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Endotoxin contamination alters macrophage-cancer cell interaction and therapeutic efficacy in pre-clinical 3D in vitro models. BIOMATERIALS ADVANCES 2022; 144:213220. [PMID: 36476713 DOI: 10.1016/j.bioadv.2022.213220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
The rapid developments in biofabrication, in particular 3D bioprinting, in the recent years have facilitated the need for novel biomaterials that aim to replicate the target tissue in great detail. The presence of endotoxins in these biomaterials is often an overlooked problem. In pre-clinical 3D in vitro models, endotoxins can have significant influence on cell behavior and credibility of the model. In this study we demonstrate the effects of high levels of endotoxins in commercially-available gelatin on the macrophage-cancer cell crosstalk in a 3D bioprinted co-culture model. First, it is demonstrated that, while presenting the same mechanical and structural stimuli, high levels of endotoxin can have significant influence on the metabolic activity of macrophages and cancer cells. Furthermore, this study shows that high endotoxin contamination causes a strong inflammatory reaction in macrophages and significantly inhibits the effects of a paracrine macrophage-cancer cell co-culture. At last, it is demonstrated that the differences in endotoxin levels can drastically alter the efficacy of novel macrophage modulating immunotherapies, AS1517499 and 3-methyladenine. Altogether, this study shows that endotoxin contamination in biomaterials can significantly alter intra- and intercellular communication and thereby drug efficacy, which might lead to misinterpretation of the potency and safety of the tested compounds.
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Fatima A, Tariq F, Malik MFA, Qasim M, Haq F. Copy Number Profiling of MammaPrint™ Genes Reveals Association with the Prognosis of Breast Cancer Patients. J Breast Cancer 2017; 20:246-253. [PMID: 28970850 PMCID: PMC5620439 DOI: 10.4048/jbc.2017.20.3.246] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 01/22/2023] Open
Abstract
Purpose The MammaPrint™ gene signature, currently used in clinical practice, provides prognostic information regarding the recurrence and potential metastasis in breast cancer patients. However, the prognostic information of the 70 genes included can only be estimated at the RNA expression level. In this study, we investigated whether copy number information of MammaPrint™ genes at the DNA level can be used as a prognostic tool for breast cancer, as copy number variations (CNVs) are major contributors to cancer progression. Methods We performed CNV profiling of MammaPrint™ genes in 59 breast cancer cell lines and 650 breast cancer patients, using publicly available data in The Cancer Genome Atlas (TCGA) database. Statistical analyses including Fisher exact test, chi-square test, and Kaplan-Meier survival analyses were performed. Results All MammaPrint™ genes showed recurrent CNVs, particularly in TCGA cohort. CNVs of 32 and 36 genes showed significant associations with progesterone receptor and estrogen rector, respectively. No genes showed a significant association with human epidermal growth factor receptor 2 status and lymph node status. In addition, only six genes were associated with tumor stages. RFC4, HRASLS, NMU, GPR126, SCUBE2, C20orf46, and EBF4 were associated with reduced survival and RASSF7 and ESM1 were associated with reduced disease-free survival. Conclusion Based on these findings, a concordance of CNV-based genomic rearrangement with expression profiling of these genes and their putative roles in disease tumorigenesis was established. The results suggested that the CNV profiles of the MammaPrint™ genes can be used to predict the prognosis of breast cancer patients. In addition, this approach may lead to the development of new cancer biomarkers at the DNA level.
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Affiliation(s)
- Areej Fatima
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Fomaz Tariq
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Faraz Arshad Malik
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Qasim
- Department of Pharmacology & Immune Network Pioneer Research Center, Ajou University School of Medicine, Suwon, Korea
| | - Farhan Haq
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Qian J, Chen H, Ji X, Eisenberg R, Chakravarthy AB, Mayer IA, Massion PP. A 3q gene signature associated with triple negative breast cancer organ specific metastasis and response to neoadjuvant chemotherapy. Sci Rep 2017; 7:45828. [PMID: 28387221 PMCID: PMC5384279 DOI: 10.1038/srep45828] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/06/2017] [Indexed: 02/08/2023] Open
Abstract
Triple negative breast cancers (TNBC) are aggressive tumors, with high rates of metastatic spread and targeted therapies are critically needed. We aimed to assess the prognostic and predictive value of a 3q 19-gene signature identified previously from lung cancer in a collection of 4,801 breast tumor gene expression data. The 3q gene signature had a strong association with features of aggressiveness such as high grade, hormone receptor negativity, presence of a basal-like or TNBC phenotype and reduced distant metastasis free survival. The 3q gene signature was strongly associated with lung metastasis only in TNBC (P < 0.0001, Hazard ratio (HR) 1.44, 95% confidence interval (CI), 1.31-1.60), significantly associated with brain but not bone metastasis regardless of TNBC status. The association of one 3q driver gene FXR1 with distant metastasis in TNBC (P = 0.01) was further validated by immunohistochemistry. In addition, the 3q gene signature was associated with better response to neoadjuvant chemotherapy in TNBC (P < 0.0001) but not in non-TNBC patients. Our study suggests that the 3q gene signature is a novel prognostic marker for lung and/or brain metastasis and a predictive marker for the response to neoadjuvant chemotherapy in TNBC, implying a potential role for 3q genes in the mechanism of organ-specific metastasis.
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Affiliation(s)
- Jun Qian
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Heidi Chen
- Vanderbilt Center for Quantitative Sciences, Department of Statistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiangming Ji
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rosana Eisenberg
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - A Bapsi Chakravarthy
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ingrid A Mayer
- Divsion of Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pierre P Massion
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Medical Center, Nashville, TN, USA
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Khan MI, Dębski KJ, Dabrowski M, Czarnecka AM, Szczylik C. Gene set enrichment analysis and ingenuity pathway analysis of metastatic clear cell renal cell carcinoma cell line. Am J Physiol Renal Physiol 2016; 311:F424-36. [PMID: 27279483 DOI: 10.1152/ajprenal.00138.2016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/06/2016] [Indexed: 11/22/2022] Open
Abstract
In recent years, genome-wide RNA expression analysis has become a routine tool that offers a great opportunity to study and understand the key role of genes that contribute to carcinogenesis. Various microarray platforms and statistical approaches can be used to identify genes that might serve as prognostic biomarkers and be developed as antitumor therapies in the future. Metastatic renal cell carcinoma (mRCC) is a serious, life-threatening disease, and there are few treatment options for patients. In this study, we performed one-color microarray gene expression (4×44K) analysis of the mRCC cell line Caki-1 and the healthy kidney cell line ASE-5063. A total of 1,921 genes were differentially expressed in the Caki-1 cell line (1,023 upregulated and 898 downregulated). Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) approaches were used to analyze the differential-expression data. The objective of this research was to identify complex biological changes that occur during metastatic development using Caki-1 as a model mRCC cell line. Our data suggest that there are multiple deregulated pathways associated with metastatic clear cell renal cell carcinoma (mccRCC), including integrin-linked kinase (ILK) signaling, leukocyte extravasation signaling, IGF-I signaling, CXCR4 signaling, and phosphoinositol 3-kinase/AKT/mammalian target of rapamycin signaling. The IPA upstream analysis predicted top transcriptional regulators that are either activated or inhibited, such as estrogen receptors, TP53, KDM5B, SPDEF, and CDKN1A. The GSEA approach was used to further confirm enriched pathway data following IPA.
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Affiliation(s)
- Mohammed I Khan
- Molecular Oncology Laboratory, Department of Oncology, Military Institute of Medicine, Warsaw, Poland; and
| | - Konrad J Dębski
- Bioinformatics Laboratory, Center of Neurobiology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Michał Dabrowski
- Bioinformatics Laboratory, Center of Neurobiology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Anna M Czarnecka
- Molecular Oncology Laboratory, Department of Oncology, Military Institute of Medicine, Warsaw, Poland; and
| | - Cezary Szczylik
- Molecular Oncology Laboratory, Department of Oncology, Military Institute of Medicine, Warsaw, Poland; and
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Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W. CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell 2014; 25:21-36. [PMID: 24434208 PMCID: PMC4004525 DOI: 10.1016/j.ccr.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/29/2013] [Accepted: 12/13/2013] [Indexed: 11/25/2022]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1), a coactivator for various cancer-relevant transcription factors, is overexpressed in breast cancer. To elucidate the functions of CARM1 in tumorigenesis, we knocked out CARM1 from several breast cancer cell lines using Zinc-Finger Nuclease technology, which resulted in drastic phenotypic and biochemical changes. The CARM1 KO cell lines enabled identification of CARM1 substrates, notably the SWI/SNF core subunit BAF155. Methylation of BAF155 at R1064 was found to be an independent prognostic biomarker for cancer recurrence and to regulate breast cancer cell migration and metastasis. Furthermore, CARM1-mediated BAF155 methylation affects gene expression by directing methylated BAF155 to unique chromatin regions (e.g., c-Myc pathway genes). Collectively, our studies uncover a mechanism by which BAF155 acquires tumorigenic functions via arginine methylation.
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Affiliation(s)
- Lu Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zibo Zhao
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sandeep Saha
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ailan Guo
- Cell Signaling Technology, Danvers, MA 01923, USA
| | - Kari B Wisinski
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Huang
- Department of Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Weibo Cai
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ming Yuan
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Guttery DS, Blighe K, Page K, Marchese SD, Hills A, Coombes RC, Stebbing J, Shaw JA. Hide and seek: tell-tale signs of breast cancer lurking in the blood. Cancer Metastasis Rev 2013; 32:289-302. [PMID: 23108389 DOI: 10.1007/s10555-012-9414-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Breast cancer treatment is improving due to the introduction of new drugs, guided by molecular testing of the primary tumour for mutations/oncogenic drivers (e.g. HER2 gene amplification). However, tumour tissue is not always available for molecular analysis, intra-tumoural heterogeneity is common and the "cancer genome" is known to evolve with time, particularly following treatment as resistance develops. After resection, those patients with only residual micrometastases are likely to be cured but those with radiologically detectable overt disease are not. Thus, the discovery of blood test(s) that could (1) alert clinicians to early primary or recurrent disease and (2) monitor response to treatment could impact significantly on mortality. Towards this, we and others have focused on molecular profiling of circulating nucleic acids isolated from plasma, both cell-free DNA (cfDNA) and microRNAs, and the relationship of these to circulating tumour cells (CTCs). This review considers the utility of each as circulating biomarkers in breast cancer with particular emphasis on the bioinformatic tools available to support molecular profiling.
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Affiliation(s)
- David S Guttery
- Department of Cancer Studies and Molecular Medicine, Leicester Royal Infirmary, Leicester, UK.
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Roberts JS, Christensen KD, Green RC. Using Alzheimer's disease as a model for genetic risk disclosure: implications for personal genomics. Clin Genet 2011; 80:407-14. [PMID: 21696382 PMCID: PMC3191239 DOI: 10.1111/j.1399-0004.2011.01739.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Susceptibility testing for common, complex adult-onset diseases is projected to become more commonplace as the rapid pace of genomic discoveries continues, and evidence regarding the potential benefits and harms of such testing is needed to inform medical practice and health policy. Apolipoprotein E (APOE) testing for risk of Alzheimer's disease (AD) provides a paradigm in which to examine the process and impact of disclosing genetic susceptibility for a prevalent, severe and incurable neurological condition. This review summarizes findings from a series of multi-site randomized clinical trials examining psychological and behavioral responses to various methods of genetic risk assessment for AD using APOE disclosure. We discuss challenges involved in disease risk estimation and communication and the extent to which participants comprehend and perceive utility in their genetic risk information. Findings on the psychological impact of test results are presented (e.g. distress), along with data on participants' health behavior and insurance purchasing responses (e.g. long-term care). Finally, we report comparisons of the safety and efficacy of intensive genetic counseling approaches to briefer models that emphasize streamlined processes and educational materials. The implications of these findings for the emerging field of personal genomics are discussed, with directions identified for future research.
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Affiliation(s)
- J S Roberts
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, 48109, USA.
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Wulfkuhle JD, Speer R, Pierobon M, Laird J, Espina V, Deng J, Mammano E, Yang SX, Swain SM, Nitti D, Esserman LJ, Belluco C, Liotta LA, Petricoin EF. Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res 2008; 7:1508-17. [PMID: 18257519 DOI: 10.1021/pr7008127] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Phosphoprotein driven cellular signaling events represent most of the new molecular targets for cancer treatment. Application of reverse-phase protein microarray technology for the study of ongoing signaling activity within breast tumor specimens holds great potential for elucidating and profiling signaling activity in real-time for patient-tailored therapy. Analysis of laser capture microdissection primary human breast tumors and metastatic lesions reveals pathway specific profiles and a new way to classify cancer based on functional signaling portraits. Moreover, the data demonstrate the requirement of laser capture microdissection for analysis and reveal the metastasis-specific changes that occur within a new microenvironment. Analysis of biopsy material from clinical trials for targeted therapeutics demonstrates the feasibility and utility of comprehensive signal pathway activation profiling for molecular analysis.
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Affiliation(s)
- Julia D Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, USA.
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