) and four and a half LIM domains 1 (FHL1). Immunohistochemical labeling with anti-stanniocalcin 2 antibody demonstrated its overexpression in 132/140 (94%) cases, IGFBP7 showed overexpression in 127/140 (91%) cases and overexpression of INHBA was observed in 62/105 (59%) of ESCC cases. In contrast, FHL1 expression was observed only in 12/143 (8%) of ESCC cases suggesting its possible involvement in tumor suppression. These data suggest that IGFBP7, INHBA, STC2 and FHL1 might play an important role in ESCC tumorigenesis, which can be explored in future studies. Overall, our findings open up new avenues for development of novel therapeutics and/or diagnostic approaches in ESCC.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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35
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Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, Sekhar NR, Katte TV, Pinto SM, Srikanth SM, Kumar P, Pawar H, Kashyap MK, Maharudraiah J, Ashktorab H, Smoot DT, Ramaswamy G, Kumar RV, Cheng Y, Meltzer SJ, Roa JC, Chaerkady R, Prasad TK, Harsha HC, Chatterjee A, Pandey A. SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clin Appl 2013; 7:355-66. [PMID: 23161554 PMCID: PMC3804263 DOI: 10.1002/prca.201200069] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/24/2012] [Accepted: 10/25/2012] [Indexed: 02/05/2023]
Abstract
PURPOSE Gastric cancer is a commonly occurring cancer in Asia and one of the leading causes of cancer deaths. However, there is no reliable blood-based screening test for this cancer. Identifying proteins secreted from tumor cells could lead to the discovery of clinically useful biomarkers for early detection of gastric cancer. EXPERIMENTAL DESIGN A SILAC-based quantitative proteomic approach was employed to identify secreted proteins that were differentially expressed between neoplastic and non-neoplastic gastric epithelial cells. Proteins from the secretome were subjected to SDS-PAGE and SCX-based fractionation, followed by mass spectrometric analysis on an LTQ-Orbitrap Velos mass spectrometer. Immunohistochemical labeling was employed to validate a subset of candidates using tissue microarrays. RESULTS We identified 2205 proteins in the gastric cancer secretome of which 263 proteins were overexpressed greater than fourfold in gastric cancer-derived cell lines as compared to non-neoplastic gastric epithelial cells. Three candidate proteins, proprotein convertase subtilisin/kexin type 9 (PCSK9), lectin mannose binding 2 (LMAN2), and PDGFA-associated protein 1 (PDAP1) were validated by immunohistochemical labeling. CONCLUSIONS AND CLINICAL RELEVANCE We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Nandini A. Sahasrabuddhe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577 451, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India
| | - Nirujogi Raja Sekhar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Teesta V. Katte
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Srinivas M. Srikanth
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington DC 20060, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical College, Nashville 37208, Tennessee, USA
| | - Girija Ramaswamy
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen J Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- To whom correspondence should be addressed: Akhilesh Pandey M.D., Ph.D., McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205. Tel.: 410-502-6662; Fax: 410-502-7544;
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Pawar H, Maharudraiah J, Kashyap MK, Sharma J, Srikanth SM, Choudhary R, Chavan S, Sathe G, Manju HC, Kumar KVV, Vijayakumar M, Sirdeshmukh R, Harsha HC, Prasad TSK, Pandey A, Kumar RV. Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochem 2013; 115:89-99. [PMID: 22560086 DOI: 10.1016/j.acthis.2012.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/04/2012] [Accepted: 04/15/2012] [Indexed: 02/07/2023]
Abstract
Early events in the development of esophageal squamous cell carcinoma (ESCC) are poorly understood and many of the key molecules involved have not yet been identified. We previously used isobaric tags for a relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach to identify differentially expressed proteins in ESCC tissue as compared to the adjacent normal mucosa. Cornulin was identified as one of the major downregulated molecules in ESCC. Cornulin is a member of the S100 fused-type protein family, which has an EF-hand calcium binding motif and multiple tandem repeats of specific peptide motifs. Cornulin was 5-fold downregulated in ESCC as compared to normal epithelium mirroring our previous findings in a gene expression study of ESCC. In the present study, we performed immunohistochemical validation of cornulin (CRNN) in a larger set of patients with ESCC. Downregulation of cornulin was observed in 89% (n=239) of 266 different ESCC tissues arrayed on tissue microarrays (TMAs). Expression of cornulin was observed in the prickle and functional cell layers of normal esophageal mucosa, localized predominantly in the cytoplasm and perinuclear region. The large majority of ESCC cases had little or no expression of cornulin in the carcinoma or stroma. These findings suggest that cornulin is an important molecule in normal esophageal pathology and is likely lost during the conversion of normal to neoplastic epithelium.
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Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
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37
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Kim MS, Kuppireddy SV, Sakamuri S, Singal M, Getnet D, Harsha HC, Goel R, Balakrishnan L, Jacob HKC, Kashyap MK, Tankala SG, Maitra A, Iacobuzio-Donahue CA, Jaffee E, Goggins MG, Velculescu VE, Hruban RH, Pandey A. Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). J Proteome Res 2012; 11:5556-63. [PMID: 22985314 PMCID: PMC3565537 DOI: 10.1021/pr300483r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tissue microarrays have become a valuable tool for high-throughput analysis using immunohistochemical labeling. However, the large majority of biochemical studies are carried out in cell lines to further characterize candidate biomarkers or therapeutic targets with subsequent studies in animals or using primary tissues. Thus, cell line-based microarrays could be a useful screening tool in some situations. Here, we constructed a cell microarray (CMA) containing a panel of 40 pancreatic cancer cell lines available from American Type Culture Collection in addition to those locally available at Johns Hopkins. As proof of principle, we performed immunocytochemical labeling of an epithelial cell adhesion molecule (Ep-CAM), a molecule generally expressed in the epithelium, on this pancreatic cancer CMA. In addition, selected molecules that have been previously shown to be differentially expressed in pancreatic cancer in the literature were validated. For example, we observed strong labeling of CA19-9 antigen, a prognostic and predictive marker for pancreatic cancer. We also carried out a bioinformatics analysis of a literature curated catalog of pancreatic cancer biomarkers developed previously by our group and identified two candidate biomarkers, HLA class I and transmembrane protease, serine 4 (TMPRSS4), and examined their expression in the cell lines represented on the pancreatic cancer CMAs. Our results demonstrate the utility of CMAs as a useful resource for rapid screening of molecules of interest and suggest that CMAs can become a universal standard platform in cancer research.
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Affiliation(s)
- Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sarada V. Kuppireddy
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sruthi Sakamuri
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Mukul Singal
- Government Medical College and Hospital, Chandigarh 160030, India
| | - Derese Getnet
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Harrys K. C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | - Anirban Maitra
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
| | - Christine A. Iacobuzio-Donahue
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
| | - Elizabeth Jaffee
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
| | - Michael G. Goggins
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
| | - Victor E. Velculescu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland 21231, United States
| | - Ralph H. Hruban
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Pathology Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland 21231, United States
- Corresponding Author . Fax: +1-410-502-7544.
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Kumar GSS, Venugopal AK, Kashyap MK, Raju R, Marimuthu A, Palapetta SM, Subbanayya Y, Goel R, Chawla A, Dikshit JB, Tata P, Harsha HC, Maharudraiah J, Ramachandra YL, Satishchandra P, Prasad TSK, Pandey A, Mahadevan A, Shankar SK. Gene Expression Profiling of Tuberculous Meningitis Co-infected with HIV. J Proteomics Bioinform 2012; 5:235-244. [PMID: 27053842 PMCID: PMC4820295 DOI: 10.4172/jpb.1000243] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tuberculous meningitis (TBM) is a fatal form of Mycobacterium tuberculosis infection of the central nervous system (CNS). The similarities in the clinical and radiological findings in TBM cases with or without HIV make the diagnosis very challenging. Identification of genes, which are differentially expressed in brain tissues of HIV positive and HIV negative TBM patients, would enable better understanding of the molecular aspects of the infection and would also serve as an initial platform to evaluate potential biomarkers. Here, we report the identification of 796 differentially regulated genes in brain tissues of TBM patients co-infected with HIV using oligonucleotide DNA microarrays. We also performed immunohistochemical validation and confirmed the abundance of four gene products-glial fibrillary acidic protein (GFAP), serpin peptidase inhibitor, clade A member 3 (SERPINA3), thymidine phosphorylase (TYMP/ECGF1) and heat shock 70 kDa protein 8 (HSPA8). Our study paves the way for understanding the mechanism of TBM in HIV positive patients and for further validation of potential disease biomarkers.
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Affiliation(s)
- Ghantasala S. Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | - Abhilash K. Venugopal
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Rajesh Raju
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Shyam Mohan Palapetta
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014, India
| | - Yashwanth Subbanayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | - Ankit Chawla
- Armed Forces Medical College, Pune-411040, India
| | | | - Pramila Tata
- Strand Life Sciences, Bangalore 560024, Karnataka, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Y. L. Ramachandra
- Department of Biotechnology, Kuvempu University, Shimoga 577451, India
| | | | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding authors: Akhilesh Pandey, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, USA, Tel: 410-502-6662; Fax: 410-502-7544; , S. K. Shankar, Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India, Tel: 91-080-26995001/5002; Fax: 91-080-26564830;
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - S. K. Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
- Corresponding authors: Akhilesh Pandey, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, USA, Tel: 410-502-6662; Fax: 410-502-7544; , S. K. Shankar, Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India, Tel: 91-080-26995001/5002; Fax: 91-080-26564830;
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Telikicherla D, Marimuthu A, Kashyap MK, Ramachandra YL, Mohan S, Roa JC, Maharudraiah J, Pandey A. Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. Clin Proteomics 2012; 9:7. [PMID: 22709790 PMCID: PMC3439379 DOI: 10.1186/1559-0275-9-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/08/2012] [Indexed: 02/07/2023] Open
Abstract
The molecular events that lead to malignant transformation and subsequent metastasis of breast carcinoma include alterations in the cells at genome, transcriptome and proteome levels. In this study, we used publicly available gene expression databases to identify those candidate genes which are upregulated at the mRNA level in breast cancers but have not been systematically validated at the protein level. Based on an extensive literature search, we identified ribosome binding protein 1 (RRBP1) as a candidate that is upregulated at the mRNA level in five different studies but its protein expression had not been investigated. Immunohistochemical labeling of breast cancer tissue microarrays was carried out to determine the expression of RRBP1 in a large panel of breast cancers. We found that RRBP1 was overexpressed in 84% (177/219) of breast carcinoma cases tested. The subcellular localization of RRBP1 was mainly observed to be in the cytoplasm with intense staining in the perinuclear region. Our findings suggest that RRBP1 is an interesting molecule that can be further studied for its potential to serve as a breast cancer biomarker. This study also demonstrates how the integration of biological data from available resources in conjunction with systematic evaluation approaches can be successfully applied to clinical proteomics.
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Affiliation(s)
- Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
| | - Y L Ramachandra
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577451, India
| | - Sujatha Mohan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Research Unit for Immunoinformatics, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
- Department of Pathology and Laboratory Medicine, Icon Hospitals, Bangalore 560027, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, USA
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40
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Telikicherla D, Maharudraiah J, Pawar H, Marimuthu A, Kashyap MK, Ramachandra YL, Roa JC, Pandey A. Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. J Proteomics Bioinform 2012; 5:122-126. [PMID: 26843789 PMCID: PMC4734396 DOI: 10.4172/jpb.1000223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gene expression profiling studies on breast cancer have generated catalogs of differentially expressed genes. However, many of these genes have not been investigated for their expression at the protein level. It is possible to systematically evaluate such genes in a high-throughput fashion for their overexpression at the protein level using breast cancer tissue microarrays. Our strategy involved integration of information from publicly available repositories of gene expression to prepare a list of genes upregulated at the mRNA level in breast cancer followed by curation of the published literature to identify those genes that were not tested for overexpression at the protein level. We identified Kinesin Associated Protein 3 (KIFAP3) as one such molecule for further validation at the protein level. Immunohistochemical labeling of KIFAP3 using breast cancer tissue microarrays revealed overexpression of KIFAP3 protein in 84% (240/285) of breast cancers indicating the utility of our integrated approach of combining computational analysis with experimental biology.
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Affiliation(s)
- Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta-577451, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Department of Pathology, Raja Rajeshwari Medical College and Hospital, Bangalore-560074, India
- Manipal University, Madhav Nagar, Manipal-576104, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
- Rajiv Gandhi University of Health Sciences, Bangalore-560041, India
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore-560029, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore-560 066, India
| | - Y. L. Ramachandra
- Department of Biotechnology, Kuvempu University, Shankaraghatta-577451, India
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author: Akhilesh Pandey M.D., Ph.D., McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, USA, Tel: 410-502-6662; Fax: 410-502-7544;
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41
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Pawar H, Kashyap MK, Sahasrabuddhe NA, Renuse S, Harsha HC, Kumar P, Sharma J, Kandasamy K, Marimuthu A, Nair B, Rajagopalan S, Maharudraiah J, Premalatha CS, Kumar KVV, Vijayakumar M, Chaerkady R, Prasad TSK, Kumar RV, Pandey A. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biol Ther 2011; 12:510-22. [PMID: 21743296 PMCID: PMC3218592 DOI: 10.4161/cbt.12.6.16833] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the top ten most frequent malignancies worldwide. In this study, our objective was to identify potential biomarkers for ESCC through a quantitative proteomic approach using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. We compared the protein expression profiles of ESCC tumor tissues with the corresponding adjacent normal tissue from ten patients. LC-MS/MS analysis of strong cation exchange chromatography fractions was carried out on an Accurate Mass QTOF mass spectrometer, which led to the identification of 687 proteins. In all, 257 proteins were identified as differentially expressed in ESCC as compared to normal. We found several previously known protein biomarkers to be upregulated in ESCC including thrombospondin 1 (THBS1), periostin 1 (POSTN) and heat shock 70 kDa protein 9 (HSPA9) confirming the validity of our approach. In addition, several novel proteins that had not been reported previously were identified in our screen. These novel biomarker candidates included prosaposin (PSAP), plectin 1 (PLEC1) and protein disulfide isomerase A 4 (PDIA4) that were further validated to be overexpressed by immunohistochemical labeling using tissue microarrays. The success of our study shows that this mass spectrometric strategy can be applied to cancers in general to develop a panel of candidate biomarkers, which can then be validated by other techniques.
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Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
- Department of Pathology; Kidwai Memorial Institute of Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Nandini A Sahasrabuddhe
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Santosh Renuse
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - HC Harsha
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Praveen Kumar
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Jyoti Sharma
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
| | - Kumaran Kandasamy
- Institute of Bioinformatics; International Technology Park; Bangalore, India
| | - Arivusudar Marimuthu
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
| | - Bipin Nair
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
| | | | - Jagadeesha Maharudraiah
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- RajaRajeswari Medical College; Bangalore, India
| | | | | | - M Vijayakumar
- Department of Surgical Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Raghothama Chaerkady
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Thotterthodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore, India
- Manipal University; Manipal, India
- Centre of Excellence in Bioinformatics; School of Life Sciences; Pondicherry University; Pondicherry, India
| | - Rekha V Kumar
- Department of Pathology; Kidwai Memorial Institute of Oncology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Oncology; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Pathology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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42
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Marimuthu A, Jacob HK, Jakharia A, Subbannayya Y, Keerthikumar S, Kashyap MK, Goel R, Balakrishnan L, Dwivedi S, Pathare S, Dikshit JB, Maharudraiah J, Singh S, Sameer Kumar GS, Vijayakumar M, Veerendra Kumar KV, Premalatha CS, Tata P, Hariharan R, Roa JC, Prasad T, Chaerkady R, Kumar RV, Pandey A. Gene Expression Profiling of Gastric Cancer. J Proteomics Bioinform 2011; 4:74-82. [PMID: 27030788 PMCID: PMC4809432 DOI: pmid/27030788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent's whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Harrys K.C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Aniruddha Jakharia
- Department of Zoology, Gauhati University, Guwahati 781014, Assam, India
- Imgenex India, Bhubaneswar 751024, Orissa, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore, 560041, Karnataka, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Sutopa Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam 690525, Kerala, India
| | | | | | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- RajaRajeswari Medical college, Bangalore, 560074, India
| | - Sujay Singh
- Imgenex India, Bhubaneswar 751024, Orissa, India
- Imgenex Corporation, San Diego 92121, California, USA
| | - Ghantasala S Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - M. Vijayakumar
- Departments of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
| | | | | | - Pramila Tata
- Strand Life Sciences, Bangalore 560024, Karnataka, India
| | | | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - T.S.K Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
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Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TSK, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biol Ther 2010; 10:796-810. [PMID: 20686364 PMCID: PMC3093916 DOI: 10.4161/cbt.10.8.12914] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The identification of secreted proteins that are differentially expressed between non-neoplastic and esophageal squamous cell carcinoma (ESCC) cells can provide potential biomarkers of ESCC. We used a SILAC-based quantitative proteomic approach to compare the secretome of ESCC cells with that of non-neoplastic esophageal squamous epithelial cells. Proteins were resolved by SDS-PAGE, and tandem mass spectrometry analysis (LC-MS/MS) of in-gel trypsin-digested peptides was carried out on a high-accuracy qTOF mass spectrometer. In total, we identified 441 proteins in the combined secretomes, including 120 proteins with > 2-fold upregulation in the ESCC secretome vs. that of non-neoplastic esophageal squamous epithelial cells. In this study, several potential protein biomarkers previously known to be increased in ESCC including matrix metalloproteinase 1, transferrin receptor, and transforming growth factor beta-induced 68 kDa were identified as overexpressed in the ESCC-derived secretome. In addition, we identified several novel proteins that have not been previously reported to be associated with ESCC. Among the novel candidate proteins identified, protein disulfide isomerase family a member 3 (PDIA3), GDP dissociation inhibitor 2 (GDI2), and lectin galactoside binding soluble 3 binding protein (LGALS3BP) were further validated by immunoblot analysis and immunohistochemical labeling using tissue microarrays. This tissue microarray analysis showed overexpression of protein disulfide isomerase family a member 3, GDP dissociation inhibitor 2, and lectin galactoside binding soluble 3 binding protein in 93%, 93% and 87% of 137 ESCC cases, respectively. Hence, we conclude that these potential biomarkers are excellent candidates for further evaluation to test their role and efficacy in the early detection of ESCC.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biotechnology; Kuvempu University; Shimoga, India
| | - HC Harsha
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Department of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
| | - Nandini A Sahasrabuddhe
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Manipal University; Manipal, Karnataka India
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Manipal University; Manipal, Karnataka India
| | | | | | - Kumaran Kandasamy
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biotechnology; Kuvempu University; Shimoga, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- Rajiv Gandhi University of Health Sciences; Bangalore, India
| | | | - Riaz Mahmood
- Department of Biotechnology; Kuvempu University; Shimoga, India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park; Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Stephen J Meltzer
- Department of Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Oncology; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Rekha V Kumar
- Department of Pathology; Kidwai Memorial Institute of Oncology; Bangalore, India
| | - Anil K Rustgi
- Division of Gastroenterology; Department of Medicine and Genetics; Abramson Cancer Center; University of Pennsylvania; Philadelphia, Pennsylvania USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore, MD USA
- Department of Pathology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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Kashyap MK, Marimuthu A, Peri S, Kumar GSS, Jacob HK, Prasad TSK, Mahmood R, Kumar KVV, Kumar MV, Meltzer SJ, Montgomery EA, Kumar RV, Pandey A. Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers (Basel) 2010; 2:133-42. [PMID: 24281036 PMCID: PMC3827595 DOI: 10.3390/cancers2010133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/08/2010] [Accepted: 02/20/2010] [Indexed: 02/07/2023] Open
Abstract
To identify biomarkers for early detection for esophageal squamous cell carcinoma (ESCC), we previously carried out a genome-wide gene expression profiling study using an oligonucleotide microarray platform. This analysis led to identification of several transcripts that were significantly upregulated in ESCC compared to the adjacent normal epithelium. In the current study, we performed immunohistochemical analyses of protein products for two candidates genes identified from the DNA microarray analysis, periostin (POSTN) and lumican (LUM), using tissue microarrays. Increased expression of both periostin and lumican was observed in 100% of 137 different ESCC samples arrayed on tissue microarrays. Increased expression of periostin and lumican was observed in carcinoma as well as in stromal cell in the large majority of cases. These findings suggest that these candidates can be investigated in the sera of ESCC patients using ELISA or multiple reaction monitoring (MRM) type assays to further explore their utility as biomarkers.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Suraj Peri
- Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA; E-Mail: (S.P.)
| | - Ghantasala S. Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - Harrys K.C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; E-Mails: (M.K.K.); (A.M.); (G.S.S.K.); (T.S.K.P.)
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Riaz Mahmood
- Department of Biotechnology, Kuvempu University, Shimoga District, Karnataka 577451, India; E-Mail: (R.M.)
| | - K. V. Veerendra Kumar
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India; E-Mails: (K.V.V.K.); (M.V.)
| | - M. Vijaya Kumar
- Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India; E-Mails: (K.V.V.K.); (M.V.)
| | - Stephen J. Meltzer
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (S.J.M.)
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth A. Montgomery
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (E.A.M.)
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029, India
- Authors to whom correspondence should be addressed; E-Mail: (A.P.) ; (R.V.K.); Tel.: +1-410-502-6662; Fax: +1-410-502-7544 (A.P.); Tel.: +91-80-656-708; Fax: +91-80-6560723 (R.V.K.).
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (H.K.C.J.)
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; E-Mail: (E.A.M.)
- Authors to whom correspondence should be addressed; E-Mail: (A.P.) ; (R.V.K.); Tel.: +1-410-502-6662; Fax: +1-410-502-7544 (A.P.); Tel.: +91-80-656-708; Fax: +91-80-6560723 (R.V.K.).
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Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LDN, Goel R, Mathivanan S, Marimuthu A, Kashyap M, Vizza RF, Mayer RJ, DeCaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. A compendium of potential biomarkers of pancreatic cancer. PLoS Med 2009; 6:e1000046. [PMID: 19360088 PMCID: PMC2661257 DOI: 10.1371/journal.pmed.1000046] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Akhilesh Pandey and colleagues describe a compendium of potential biomarkers that can be systematically validated by the pancreatic cancer community.
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Affiliation(s)
- H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kumaran Kandasamy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Prathibha Ranganathan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sandhya Rani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Subhashri Ramabadran
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sashikanth Gollapudi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Sutopa B. Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Deepthi Telikicherla
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | | | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Suresh Mathivanan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal University, Manipal, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Manoj Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Robert F. Vizza
- The Lustgarten Foundation for Pancreatic Cancer Research, Bethpage, New York, United States of America
| | - Robert J. Mayer
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - James A. DeCaprio
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samir M. Hanash
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ralph H. Hruban
- Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
- Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
- * E-mail:
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Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. Temporal analysis of neural differentiation using quantitative proteomics. J Proteome Res 2009; 8:1315-26. [PMID: 19173612 PMCID: PMC2693473 DOI: 10.1021/pr8006667] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ability to derive neural progenitors, differentiated neurons and glial cells from human embryonic stem cells (hESCs) with high efficiency holds promise for a number of clinical applications. However, investigating the temporal events is crucial for defining the underlying mechanisms that drive this process of differentiation along different lineages. We carried out quantitative proteomic profiling using a multiplexed approach capable of analyzing eight different samples simultaneously to monitor the temporal dynamics of protein abundance as human embryonic stem cells differentiate into motor neurons or astrocytes. With this approach, a catalog of approximately 1200 proteins along with their relative quantitative expression patterns was generated. The differential expression of the large majority of these proteins has not previously been reported or studied in the context of neural differentiation. As expected, two of the widely used markers of pluripotency, alkaline phosphatase (ALPL) and LIN28, were found to be downregulated during differentiation, while S-100 and tenascin C were upregulated in astrocytes. Neurofilament 3 protein, doublecortin and CAM kinase-like 1 and nestin proteins were upregulated during motor neuron differentiation. We identified a number of proteins whose expression was largely confined to specific cell types, embryonic stem cells, embryoid bodies and differentiating motor neurons. For example, glycogen phosphorylase (PYGL) and fatty acid binding protein 5 (FABP5) were enriched in ESCs, while beta spectrin (SPTBN5) was highly expressed in embryoid bodies. Karyopherin, heat shock 27 kDa protein 1 and cellular retinoic acid binding protein 2 (CRABP2) were upregulated in differentiating motor neurons but were downregulated in mature motor neurons. We validated some of the novel markers of the differentiation process using immunoblotting and immunocytochemical labeling. To our knowledge, this is the first large-scale temporal proteomic profiling of human stem cell differentiation into neural cell types highlighting proteins with limited or undefined roles in neural fate.
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Affiliation(s)
- Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
- To whom correspondence should be addressed. E-mail: and E-mail:
| | - Candace L. Kerr
- Institute for Cell Engineering, Department of Obstetrics and Gynecology, Baltimore, MD, 21205, USA
- To whom correspondence should be addressed. E-mail: and E-mail:
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
| | - Dhanashree S. Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
| | - Marjan Gucek
- Institute of Basic Biomedical Sciences, Baltimore, MD, 21205, USA
| | - John D. Gearhart
- Institute for Cell Engineering, Department of Obstetrics and Gynecology, Baltimore, MD, 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Baltimore, MD, 21205, USA
- Department of Pathology and Oncology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
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Kashyap MK, Marimuthu A, Kishore CJH, Peri S, Keerthikumar S, Prasad TSK, Mahmood R, Rao S, Ranganathan P, Sanjeeviah RC, Vijayakumar M, Kumar KVV, Montgomery EA, Kumar RV, Pandey A. Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther 2009; 8:36-46. [PMID: 18981721 DOI: 10.4161/cbt.8.1.7090] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer of the esophagus is of two main types, each with distinct etiological and pathological characteristics. Esophageal squamous cell carcinoma (ESCC) is predominant type of esophageal cancers worldwide comprising almost 95% of cases. While ESCC is prevalent in the developing world, esophageal adenocarcinoma is commonly seen in the developed country, usually in association with Barrett's esophagus. In spite of its higher prevalence, ESCC has not been studied as intensively as esophageal adenocarcinoma. ESCC and esophageal adenocarcinoma are common cancers worldwide with poor survival rate among patients mainly because both of these cancers lack early biomarkers of identification. Molecular mechanisms contributing to initiation and progression of esophageal squamous cell carcinoma are still poorly understood. Development of DNA microarray technology allows high-throughput identification of gene expression profiles in cancers. In order to identify molecules as candidates for early diagnosis and/or as therapeutic targets, we analyzed the mRNA expression profiles of 20 cases of ESCC using whole genome DNA microarrays. A total of 2,235 genes were differentially regulated in the tumors as compared to the corresponding adjacent normal epithelium of which 881 were significantly upregulated. We validated two molecules that were not previously reported to be overexpressed in ESCC, oral cancer overexpressed 2 (ORAOV2) and fibroblast activation protein (FAP), by immunohistochemical labeling of tissue microarrays and archival tissue sections and found that they were overexpressed in 98% (116/118) and 68% (79/116) of cases, respectively. By gene enrichment analysis, we identified significant downregulation of several genes in the arachidonic acid metabolic pathway. Overall, using this approach we have identified a number of promising novel candidates that can be validated further for their potential to serve as biomarkers for ESCC.
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Affiliation(s)
- Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009; 37:D767-72. [PMID: 18988627 PMCID: PMC2686490 DOI: 10.1093/nar/gkn892] [Citation(s) in RCA: 2223] [Impact Index Per Article: 148.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.
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Affiliation(s)
- T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Renu Goel
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kumaran Kandasamy
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Shivakumar Keerthikumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sameer Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Suresh Mathivanan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Deepthi Telikicherla
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Beema Shafreen
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Abhilash Venugopal
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sutopa Banerjee
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Devi S. Somanathan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Aimy Sebastian
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sandhya Rani
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Somak Ray
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - C. J. Harrys Kishore
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sashi Kanth
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mukhtar Ahmed
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Riaz Mohmood
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Y. L. Ramachandra
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - V. Krishna
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - B. Abdul Rahiman
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sujatha Mohan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Prathibha Ranganathan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Subhashri Ramabadran
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka, India, McKusick-Nathans Institute of Genetic Medicine, Department of Biological Chemistry and Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
- *To whom correspondence should be addressed. Tel: +410 502 6662; Fax: +410 502 7544;
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Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A 2008; 105:14112-7. [PMID: 18776048 PMCID: PMC2531065 DOI: 10.1073/pnas.0806158105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We have used unbiased phosphoproteomic approaches, based on quantitative mass spectrometry using stable isotope labeling with amino acids in cell culture (SILAC), to identify tyrosine phosphorylated proteins in isogenic human bronchial epithelial cells (HBECs) and human lung adenocarcinoma cell lines, expressing either of the two mutant alleles of EGFR (L858R and Del E746-A750), or a mutant KRAS allele, which are common in human lung adenocarcinomas. Tyrosine phosphorylation of signaling molecules was greater in HBECs expressing the mutant EGFRs than in cells expressing WT EGFR or mutant KRAS. Receptor tyrosine kinases (such as EGFR, ERBB2, MET, and IGF1R), and Mig-6, an inhibitor of EGFR signaling, were more phosphorylated in HBECs expressing mutant EGFR than in cells expressing WT EGFR or mutant RAS. Phosphorylation of some proteins differed in the two EGFR mutant-expressing cells; for example, some cell junction proteins (beta-catenin, plakoglobin, and E-cadherin) were more phosphorylated in HBECs expressing L858R EGFR than in cells expressing Del EGFR. There were also differences in degree of phosphorylation at individual tyrosine sites within a protein; for example, a previously uncharacterized phosphorylation site in the nucleotide-binding loop of the kinase domains of EGFR (Y727), ERBB2 (Y735), or ERBB4 (Y733), is phosphorylated significantly more in HBECs expressing the deletion mutant than in cells expressing the wild type or L858R EGFR. Signaling molecules not previously implicated in ERBB signaling, such as polymerase transcript release factor (PTRF), were also phosphorylated in cells expressing mutant EGFR. Bayesian network analysis of these and other datasets revealed that PTRF might be a potentially important component of the ERBB signaling network.
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Affiliation(s)
- Udayan Guha
- *Programs in Cancer Biology and Genetics, and
- †To whom correspondence may be addressed. E-mail: or
| | - Raghothama Chaerkady
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - Arivusudar Marimuthu
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - A. Scott Patterson
- ‖Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
| | - Manoj K. Kashyap
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - H. C. Harsha
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
- ¶Institute of Bioinformatics, Bangalore 560066, India;
| | - Mitsuo Sato
- **Department of Clinical Oncology and Chemotherapy, Nagoya University School of Medicine, Nagoya, Japan 466-8550; and
| | - Joel S. Bader
- ‖Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
| | - Alex E. Lash
- ††Comptational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065;
| | - John D. Minna
- ‡‡Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Akhilesh Pandey
- ‡McKusick-Nathans Institute for Genetic Medicine and
- Departments of §Biological Chemistry and Oncology, and
| | - Harold E. Varmus
- *Programs in Cancer Biology and Genetics, and
- †To whom correspondence may be addressed. E-mail: or
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