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Moon S, Kim HJ, Lee Y, Lee YJ, Jung S, Lee JS, Hahn SH, Kim K, Roh JY, Nam S. Oncogenic signaling pathways and hallmarks of cancer in Korean patients with acral melanoma. Comput Biol Med 2023; 154:106602. [PMID: 36716688 DOI: 10.1016/j.compbiomed.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/23/2022] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Acral melanoma (AM), a rare subtype of cutaneous melanoma, shows higher incidence in Asians, including Koreans, than in Caucasians. However, the genetic modification associated with AM in Koreans is not well known and has not been comprehensively investigated in terms of oncogenic signaling, and hallmarks of cancer. We performed whole-exome and RNA sequencing for Korean patients with AM and acquired the genetic alterations and gene expression profiles. KIT alterations (previously known to be recurrent alterations in AM) and CDK4/CCND1 copy number amplifications were identified in the patients. Genetic and transcriptomic alterations in patients with AM were functionally converge to the hallmarks of cancer and oncogenic pathways, including 'proliferative signal persistence', 'apoptotic resistance', and 'activation of invasion and metastasis', despite the heterogeneous somatic mutation profiles of Korean patients with AM. This study may provide a molecular understanding for therapeutic strategy for AM.
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Affiliation(s)
- SeongRyeol Moon
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon, 21999, South Korea
| | - Hee Joo Kim
- Department of Dermatology, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, South Korea
| | - Yeeun Lee
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon, 21999, South Korea
| | - Yu Joo Lee
- Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, South Korea
| | - Sungwon Jung
- Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, South Korea
| | - Jin Sook Lee
- Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, South Korea; Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children's Hospital, Seoul, 03080, South Korea
| | - Si Houn Hahn
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | | | - Joo Young Roh
- Department of Dermatology, Ewha Womans University College of Medicine, Seoul Hospital, Seoul, 07804, South Korea.
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon, 21999, South Korea; Department of Genome Medicine and Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, South Korea; AI Convergence Center for Medical Science, Gachon University College of Medicine, Incheon, 21565, South Korea.
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High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs. PLoS Genet 2021; 17:e1009732. [PMID: 34437536 PMCID: PMC8439493 DOI: 10.1371/journal.pgen.1009732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 09/14/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer patients exhibit a broad range of inter-individual variability in response and toxicity to widely used anticancer drugs, and genetic variation is a major contributor to this variability. To identify new genes that influence the response of 44 FDA-approved anticancer drug treatments widely used to treat various types of cancer, we conducted high-throughput screening and genome-wide association mapping using 680 lymphoblastoid cell lines from the 1000 Genomes Project. The drug treatments considered in this study represent nine drug classes widely used in the treatment of cancer in addition to the paclitaxel + epirubicin combination therapy commonly used for breast cancer patients. Our genome-wide association study (GWAS) found several significant and suggestive associations. We prioritized consistent associations for functional follow-up using gene-expression analyses. The NAD(P)H quinone dehydrogenase 1 (NQO1) gene was found to be associated with the dose-response of arsenic trioxide, erlotinib, trametinib, and a combination treatment of paclitaxel + epirubicin. NQO1 has previously been shown as a biomarker of epirubicin response, but our results reveal novel associations with these additional treatments. Baseline gene expression of NQO1 was positively correlated with response for 43 of the 44 treatments surveyed. By interrogating the functional mechanisms of this association, the results demonstrate differences in both baseline and drug-exposed induction. In the burgeoning field of personalized medicine, genetic variation is recognized as a major contributor to patients’ differential responses to drugs. Lymphoblastoid cell lines (LCLs) are a consistent and convenient representation of cells used for in vitro research. Human genome sequencing with LCLs can identify new genes that influence individuals’ drug responses, including the dose-response relationship, which describes the relationship between physiological response and the amount of exposure to a substance. In this work, we conduct high-throughput screening and genome-wide association mapping using 680 LCLs from the 1000 Genomes Project to identify new genes that influence individual response to 44 widely used anticancer drugs. We found the NQO1 gene to be associated with the dose-response of several drugs, namely arsenic trioxide, erlotinib, trametinib, and the paclitaxel + epirubicin combination, and performed follow-up analyses to better understand its functional role in drug response. Our results indicate NQO1 expression is correlated with increased drug resistance and provide some evidence that SNP rs1800566 influences drug response by altering protein activity for these four treatments. With further research, NQO1 has potential use as a therapeutic target, for example, suppressing NQO1 expression to increase sensitivity to particular drugs.
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Unterholzner J, Millischer V, Wotawa C, Sawa A, Lanzenberger R. Making Sense of Patient-Derived iPSCs, Transdifferentiated Neurons, Olfactory Neuronal Cells, and Cerebral Organoids as Models for Psychiatric Disorders. Int J Neuropsychopharmacol 2021; 24:759-775. [PMID: 34216465 PMCID: PMC8538891 DOI: 10.1093/ijnp/pyab037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/30/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022] Open
Abstract
The improvement of experimental models for disorders requires a constant approximation towards the dysregulated tissue. In psychiatry, where an impairment of neuronal structure and function is assumed to play a major role in disease mechanisms and symptom development, this approximation is an ongoing process implicating various fields. These include genetic, animal, and post-mortem studies. To test hypotheses generated through these studies, in vitro models using non-neuronal cells such as fibroblasts and lymphocytes have been developed. For brain network disorders, cells with neuronal signatures would, however, represent a more adequate tissue. Considering the limited accessibility of brain tissue, research has thus turned towards neurons generated from induced pluripotent stem cells as well as directly induced neurons, cerebral organoids, and olfactory neuroepithelium. Regarding the increasing importance and amount of research using these neuronal cells, this review aims to provide an overview of all these models to make sense of the current literature. The development of each model system and its use as a model for the various psychiatric disorder categories will be laid out. Also, advantages and limitations of each model will be discussed, including a reflection on implications and future perspectives.
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Affiliation(s)
- Jakob Unterholzner
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Vincent Millischer
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria,Neurogenetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Wotawa
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria
| | - Akira Sawa
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA,Departments of Psychiatry, Neuroscience, Biomedical Engineering and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Austria,Correspondence: Prof. Rupert Lanzenberger, MD, PD, NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab, Department of Psychiatry and Psychotherapy, Medical University of Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria ()
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Kartini D, Taher A, Panigoro SS, Setiabudy R, Jusman SW, Haryana SM, Murdani A, Rustamadji P, Karisyah A, Rasyid SH. Melatonin effect on hypoxia inducible factor-1α and clinical response in patients with oral squamous cell carcinoma receiving neoadjuvant chemotherapy: A randomized controlled trial. J Carcinog 2021; 20:5. [PMID: 34429714 PMCID: PMC8335757 DOI: 10.4103/jcar.jcar_19_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 11/25/2022] Open
Abstract
CONTEXT Chemoresistance is a major issue in patients with locally advanced oral squamous cell carcinoma (OSCC). In this study, we evaluated the effectiveness of melatonin in conjunction with neoadjuvant chemotherapy (NC) on hypoxia-inducible factor-1α (HIF-1α) expression and clinical response in locally advanced OSCC patients. AIMS To study the effects of melatonin on HIF-1α expression and its effect on the clinical response of patients with locally advanced OSCC. SETTINGS AND DESIGN A randomized controlled trial was conducted, wherein patients were recruited from several hospitals in Jakarta, Indonesia. Patients were randomized into two groups using computerized block randomization. SUBJECTS AND METHODS Both groups were given NC, with treatment group receiving melatonin. Outcomes measured in this study were HIF-1α expression from tissue samples and clinical response based on the RECIST 1.1 criteria. Twenty-five patients completed the study protocol and were included in the data analysis. STATISTICAL ANALYSIS USED Shapiro-Wilk test was used to test the data normality. For data with normal distribution, we conducted an independent t-test to compare between the two groups. Data with abnormal distribution were analyzed using Mann-Whitney U-test. The mean difference between the two groups was analyzed using Shapiro-Wilk normality test. RESULTS Our study showed a significant decrease in HIF-1α expression in the melatonin group compared to the placebo group (P < 0.05, relative risk 3.08). However, the degree of reduction of HIF-1α expression in the melatonin group did not differ significantly (P = 0.301). CONCLUSIONS Our study showed that melatonin administered at 20 mg/day could reduce the expression of HIF-1α and residual tumor percentage, but did not affect the clinical response in OSCC patients.
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Affiliation(s)
- Diani Kartini
- Oncology Division, Department of Surgery, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Akmal Taher
- Department of Urology, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sonar Soni Panigoro
- Oncology Division, Department of Surgery, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Rianto Setiabudy
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sri Widia Jusman
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Abdullah Murdani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Primariadewi Rustamadji
- Department of Pathological Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Adlina Karisyah
- Oncology Division, Department of Surgery, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sani Hadiyan Rasyid
- Oncology Division, Department of Surgery, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Di Francia R, Crisci S, De Monaco A, Cafiero C, Re A, Iaccarino G, De Filippi R, Frigeri F, Corazzelli G, Micera A, Pinto A. Response and Toxicity to Cytarabine Therapy in Leukemia and Lymphoma: From Dose Puzzle to Pharmacogenomic Biomarkers. Cancers (Basel) 2021; 13:cancers13050966. [PMID: 33669053 PMCID: PMC7956511 DOI: 10.3390/cancers13050966] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary In this review, the authors propose a crosswise examination of cytarabine-related issues ranging from the spectrum of clinical activity and severe toxicities, through updated cellular pharmacology and drug formulations, to the genetic variants associated with drug-induced phenotypes. Cytarabine (cytosine arabinoside; Ara-C) in multiagent chemotherapy regimens is often used for leukemia or lymphoma treatments, as well as neoplastic meningitis. Chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. The individual variability in clinical response to Leukemia & Lymphoma treatments among patients appears to be associated with intracellular accumulation of Ara-CTP due to genetic variants related to metabolic enzymes. The review provides exhaustive information on the effects of Ara-C-based therapies, the adverse drug reaction will also be provided including bone pain, ocular toxicity (corneal pain, keratoconjunctivitis, and blurred vision), maculopapular rash, and occasional chest pain. Evidence for predicting the response to cytarabine-based treatments will be highlighted, pointing at their significant impact on the routine management of blood cancers. Abstract Cytarabine is a pyrimidine nucleoside analog, commonly used in multiagent chemotherapy regimens for the treatment of leukemia and lymphoma, as well as for neoplastic meningitis. Ara-C-based chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. Several studies suggest that the individual variability in clinical response to Leukemia & Lymphoma treatments among patients, underlying either Ara-C mechanism resistance or toxicity, appears to be associated with the intracellular accumulation and retention of Ara-CTP due to genetic variants related to metabolic enzymes. Herein, we reported (a) the latest Pharmacogenomics biomarkers associated with the response to cytarabine and (b) the new drug formulations with optimized pharmacokinetics. The purpose of this review is to provide readers with detailed and comprehensive information on the effects of Ara-C-based therapies, from biological to clinical practice, maintaining high the interest of both researcher and clinical hematologist. This review could help clinicians in predicting the response to cytarabine-based treatments.
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Affiliation(s)
- Raffaele Di Francia
- Italian Association of Pharmacogenomics and Molecular Diagnostics, 60126 Ancona, Italy;
| | - Stefania Crisci
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Angela De Monaco
- Clinical Patology, ASL Napoli 2 Nord, “S.M. delle Grazie Hospital”, 80078 Pozzuoli, Italy;
| | - Concetta Cafiero
- Medical Oncology, S.G. Moscati, Statte, 74010 Taranto, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Agnese Re
- Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Giancarla Iaccarino
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Rosaria De Filippi
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
- Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy
| | | | - Gaetano Corazzelli
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Alessandra Micera
- Research and Development Laboratory for Biochemical, Molecular and Cellular Applications in Ophthalmological Sciences, IRCCS—Fondazione Bietti, 00184 Rome, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Antonio Pinto
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
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Akhtari FS, Havener TM, Hertz DL, Ash J, Larson A, Carey LA, McLeod HL, Motsinger-Reif AA. Race and smoking status associated with paclitaxel drug response in patient-derived lymphoblastoid cell lines. Pharmacogenet Genomics 2021; 31:48-52. [PMID: 32941389 PMCID: PMC8320509 DOI: 10.1097/fpc.0000000000000419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The use of ex-vivo model systems to provide a level of forecasting for in-vivo characteristics remains an important need for cancer therapeutics. The use of lymphoblastoid cell lines (LCLs) is an attractive approach for pharmacogenomics and toxicogenomics, due to their scalability, efficiency, and cost-effectiveness. There is little data on the impact of demographic or clinical covariates on LCL response to chemotherapy. Paclitaxel sensitivity was determined in LCLs from 93 breast cancer patients from the University of North Carolina Lineberger Comprehensive Cancer Center Breast Cancer Database to test for potential associations and/or confounders in paclitaxel dose-response assays. Measures of paclitaxel cell viability were associated with patient data included treatment regimens, cancer status, demographic and environmental variables, and clinical outcomes. We used multivariate analysis of variance to identify the in-vivo variables associated with ex-vivo dose-response. In this unique dataset that includes both in-vivo and ex-vivo data from breast cancer patients, race (P = 0.0049) and smoking status (P = 0.0050) were found to be significantly associated with ex-vivo dose-response in LCLs. Racial differences in clinical dose-response have been previously described, but the smoking association has not been reported. Our results indicate that in-vivo smoking status can influence ex-vivo dose-response in LCLs, and more precise measures of covariates may allow for more precise forecasting of clinical effect. In addition, understanding the mechanism by which exposure to smoking in-vivo effects ex-vivo dose-response in LCLs may open up new avenues in the quest for better therapeutic prediction.
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Affiliation(s)
- Farida S. Akhtari
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Tammy M. Havener
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, 48109, USA
| | - Jeremy Ash
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Alexandra Larson
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| | - Lisa A. Carey
- Division of Hematology/Oncology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Howard L. McLeod
- University of South Florida Taneja College of Pharmacy, Tampa, FL 33612, USA
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alison A. Motsinger-Reif
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
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Kartini D, Taher A, Panigoro SS, Setiabudy R, Jusman SW, Haryana SM, Abdullah M, Rustamadji P, Purwanto DJ, Sutandyo N, Suroyo I, Siregar BH, Maruli H, Sungkar S. Effect of melatonin supplementation in combination with neoadjuvant chemotherapy to miR-210 and CD44 expression and clinical response improvement in locally advanced oral squamous cell carcinoma: a randomized controlled trial. J Egypt Natl Canc Inst 2020; 32:12. [PMID: 32372215 DOI: 10.1186/s43046-020-0021-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/31/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Squamous cell carcinoma of the oral cavity (OSCC) is the sixth most common malignancy. Surgery is mainstay treatment for oral cancers. Surgery in locally advanced OSCC presents many challenges primarily because the head and neck have critical structures that can be damaged by tumor or treatment. It is thought that neoadjuvant chemotherapy (NC) in locally advanced OSCC is able to shrink tumor size. Chemoresistancy is a problem due to hypoxic microenvironment characterized by increased expression of HIF-1α. It is also regulated by miR-210 as well as increased expression of CD44 and CD133. Melatonin has a powerful antioxidant and oncostatic effects that are expected to improve tumor hypoxia and clinical response. Fifty patients with OSCC were included and randomized. miR-210 and CD44 expression were measured before and after intervention using qRT-PCR absolute quantification, and clinical response was evaluated according to RECIST 1.1 criteria. This study aims to determine the effect of melatonin in improving the clinical response of patients with locally advanced oral squamous cell carcinoma (OSCC) after neoadjuvant chemotherapy to miR-210 and CD44 expression. RESULTS Melatonin administration reduced miR-210 levels but not significant (p = 0.767). CD44 expression also decreased in the melatonin group compared with placebo yet was not significant (p = 0.103). There was a decrease in the expression of miR-210 and CD44 followed by a decrease in the percentage of residual tumor but not significant (p = 0.114). CONCLUSION In OSCC, the addition of 20-mg melatonin to neoadjuvant chemotherapy (NC) reduced the expression of miR-210 and CD44 and decreased the percentage of tumor residue; however, no statistically significant result was observed. TRIAL REGISTRATION This study is registered to ClinicalTrials.gov under trial registration number: NCT04137627 with date of registration on October 22, 2019-retrospectively registered, accessible from: https://clinicaltrials.gov/ct2/show/NCT04137627.
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Affiliation(s)
- Diani Kartini
- Oncology Division, Department of Surgery, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, 10430, Indonesia.
| | - Akmal Taher
- Department of Urology, Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sonar Soni Panigoro
- Oncology Division, Department of Surgery, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, 10430, Indonesia
| | - Rianto Setiabudy
- Department of Pharmacology and Therapeutics, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Sri Widia Jusman
- Department of Biochemistry and Molecular Genetics, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Murdani Abdullah
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Primariadewi Rustamadji
- Department of Pathological Anatomy, Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Denni Joko Purwanto
- Department of Surgical Oncology, Dharmais Hospital, National Cancer Center, Jakarta, Indonesia
| | - Noorwati Sutandyo
- Department of Hematology and Medical Oncology, Dharmais Hospital, National Cancer Center, Jakarta, Indonesia
| | - Indrati Suroyo
- Department of Radiology, Dr. Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Budi Harapan Siregar
- Oncology Division, Department of Surgery, Persahabatan General Hospital, Jakarta, Indonesia
| | - Haris Maruli
- Oncology Division, Department of Surgery, Persahabatan General Hospital, Jakarta, Indonesia
| | - Saleha Sungkar
- Department of Parasitology, Dr. Cipto Mangunkusumo National Central General Hospital, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
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Fustin JM, Li M, Gao B, Chen Q, Cheng T, Stewart AG. Rhythm on a chip: circadian entrainment in vitro is the next frontier in body-on-a chip technology. Curr Opin Pharmacol 2019; 48:127-136. [PMID: 31600661 DOI: 10.1016/j.coph.2019.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023]
Abstract
Organoids, bioprinted mini-tissues and body-on-a-chip technologies are poised to transform the practice of preclinical pharmacology, with a view to achieving better predictive value. We review the need for further refinement in static and dynamic biomechanical aspects of such microenvironments. Further consideration of the developments required in perfusion systems to enable delivery of an appropriate soluble microenvironment are argued. We place particular emphasis on a major deficiency in these systems, being the absence or aberrant circadian behaviour of cells used in such settings, and consider the technical challenges that are needing to be met in order to achieve rhythm-on-a-chip.
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Affiliation(s)
- Jean-Michel Fustin
- Laboratory of Molecular Metabology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Meina Li
- ARC Centre for Personalised Therapeutics Technologies, Department of Pharmacology & Therapeutics, School of Biomedical Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bryan Gao
- ARC Centre for Personalised Therapeutics Technologies, Department of Pharmacology & Therapeutics, School of Biomedical Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Qianyu Chen
- ARC Centre for Personalised Therapeutics Technologies, Department of Pharmacology & Therapeutics, School of Biomedical Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tianhong Cheng
- ARC Centre for Personalised Therapeutics Technologies, Department of Pharmacology & Therapeutics, School of Biomedical Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alastair G Stewart
- ARC Centre for Personalised Therapeutics Technologies, Department of Pharmacology & Therapeutics, School of Biomedical Science, University of Melbourne, Parkville, Victoria 3010, Australia.
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Pillai DK, Amachawadi RG, Baca G, Narayanan S, Nagaraja T. Leukotoxic activity of Fusobacterium necrophorum of cattle origin. Anaerobe 2019; 56:51-56. [DOI: 10.1016/j.anaerobe.2019.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 11/16/2022]
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Yao F, Madani Tonekaboni SA, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B. Tissue specificity of in vitro drug sensitivity. J Am Med Inform Assoc 2019; 25:158-166. [PMID: 29016819 DOI: 10.1093/jamia/ocx062] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/22/2017] [Indexed: 12/11/2022] Open
Abstract
Objectives We sought to investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in drug clinical indications. Materials and Methods We leveraged the curated cell line response data from PharmacoGx and applied an enrichment algorithm on drug sensitivity values' area under the drug dose-response curves (AUCs) with and without adjustment for general level of drug sensitivity. Results We observed tissue specificity in 63% of tested drugs, with 8% of total interactions deemed significant (false discovery rate <0.05). By restricting the drug-tissue interactions to those with AUC > 0.2, we found that in 52% of interactions, the tissue was predictive of drug sensitivity (concordance index > 0.65). When compared with clinical indications, the observed overlap was weak (Matthew correlation coefficient, MCC = 0.0003, P > .10). Discussion While drugs exhibit significant tissue specificity in vitro, there is little overlap with clinical indications. This can be attributed to factors such as underlying biological differences between in vitro models and patient tumors, or the inability of tissue-specific drugs to bring additional benefits beyond gold standard treatments during clinical trials. Conclusion Our meta-analysis of pan-cancer drug screening datasets indicates that most tested drugs exhibit tissue-specific sensitivities in a large panel of cancer cell lines. However, the observed preclinical results do not translate to the clinical setting. Our results suggest that additional research into showing parallels between preclinical and clinical data is required to increase the translational potential of in vitro drug screening.
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Affiliation(s)
- Fupan Yao
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Petr Smirnov
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nehme El-Hachem
- Integrative Systems Biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Mark Freeman
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Venkata Satya Kumar Manem
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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11
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Sivadas A, Scaria V. Population-scale genomics-Enabling precision public health. ADVANCES IN GENETICS 2018; 103:119-161. [PMID: 30904093 DOI: 10.1016/bs.adgen.2018.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The current excitement for affordable genomics technologies and national precision medicine initiatives marks a turning point in worldwide healthcare practices. The last decade of global population sequencing efforts has defined the enormous extent of genetic variation in the human population resulting in insights into differential disease burden and response to therapy within and between populations. Population-scale pharmacogenomics helps to provide insights into the choice of optimal therapies and an opportunity to estimate, predict and minimize adverse events. Such an approach can potentially empower countries to formulate national selection and dosing policies for therapeutic agents thereby promoting public health with precision. We review the breadth and depth of worldwide population-scale sequencing efforts and its implications for the implementation of clinical pharmacogenetics toward making precision medicine a reality.
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Affiliation(s)
- Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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12
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Zhang Q, Li J, Middleton A, Bhattacharya S, Conolly RB. Bridging the Data Gap From in vitro Toxicity Testing to Chemical Safety Assessment Through Computational Modeling. Front Public Health 2018; 6:261. [PMID: 30255008 PMCID: PMC6141783 DOI: 10.3389/fpubh.2018.00261] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
Chemical toxicity testing is moving steadily toward a human cell and organoid-based in vitro approach for reasons including scientific relevancy, efficiency, cost, and ethical rightfulness. Inferring human health risk from chemical exposure based on in vitro testing data is a challenging task, facing various data gaps along the way. This review identifies these gaps and makes a case for the in silico approach of computational dose-response and extrapolation modeling to address many of the challenges. Mathematical models that can mechanistically describe chemical toxicokinetics (TK) and toxicodynamics (TD), for both in vitro and in vivo conditions, are the founding pieces in this regard. Identifying toxicity pathways and in vitro point of departure (PoD) associated with adverse health outcomes requires an understanding of the molecular key events in the interacting transcriptome, proteome, and metabolome. Such an understanding will in turn help determine the sets of sensitive biomarkers to be measured in vitro and the scope of toxicity pathways to be modeled in silico. In vitro data reporting both pathway perturbation and chemical biokinetics in the culture medium serve to calibrate the toxicity pathway and virtual tissue models, which can then help predict PoDs in response to chemical dosimetry experienced by cells in vivo. Two types of in vitro to in vivo extrapolation (IVIVE) are needed. (1) For toxic effects involving systemic regulations, such as endocrine disruption, organism-level adverse outcome pathway (AOP) models are needed to extrapolate in vitro toxicity pathway perturbation to in vivo PoD. (2) Physiologically-based toxicokinetic (PBTK) modeling is needed to extrapolate in vitro PoD dose metrics into external doses for expected exposure scenarios. Linked PBTK and TD models can explore the parameter space to recapitulate human population variability in response to chemical insults. While challenges remain for applying these modeling tools to support in vitro toxicity testing, they open the door toward population-stratified and personalized risk assessment.
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Affiliation(s)
- Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Jin Li
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Sudin Bhattacharya
- Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - Rory B Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Durham, NC, United States
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13
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Robust imaging and gene delivery to study human lymphoblastoid cell lines. J Hum Genet 2018; 63:945-955. [DOI: 10.1038/s10038-018-0483-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
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14
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Eguchi T, Sogawa C, Okusha Y, Uchibe K, Iinuma R, Ono K, Nakano K, Murakami J, Itoh M, Arai K, Fujiwara T, Namba Y, Murata Y, Ohyama K, Shimomura M, Okamura H, Takigawa M, Nakatsura T, Kozaki KI, Okamoto K, Calderwood SK. Organoids with cancer stem cell-like properties secrete exosomes and HSP90 in a 3D nanoenvironment. PLoS One 2018; 13:e0191109. [PMID: 29415026 PMCID: PMC5802492 DOI: 10.1371/journal.pone.0191109] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/28/2017] [Indexed: 12/12/2022] Open
Abstract
Ability to form cellular aggregations such as tumorspheres and spheroids have been used as a morphological marker of malignant cancer cells and in particular cancer stem cells (CSC). However, the common definition of the types of cellular aggregation formed by cancer cells has not been available. We examined morphologies of 67 cell lines cultured on three dimensional morphology enhancing NanoCulture Plates (NCP) and classified the types of cellular aggregates that form. Among the 67 cell lines, 49 cell lines formed spheres or spheroids, 8 cell lines formed grape-like aggregation (GLA), 8 cell lines formed other types of aggregation, and 3 cell lines formed monolayer sheets. Seven GLA-forming cell lines were derived from adenocarcinoma among the 8 lines. A neuroendocrine adenocarcinoma cell line PC-3 formed asymmetric GLA with ductal structures on the NCPs and rapidly growing asymmetric tumors that metastasized to lymph nodes in immunocompromised mice. In contrast, another adenocarcinoma cell line DU-145 formed spheroids in vitro and spheroid-like tumors in vivo that did not metastasize to lymph nodes until day 50 after transplantation. Culture in the 3D nanoenvironment and in a defined stem cell medium enabled the neuroendocrine adenocarcinoma cells to form slowly growing large organoids that expressed multiple stem cell markers, neuroendocrine markers, intercellular adhesion molecules, and oncogenes in vitro. In contrast, the more commonly used 2D serum-contained environment reduced intercellular adhesion and induced mesenchymal transition and promoted rapid growth of the cells. In addition, the 3D stemness nanoenvironment promoted secretion of HSP90 and EpCAM-exosomes, a marker of CSC phenotype, from the neuroendocrine organoids. These findings indicate that the NCP-based 3D environment enables cells to form stem cell tumoroids with multipotency and model more accurately the in vivo tumor status at the levels of morphology and gene expression.
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Affiliation(s)
- Takanori Eguchi
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Chiharu Sogawa
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuka Okusha
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kenta Uchibe
- Department of Oral Morphology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | | | - Kisho Ono
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Keisuke Nakano
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Jun Murakami
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
- Department of Oral Diagnosis and Dent-maxillofacial Radiology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Manabu Itoh
- JSR Life Sciences Corporation, Tsukuba, Japan
| | - Kazuya Arai
- JSR Life Sciences Corporation, Tsukuba, Japan
| | - Toshifumi Fujiwara
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuri Namba
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yoshiki Murata
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kazumi Ohyama
- Radio Isotope Research Center, Okayama University Dental School, Okayama, Japan
| | - Manami Shimomura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Hirohiko Okamura
- Department of Oral Morphology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masaharu Takigawa
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Ken-ichi Kozaki
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kuniaki Okamoto
- Department of Dental Pharmacology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Stuart K. Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
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Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. Sci Rep 2018; 8:733. [PMID: 29335598 PMCID: PMC5768793 DOI: 10.1038/s41598-017-19004-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0.05) using the Genotype-Tissue Expression data and found evidence for their clinical relevance using integrated molecular profiling and lung adenocarcinoma survival data from The Cancer Genome Atlas project. We identified 39 miRNAs with significant differential expression (BH adjusted p < 0.05) in LCLs. We developed a gene expression based imputation model of drug sensitivity, quantified its prediction performance, and found a significant correlation of the imputed phenotype generated from expression data with survival time in lung adenocarcinoma patients. Differentially expressed genes (MTHFD2 and SUFU) that are putative targets of differentially expressed miRNAs also showed differential perturbation in A549 fusion lung tumor cells with further replication in A549 cells. Our study suggests pemetrexed may be used in combination with agents that target miRNAs to increase its cytotoxicity.
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16
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Hillger JM, Lieuw WL, Heitman LH, IJzerman AP. Label-free technology and patient cells: from early drug development to precision medicine. Drug Discov Today 2017; 22:1808-1815. [PMID: 28778587 DOI: 10.1016/j.drudis.2017.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/10/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
Abstract
Drug development requires physiologically more appropriate model systems and assays to increase understanding of drug action and pathological processes in individual humans. Specifically, patient-derived cells offer great opportunities as representative cellular model systems. Moreover, with novel label-free cellular assays, it is often possible to investigate complex biological processes in their native environment. Combining these two offers distinct opportunities for increasing physiological relevance. Here, we review impedance-based label-free technologies in the context of patient samples, focusing on commonly used cell types, including fibroblasts, blood components, and stem cells. Applications extend as far as tissue-on-a-chip models. Thus, applying label-free technologies to patient samples can produce highly biorelevant data and, with them, unique opportunities for drug development and precision medicine.
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Affiliation(s)
- Julia M Hillger
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Wai-Ling Lieuw
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands.
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17
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Gallo A, Vella S, Miele M, Timoneri F, Di Bella M, Bosi S, Sciveres M, Conaldi PG. Global profiling of viral and cellular non-coding RNAs in Epstein-Barr virus-induced lymphoblastoid cell lines and released exosome cargos. Cancer Lett 2016; 388:334-343. [PMID: 27956246 DOI: 10.1016/j.canlet.2016.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
The human EBV-transformed lymphoblastoid cell line (LCL), obtained by infecting peripheral blood monocular cells with Epstein-Barr Virus, has been extensively used for human genetic, pharmacogenomic, and immunologic studies. Recently, the role of exosomes has also been indicated as crucial in the crosstalk between EBV and the host microenvironment. Because the role that the LCL and LCL exosomal cargo might play in maintaining persistent infection, and since little is known regarding the non-coding RNAs of LCL, the aim of our work was the comprehensive characterization of this class of RNA, cellular and viral miRNAs, and cellular lncRNAs, in LCL compared with PBMC derived from the same donors. In this study, we have demonstrated, for the first time, that all the viral miRNAs expressed by LCL are also packaged in the exosomes, and we found that two miRNAs, ebv-miR-BART3 and ebv-miR-BHRF1-1, are more abundant in the exosomes, suggesting a microvescicular viral microRNA transfer. In addition, lncRNA profiling revealed that LCLs were enriched in lncRNA H19 and H19 antisense, and released these through exosomes, suggesting a leading role in the regulation of the tumor microenvironment.
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Affiliation(s)
- Alessia Gallo
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy.
| | - Serena Vella
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy
| | | | | | | | | | - Marco Sciveres
- Pediatric Hepatology and Liver Transplantation, IRCCS ISMETT, University of Pittsburgh Medical Center, Palermo, Italy
| | - Pier Giulio Conaldi
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy; Fondazione Ri.MED, Italy
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18
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Investigating Leber's hereditary optic neuropathy: Cell models and future perspectives. Mitochondrion 2016; 32:19-26. [PMID: 27847334 DOI: 10.1016/j.mito.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/19/2023]
Abstract
Leber's hereditary optic neuropathy (LHON) was the first human disease found to be associated with a mitochondrial DNA (mtDNA) point mutation. The most common LHON mutations are 11778G>A, 3460G>A or 14484T>C. The most common clinical features of LHON are optic nerve and retina atrophy. The affected tissue is not available for studies, therefore a variety of other cell types are used. However, all models face difficulties and limitations in mitochondrial disease research. The advantages and disadvantages of different cell models used to study LHON, recent advances in animal model generation and novel approaches in this field are discussed.
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Chambliss AB, Chan DW. Precision medicine: from pharmacogenomics to pharmacoproteomics. Clin Proteomics 2016; 13:25. [PMID: 27708556 PMCID: PMC5037608 DOI: 10.1186/s12014-016-9127-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
Disease progression and drug response may vary significantly from patient to patient. Fortunately, the rapid development of high-throughput ‘omics’ technologies has allowed for the identification of potential biomarkers that may aid in the understanding of the heterogeneities in disease development and treatment outcomes. However, mechanistic gaps remain when the genome or the proteome are investigated independently in response to drug treatment. In this article, we discuss the current status of pharmacogenomics in precision medicine and highlight the needs for concordant analysis at the proteome and metabolome levels via the more recently-evolved fields of pharmacoproteomics, toxicoproteomics, and pharmacometabolomics. Integrated ‘omics’ investigations will be critical in piecing together targetable mechanisms of action for both drug development and monitoring of therapy in order to fully apply precision medicine to the clinic.
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Affiliation(s)
- Allison B Chambliss
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA ; Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033 USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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20
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A Novel High-Throughput 3D Screening System for EMT Inhibitors: A Pilot Screening Discovered the EMT Inhibitory Activity of CDK2 Inhibitor SU9516. PLoS One 2016; 11:e0162394. [PMID: 27622654 PMCID: PMC5021355 DOI: 10.1371/journal.pone.0162394] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/22/2016] [Indexed: 11/21/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a crucial pathological event in cancer, particularly in tumor cell budding and metastasis. Therefore, control of EMT can represent a novel therapeutic strategy in cancer. Here, we introduce an innovative three-dimensional (3D) high-throughput screening (HTS) system that leads to an identification of EMT inhibitors. For the establishment of the novel 3D-HTS system, we chose NanoCulture Plates (NCP) that provided a gel-free micro-patterned scaffold for cells and were independent of other spheroid formation systems using soft-agar. In the NCP-based 3D cell culture system, A549 lung cancer cells migrated, gathered, and then formed multiple spheroids within 7 days. Live cell imaging experiments showed that an established EMT-inducer TGF-β promoted peripheral cells around the core of spheroids to acquire mesenchymal spindle shapes, loss of intercellular adhesion, and migration from the spheroids. Along with such morphological change, EMT-related gene expression signatures were altered, particularly alteration of mRNA levels of ECAD/CDH1, NCAD/CDH2, VIM and ZEB1/TCF8. These EMT-related phenotypic changes were blocked by SB431542, a TGF-βreceptor I (TGFβR1) inhibitor. Inside of the spheroids were highly hypoxic; in contrast, spheroid-derived peripheral migrating cells were normoxic, revealed by visualization and quantification using Hypoxia Probe. Thus, TGF-β-triggered EMT caused spheroid hypoplasia and loss of hypoxia. Spheroid EMT inhibitory (SEMTIN) activity of SB431542 was calculated from fluorescence intensities of the Hypoxia Probe, and then was utilized in a drug screening of EMT-inhibitory small molecule compounds. In a pilot screening, 9 of 1,330 compounds were above the thresholds of the SEMTIN activity and cell viability. Finally, two compounds SB-525334 and SU9516 showed SEMTIN activities in a dose dependent manner. SB-525334 was a known TGFβR1 inhibitor. SU9516 was a cyclin-dependent kinase 2 (CDK2) inhibitor, which we showed also had an EMT-inhibitory activity. The half maximal inhibitory concentration (IC50) of SB-525334 and SU9516 were 0.31 μM and 1.21 μM, respectively, while IC50 of SB431542 was 2.38 μM. Taken together, it was shown that this 3D NCP-based HTS system was useful for screening of EMT-regulatory drugs.
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Grassi MA, Rao VR, Chen S, Cao D, Gao X, Cleary PA, Huang RS, Paterson AD, Natarajan R, Rehman J, Kern TS. Lymphoblastoid Cell Lines as a Tool to Study Inter-Individual Differences in the Response to Glucose. PLoS One 2016; 11:e0160504. [PMID: 27509144 PMCID: PMC4979894 DOI: 10.1371/journal.pone.0160504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/20/2016] [Indexed: 01/15/2023] Open
Abstract
Background White blood cells have been shown in animal studies to play a central role in the pathogenesis of diabetic retinopathy. Lymphoblastoid cells are immortalized EBV-transformed primary B-cell leukocytes that have been extensively used as a model for conditions in which white blood cells play a primary role. The purpose of this study was to investigate whether lymphoblastoid cell lines, by retaining many of the key features of primary leukocytes, can be induced with glucose to demonstrate relevant biological responses to those found in diabetic retinopathy. Methods Lymphoblastoid cell lines were obtained from twenty-three human subjects. Differences between high and standard glucose conditions were assessed for expression, endothelial adhesion, and reactive oxygen species. Results Collectively, stimulation of the lymphoblastoid cell lines with high glucose demonstrated corresponding changes on molecular, cellular and functional levels. Lymphoblastoid cell lines up-regulated expression of a panel of genes associated with the leukocyte-mediated inflammation found in diabetic retinopathy that include: a cytokine (IL-1B fold change = 2.11, p-value = 0.02), an enzyme (PKCB fold change = 2.30, p-value = 0.01), transcription factors (NFKB-p50 fold change = 2.05, p-value = 0.01), (NFKB-p65 fold change = 2.82, p-value = 0.003), and an adhesion molecule (CD18 fold change = 2.59, 0.02). Protein expression of CD18 was also increased (p-value = 2.14x10-5). The lymphoblastoid cell lines demonstrated increased adhesiveness to endothelial cells (p = 1.28x10-5). Reactive oxygen species were increased (p = 2.56x10-6). Significant inter-individual variation among the lymphoblastoid cell lines in these responses was evident (F = 18.70, p < 0.0001). Conclusions Exposure of lymphoblastoid cell lines derived from different human subjects to high glucose demonstrated differential and heterogeneous gene expression, adhesion, and cellular effects that recapitulated features found in the diabetic state. Lymphoblastoid cells may represent a useful tool to guide an individualized understanding of the development and potential treatment of diabetic complications like retinopathy.
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Affiliation(s)
- Michael A. Grassi
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Vidhya R. Rao
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Dingcai Cao
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Xiaoyu Gao
- The Biostatistics Center, George Washington University, Rockville, Maryland, United States of America
| | - Patricia A. Cleary
- The Biostatistics Center, George Washington University, Rockville, Maryland, United States of America
| | - R. Stephanie Huang
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Andrew D. Paterson
- Genetics and Genome Biology Research Institute, Sickkids, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Jalees Rehman
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Timothy S. Kern
- Departments of Medicine and Pharmacology Case Western Reserve University, Cleveland, Ohio, United States of America, and the Veterans Administration Medical Center Research Service 151, Cleveland, Ohio, United States of America
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Morrison G, Liu C, Wing C, Delaney SM, Zhang W, Dolan ME. Evaluation of inter-batch differences in stem-cell derived neurons. Stem Cell Res 2015; 16:140-8. [PMID: 26774046 DOI: 10.1016/j.scr.2015.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 01/24/2023] Open
Abstract
Differentiated cells retain the genetic information of the donor but the extent to which phenotypic differences between donors or batches of differentiated cells are explained by variation introduced during the differentiation process is not fully understood. In this study, we evaluated four separate batches of commercially available neurons originating from the same iPSCs to investigate whether the differentiation process used in manufacturing iPSCs to neurons affected genome-wide gene expression and modified cytosines, or neuronal sensitivity to drugs. No significant changes in gene expression, as measured by RNA-Seq, or cytosine modification levels, as measured by the Illumina 450K arrays, were observed between batches relative to changes over time. As expected, neurotoxic chemotherapeutics affected neuronal outgrowth, but no inter-batch differences were observed in sensitivity to paclitaxel, vincristine and cisplatin. As a testament to the utility of the model for studies of neuropathy, we observed that genes involved in neuropathy had relatively higher expression levels in these samples across different time points. Our results suggest that the process used to differentiate iPSCs into neurons is consistent, resulting in minimal intra-individual variability across batches. Therefore, this model is reasonable for studies of human neuropathy, druggable targets to prevent neuropathy, and other neurological diseases.
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Affiliation(s)
- Gladys Morrison
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, IL 60637, USA
| | - Cong Liu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Claudia Wing
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Shannon M Delaney
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Wei Zhang
- Department of Preventive Medicine & The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - M Eileen Dolan
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, IL 60637, USA; Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
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23
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Dong Z, Liu Y, Duan L, Bekele D, Naidu R. Uncertainties in human health risk assessment of environmental contaminants: A review and perspective. ENVIRONMENT INTERNATIONAL 2015; 85:120-32. [PMID: 26386465 DOI: 10.1016/j.envint.2015.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 05/24/2023]
Abstract
Addressing uncertainties in human health risk assessment is a critical issue when evaluating the effects of contaminants on public health. A range of uncertainties exist through the source-to-outcome continuum, including exposure assessment, hazard and risk characterisation. While various strategies have been applied to characterising uncertainty, classical approaches largely rely on how to maximise the available resources. Expert judgement, defaults and tools for characterising quantitative uncertainty attempt to fill the gap between data and regulation requirements. The experiences of researching 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) illustrated uncertainty sources and how to maximise available information to determine uncertainties, and thereby provide an 'adequate' protection to contaminant exposure. As regulatory requirements and recurring issues increase, the assessment of complex scenarios involving a large number of chemicals requires more sophisticated tools. Recent advances in exposure and toxicology science provide a large data set for environmental contaminants and public health. In particular, biomonitoring information, in vitro data streams and computational toxicology are the crucial factors in the NexGen risk assessment, as well as uncertainties minimisation. Although in this review we cannot yet predict how the exposure science and modern toxicology will develop in the long-term, current techniques from emerging science can be integrated to improve decision-making.
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Affiliation(s)
- Zhaomin Dong
- The Faculty of Science and Information Technology, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Mawson Lakes, SA 5095, Australia
| | - Yanju Liu
- The Faculty of Science and Information Technology, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Mawson Lakes, SA 5095, Australia
| | - Luchun Duan
- The Faculty of Science and Information Technology, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Mawson Lakes, SA 5095, Australia
| | - Dawit Bekele
- The Faculty of Science and Information Technology, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Mawson Lakes, SA 5095, Australia
| | - Ravi Naidu
- The Faculty of Science and Information Technology, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Mawson Lakes, SA 5095, Australia.
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24
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Whole-cell biosensor for label-free detection of GPCR-mediated drug responses in personal cell lines. Biosens Bioelectron 2015; 74:233-42. [DOI: 10.1016/j.bios.2015.06.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]
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25
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Hunsberger JG, Efthymiou AG, Malik N, Behl M, Mead IL, Zeng X, Simeonov A, Rao M. Induced Pluripotent Stem Cell Models to Enable In Vitro Models for Screening in the Central Nervous System. Stem Cells Dev 2015; 24:1852-64. [PMID: 25794298 PMCID: PMC4533087 DOI: 10.1089/scd.2014.0531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/20/2015] [Indexed: 12/23/2022] Open
Abstract
There is great need to develop more predictive drug discovery tools to identify new therapies to treat diseases of the central nervous system (CNS). Current nonpluripotent stem cell-based models often utilize non-CNS immortalized cell lines and do not enable the development of personalized models of disease. In this review, we discuss why in vitro models are necessary for translational research and outline the unique advantages of induced pluripotent stem cell (iPSC)-based models over those of current systems. We suggest that iPSC-based models can be patient specific and isogenic lines can be differentiated into many neural cell types for detailed comparisons. iPSC-derived cells can be combined to form small organoids, or large panels of lines can be developed that enable new forms of analysis. iPSC and embryonic stem cell-derived cells can be readily engineered to develop reporters for lineage studies or mechanism of action experiments further extending the utility of iPSC-based systems. We conclude by describing novel technologies that include strategies for the development of diversity panels, novel genomic engineering tools, new three-dimensional organoid systems, and modified high-content screens that may bring toxicology into the 21st century. The strategic integration of these technologies with the advantages of iPSC-derived cell technology, we believe, will be a paradigm shift for toxicology and drug discovery efforts.
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Affiliation(s)
| | | | - Nasir Malik
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland
| | - Mamta Behl
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Ivy L. Mead
- Wake Forest Institute for Regenerative Medicine, Winston-Salem, North Carolina
| | - Xianmin Zeng
- Buck Institute for Age Research, Novato, California
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland
| | - Mahendra Rao
- New York Stem Cell Foundation, New York, New York
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Beam AL, Motsinger-Reif AA, Doyle J. An investigation of gene-gene interactions in dose-response studies with Bayesian nonparametrics. BioData Min 2015; 8:6. [PMID: 25691918 PMCID: PMC4330980 DOI: 10.1186/s13040-015-0039-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 01/18/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Best practice for statistical methodology in cell-based dose-response studies has yet to be established. We examine the ability of MANOVA to detect trait-associated genetic loci in the presence of gene-gene interactions. We present a novel Bayesian nonparametric method designed to detect such interactions. RESULTS MANOVA and the Bayesian nonparametric approach show good ability to detect trait-associated genetic variants under various possible genetic models. It is shown through several sets of analyses that this may be due to marginal effects being present, even if the underlying genetic model does not explicitly contain them. CONCLUSIONS Understanding how genetic interactions affect drug response continues to be a critical goal. MANOVA and the novel Bayesian framework present a trade-off between computational complexity and model flexibility.
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Affiliation(s)
- Andrew L Beam
- Center for Biomedical Informatics, Boston, Massachusetts
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina ; Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | - Jon Doyle
- Department of Computer Science, North Carolina State University, Raleigh, North Carolina
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27
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Brown CC, Havener TM, Medina MW, Jack JR, Krauss RM, McLeod HL, Motsinger-Reif AA. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Pharmacogenomics 2015; 15:137-46. [PMID: 24444404 DOI: 10.2217/pgs.13.213] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Association mapping with lymphoblastoid cell lines (LCLs) is a promising approach in pharmacogenomics research, and in the current study we utilized LCLs to perform association mapping for 29 chemotherapy drugs. MATERIALS & METHODS Currently, we use LCLs to perform genome-wide association mapping of the cytotoxic response of 520 European-Americans to 29 different anticancer drugs; the largest LCL study to date. A novel association approach using a multivariate analysis of covariance design was employed with the software program MAGWAS, testing for differences in the dose-response profiles between genotypes without making assumptions about the response curve or the biologic mode of association. Additionally, by classifying 25 of the 29 drugs into eight families according to structural and mechanistic relationships, MAGWAS was used to test for associations that were shared across each drug family. Finally, a unique algorithm using multivariate responses and multiple linear regressions across pairs of response curves was used for unsupervised clustering of drugs. RESULTS Among the single-drug studies, suggestive associations were obtained for 18 loci, 12 within/near genes. Three of these, MED12L, CHN2 and MGMT, have been previously implicated in cancer pharmacogenomics. The drug family associations resulted in four additional suggestive loci (three contained within/near genes). One of these genes, HDAC4, associated with the DNA alkylating agents, shows possible clinical interactions with temozolomide. For the drug clustering analysis, 18 of 25 drugs clustered into the appropriate family. CONCLUSION This study demonstrates the utility of LCLs in identifying genes that have clinical importance in drug response and for assigning unclassified agents to specific drug families, and proposes new candidate genes for follow-up in a large number of chemotherapy drugs.
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Affiliation(s)
- Chad C Brown
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
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Meng X, Wang G, Guan R, Jia X, Gao W, Wu J, Yu J, Liu P, Yu Y, Sun W, Dong H, Fu S. Predicting chemosensitivity to gemcitabine and cisplatin based on gene polymorphisms and mRNA expression in non-small-cell lung cancer cells. Pharmacogenomics 2015; 16:23-34. [DOI: 10.2217/pgs.14.159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: We used a panel of 17 non-small-cell lung cancer cell lines to investigate whether the presence of polymorphisms in the RRM1, ERCC1, ABCB1 and MTHFR genes and alterations in their mRNA expression can affect the in vitro chemosensitivity to cisplatin and gemcitabine. Materials & methods: Polymorphisms in these genes were evaluated by direct sequencing. mRNA expression levels were assessed by realtime PCR. In vitro chemosensitivity to cisplatin and gemcitabine was expressed as IC50 values, using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay. Results: There was a significant, positive correlation between RRM1 mRNA expression and IC50 values for gemcitabine (r = 0.6533, p = 0.0045), and there was a significant, negative correlation between ABCB1 mRNA expression and IC50 values for cisplatin (r = -0.5459, p = 0.0287). When examining the association between the polymorphisms and IC50, we found that only the MTHFR 1298A>C polymorphism showed a tendency to be more chemosensitive to gemcitabine (p = 0.0440). Conclusion: These in vitro results suggest that mRNA expression levels of the RRM1 and ABCB1 genes may be useful indicators of chemosensitivity to gemcitabine and cisplatin, respectively. The MTHFR 1298A>C polymorphism was associated with gemcitabine chemosensitivity, which require further functional analysis with co-expressed genes and should be explored in prospective clinical studies to determine its potential clinical application as a predictive biomarker. Original submitted 11 February 2014; Revision submitted 3 November 2014
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Affiliation(s)
- Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Geng Wang
- Department of Anatomy, Harbin Medical University, Harbin 150081, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Wei Gao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jingcui Yu
- The Second Affiliated Hospital, Harbin Medical University, Harbin 150081, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Haiying Dong
- Department of Internal Medicine-Oncology, Zhejiang Province People's Hospital, Hangzhou 310014, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
- Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin 150081, China
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29
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Hemnes AR, Trammell AW, Archer SL, Rich S, Yu C, Nian H, Penner N, Funke M, Wheeler L, Robbins IM, Austin ED, Newman JH, West J. Peripheral blood signature of vasodilator-responsive pulmonary arterial hypertension. Circulation 2014; 131:401-9; discussion 409. [PMID: 25361553 DOI: 10.1161/circulationaha.114.013317] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Heterogeneity in response to treatment of pulmonary arterial hypertension (PAH) is a major challenge to improving outcome in this disease. Although vasodilator-responsive PAH (VR-PAH) accounts for a minority of cases, VR-PAH has a pronounced response to calcium channel blockers and better survival than vasodilator-nonresponsive PAH (VN-PAH). We hypothesized that VR-PAH has a different molecular cause from VN-PAH that can be detected in the peripheral blood. METHODS AND RESULTS Microarrays of cultured lymphocytes from VR-PAH and VN-PAH patients followed at Vanderbilt University were performed with quantitative polymerase chain reaction performed on peripheral blood for the 25 most different genes. We developed a decision tree to identify VR-PAH patients on the basis of the results with validation in a second VR-PAH cohort from the University of Chicago. We found broad differences in gene expression patterns on microarray analysis including cell-cell adhesion factors and cytoskeletal and rho-GTPase genes. Thirteen of 25 genes tested in whole blood were significantly different: EPDR1, DSG2, SCD5, P2RY5, MGAT5, RHOQ, UCHL1, ZNF652, RALGPS2, TPD52, MKNL1, RAPGEF2, and PIAS1. Seven decision trees were built with the use of expression levels of 2 genes as the primary genes: DSG2, a desmosomal cadherin involved in Wnt/β-catenin signaling, and RHOQ, which encodes a cytoskeletal protein involved in insulin-mediated signaling. These trees correctly identified 5 of 5 VR-PAH patients in the validation cohort. CONCLUSIONS VR-PAH and VN-PAH can be differentiated with the use of RNA expression patterns in peripheral blood. These differences may reflect different molecular causes of the 2 PAH phenotypes. This biomarker methodology may identify PAH patients who have a favorable treatment response.
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Affiliation(s)
- Anna R Hemnes
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.).
| | - Aaron W Trammell
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Stephen L Archer
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Stuart Rich
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Chang Yu
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Hui Nian
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Niki Penner
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Mitchell Funke
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Lisa Wheeler
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Ivan M Robbins
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - Eric D Austin
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - John H Newman
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
| | - James West
- From the Division of Allergy, Pulmonary, and Critical Care Medicine (A.R.H., A.W.T., N.P., M.F., L.W., I.M.R., J.H.N., J.W.) and Department of Biostatistics (C.Y., H.N.), Vanderbilt University School of Medicine, Nashville, TN; Department of Medicine, Queen's University, Kingston, Ontario, Canada (S.L.A.); Division of Cardiology, University of Chicago, Chicago, IL (S.R.); and Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN (E.D.A.)
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Suzuki OT, Frick A, Parks BB, Trask OJ, Butz N, Steffy B, Chan E, Scoville DK, Healy E, Benton C, McQuaid PE, Thomas RS, Wiltshire T. A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes. Front Genet 2014; 5:272. [PMID: 25221565 PMCID: PMC4148776 DOI: 10.3389/fgene.2014.00272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/24/2014] [Indexed: 12/03/2022] Open
Abstract
New approaches to toxicity testing have incorporated high-throughput screening across a broad-range of in vitro assays to identify potential key events in response to chemical or drug treatment. To date, these approaches have primarily utilized repurposed drug discovery assays. In this study, we describe an approach that combines in vitro screening with genetic approaches for the experimental identification of genes and pathways involved in chemical or drug toxicity. Primary embryonic fibroblasts isolated from 32 genetically-characterized inbred mouse strains were treated in concentration-response format with 65 compounds, including pharmaceutical drugs, environmental chemicals, and compounds with known modes-of-action. Integrated cellular responses were measured at 24 and 72 h using high-content imaging and included cell loss, membrane permeability, mitochondrial function, and apoptosis. Genetic association analysis of cross-strain differences in the cellular responses resulted in a collection of candidate loci potentially underlying the variable strain response to each chemical. As a demonstration of the approach, one candidate gene involved in rotenone sensitivity, Cybb, was experimentally validated in vitro and in vivo. Pathway analysis on the combined list of candidate loci across all chemicals identified a number of over-connected nodes that may serve as core regulatory points in toxicity pathways.
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Affiliation(s)
- Oscar T Suzuki
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Amber Frick
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Bethany B Parks
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA
| | - O Joseph Trask
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA
| | - Natasha Butz
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Brian Steffy
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Emmanuel Chan
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - David K Scoville
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Eric Healy
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA
| | - Cristina Benton
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | | | - Russell S Thomas
- The Hamner Institutes for Health Sciences, Research Triangle Park NC, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy at the University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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31
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Khsheibun R, Paperna T, Volkowich A, Lejbkowicz I, Avidan N, Miller A. Gene expression profiling of the response to interferon beta in Epstein-Barr-transformed and primary B cells of patients with multiple sclerosis. PLoS One 2014; 9:e102331. [PMID: 25025430 PMCID: PMC4099420 DOI: 10.1371/journal.pone.0102331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/16/2014] [Indexed: 01/03/2023] Open
Abstract
The effects of interferon-beta (IFN-β), one of the key immunotherapies used in multiple sclerosis (MS), on peripheral blood leukocytes and T cells have been extensively studied. B cells are a less abundant leukocyte type, and accordingly less is known about the B cell-specific response to IFN-β. To identify gene expression changes and pathways induced by IFN-β in B cells, we studied the in vitro response of human Epstein Barr-transformed B cells (lymphoblast cell lines-LCLs), and validated our results in primary B cells. LCLs were derived from an MS patient repository. Whole genome expression analysis identified 115 genes that were more than two-fold differentially up-regulated following IFN-β exposure, with over 50 previously unrecognized as IFN-β response genes. Pathways analysis demonstrated that IFN-β affected LCLs in a similar manner to other cell types by activating known IFN-β canonical pathways. Additionally, IFN-β increased the expression of innate immune response genes, while down-regulating many B cell receptor pathway genes and genes involved in adaptive immune responses. Novel response genes identified herein, NEXN, DDX60L, IGFBP4, and HAPLN3, B cell receptor pathway genes, CD79B and SYK, and lymphocyte activation genes, LAG3 and IL27RA, were validated as IFN-β response genes in primary B cells. In this study new IFN-β response genes were identified in B cells, with possible implications to B cell-specific functions. The study's results emphasize the applicability of LCLs for studies of human B cell drug response. The usage of LCLs from patient-based repositories may facilitate future studies of drug response in MS and other immune-mediated disorders with a B cell component.
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Affiliation(s)
- Rana Khsheibun
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tamar Paperna
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Anat Volkowich
- Division of Neuroimmunology and Multiple Sclerosis Center, Carmel Medical Center, Haifa, Israel
| | - Izabella Lejbkowicz
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nili Avidan
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ariel Miller
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Division of Neuroimmunology and Multiple Sclerosis Center, Carmel Medical Center, Haifa, Israel
- * E-mail:
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Hariani GD, Lam EJ, Havener T, Kwok PY, McLeod HL, Wagner MJ, Motsinger-Reif AA. Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics. BMC Res Notes 2014; 7:360. [PMID: 24924344 PMCID: PMC4068968 DOI: 10.1186/1756-0500-7-360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 05/30/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The goal of this study was to perform candidate gene association with cytotoxicity of chemotherapeutics in cell line models through resequencing and discovery of rare and low frequency variants along with common variations. Here, an association study of cytotoxicity response to 30 FDA approved drugs was conducted and we applied next generation targeted sequencing technology to discover variants from 103 candidate genes in 95 lymphoblastoid cell lines from 14 CEPH pedigrees. In this article, we called variants across 95 cell lines and performed association analysis for cytotoxic response using the Family Based Association Testing method and software. RESULTS We called 2281 variable SNP genotypes across the 103 genes for these cell lines and identified three genes of significant association within this marker set. Specifically, ATP-binding cassette, sub-family C, member 5 (ABCC5), metallothionein 1A (MT1A) and NAD(P)H dehydrogenase quinone1 (NQO1) were significantly associated with oxaliplatin drug response. The significant SNP on NQO1 (rs1800566) has been linked with poor survival rates in patients with non-small cell lung cancer treated with cisplatin (which belongs to the same class of drugs as oxaliplatin). A SNP (rs1846692) near the 5' region of MT1A was associated with arsenic trioxide. CONCLUSIONS The results from this study are promising and this serves as a proof-of-principle demonstration of the use of sequencing data in the cytotoxicity models of human cell lines. With increased sample sizes, such studies will be a fast and powerful way to associate common and rare variants with drug response; while overcoming the cost and time limitations to recruit cohorts for association study.
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Affiliation(s)
- Gunjan D Hariani
- Bioinformatics Research Center, North Carolina State University, 307 Ricks Hall, 1 Lampe Dr, Raleigh, NC 27695 CB7566, USA
| | - Ernest J Lam
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA, USA
| | - Tammy Havener
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA, USA
| | - Howard L McLeod
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
- Moffitt Cancer Center, Tampa, FL, USA
| | - Michael J Wagner
- Center for Institute of Pharmacogenomics and Individualized Therapy, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, 307 Ricks Hall, 1 Lampe Dr, Raleigh, NC 27695 CB7566, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
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Swart M, Dandara C. Genetic variation in the 3'-UTR of CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2, and UGT2B7: potential effects on regulation by microRNA and pharmacogenomics relevance. Front Genet 2014; 5:167. [PMID: 24926315 PMCID: PMC4044583 DOI: 10.3389/fgene.2014.00167] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/19/2014] [Indexed: 01/07/2023] Open
Abstract
Introduction: Pharmacogenomics research has concentrated on variation in genes coding for drug metabolizing enzymes, transporters and nuclear receptors. However, variation affecting microRNA could also play a role in drug response. This project set out to investigate potential microRNA target sites in 11 genes and the extent of variation in the 3′-UTR of six selected genes; CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2, and UGT2B7. Methods: Fifteen microRNA target prediction algorithms were used to identify microRNAs predicted to regulate 11 genes. The 3′-UTR of the 6 genes which topped the list of potential microRNA targets was sequenced in 30 black South Africans. In addition, genetic variants within these genes were investigated for interference with mRNA-microRNA interactions. Potential effects of observed variants were determined using in silico prediction tools. Results: The 11 genes coding for DMEs, transporters and nuclear receptors were predicted to be targets of microRNAs with CYP2B6, NR1I2 (PXR), CYP3A4, and CYP1A2, interacting with the most microRNAs. The majority of identified genetic variants were predicted to interfere with microRNA regulation. For example, the variant, rs1054190C in NR1I2 was predicted to result in the presence of a binding site for the microRNA miR-1250-5p, while the variant rs1054191G was predicted to result in the absence of a recognition site for miR-371b-3p, miR-4258 and miR-4707-3p. Fifteen of the seventeen, novel variants occurred within microRNA target sequences. Conclusion: The 3′-UTR harbors variation that is likely to influence regulation of specific genes by microRNA. In silico prediction followed by functional validation could aid in decoding the contribution of variation in the 3′-UTR, to some unexplained heritability that affects drug response. Understanding the specific role of each microRNA may lead to identification of markers for targeted therapy and therefore improve personalized drug treatment.
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Affiliation(s)
- Marelize Swart
- Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town Cape Town, South Africa
| | - Collet Dandara
- Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town Cape Town, South Africa
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Weng L, Ziliak D, LaCroix B, Geeleher P, Huang RS. Integrative "omic" analysis for tamoxifen sensitivity through cell based models. PLoS One 2014; 9:e93420. [PMID: 24699530 PMCID: PMC3974759 DOI: 10.1371/journal.pone.0093420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/04/2014] [Indexed: 12/25/2022] Open
Abstract
It has long been observed that tamoxifen sensitivity varies among breast cancer patients. Further, ethnic differences of tamoxifen therapy between Caucasian and African American have also been reported. Since most studies have been focused on Caucasian people, we sought to comprehensively evaluate genetic variants related to tamoxifen therapy in African-derived samples. An integrative "omic" approach developed by our group was used to investigate relationships among endoxifen (an active metabolite of tamoxifen) sensitivity, SNP genotype, mRNA and microRNA expressions in 58 HapMap YRI lymphoblastoid cell lines. We identified 50 SNPs that associate with cellular sensitivity to endoxifen through their effects on 34 genes and 30 microRNA expression. Some of these findings are shared in both Caucasian and African samples, while others are unique in the African samples. Among gene/microRNA that were identified in both ethnic groups, the expression of TRAF1 is also correlated with tamoxifen sensitivity in a collection of 44 breast cancer cell lines. Further, knock-down TRAF1 and over-expression of hsa-let-7i confirmed the roles of hsa-let-7i and TRAF1 in increasing tamoxifen sensitivity in the ZR-75-1 breast cancer cell line. Our integrative omic analysis facilitated the discovery of pharmacogenomic biomarkers that potentially affect tamoxifen sensitivity.
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Affiliation(s)
- Liming Weng
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Dana Ziliak
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Bonnie LaCroix
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Paul Geeleher
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - R. Stephanie Huang
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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Abstract
Current drug discovery is dominated by label-dependent molecular approaches, which screen drugs in the context of a predefined and target-based hypothesis in vitro. Given that target-based discovery has not transformed the industry, phenotypic screen that identifies drugs based on a specific phenotype of cells, tissues, or animals has gained renewed interest. However, owing to the intrinsic complexity in drug-target interactions, there is often a significant gap between the phenotype screened and the ultimate molecular mechanism of action sought. This paper presents a label-free strategy for early drug discovery. This strategy combines label-free cell phenotypic profiling with computational approaches, and holds promise to bridge the gap by offering a kinetic and holistic representation of the functional consequences of drugs in disease relevant cells that is amenable to mechanistic deconvolution.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning Incorporated Corning, NY, USA
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Travis LB, Fossa SD, Sesso HD, Frisina RD, Herrmann DN, Beard CJ, Feldman DR, Pagliaro LC, Miller RC, Vaughn DJ, Einhorn LH, Cox NJ, Dolan ME. Chemotherapy-induced peripheral neurotoxicity and ototoxicity: new paradigms for translational genomics. J Natl Cancer Inst 2014; 106:dju044. [PMID: 24623533 PMCID: PMC4568989 DOI: 10.1093/jnci/dju044] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 01/07/2023] Open
Abstract
In view of advances in early detection and treatment, the 5-year relative survival rate for all cancer patients combined is now approximately 66%. As a result, there are more than 13.7 million cancer survivors in the United States, with this number increasing by 2% annually. For many patients, improvements in survival have been countered by therapy-associated adverse effects that may seriously impair long-term functional status, workplace productivity, and quality of life. Approximately 20% to 40% of cancer patients given neurotoxic chemotherapy develop chemotherapy-induced peripheral neurotoxicity (CIPN), which represents one of the most common and potentially permanent nonhematologic side effects of chemotherapy. Permanent bilateral hearing loss and/or tinnitus can result from several ototoxic therapies, including cisplatin- or carboplatin-based chemotherapy. CIPN and ototoxicity represent important challenges because of the lack of means for effective prevention, mitigation, or a priori identification of high-risk patients, and few studies have applied modern genomic approaches to understand underlying mechanisms/pathways. Translational genomics, including cell-based models, now offer opportunities to make inroads for the first time to develop preventive and interventional strategies for CIPN, ototoxicity, and other treatment-related complications. This commentary provides current perspective on a successful research strategy, with a focus on cisplatin, developed by an experienced, transdisciplinary group of researchers and clinicians, representing pharmacogenomics, statistical genetics, neurology, hearing science, medical oncology, epidemiology, and cancer survivorship. Principles outlined herein are applicable to the construction of research programs in translational genomics with strong clinical relevance and highlight unprecedented opportunities to understand, prevent, and treat long-term treatment-related morbidities.
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Affiliation(s)
- Lois B Travis
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL.
| | - Sophie D Fossa
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Howard D Sesso
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Robert D Frisina
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - David N Herrmann
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Clair J Beard
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Darren R Feldman
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Lance C Pagliaro
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Robert C Miller
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - David J Vaughn
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Lawrence H Einhorn
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Nancy J Cox
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - M Eileen Dolan
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
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Integrating cell-based and clinical genome-wide studies to identify genetic variants contributing to treatment failure in neuroblastoma patients. Clin Pharmacol Ther 2014; 95:644-52. [PMID: 24549002 PMCID: PMC4029857 DOI: 10.1038/clpt.2014.37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 02/11/2014] [Indexed: 12/02/2022]
Abstract
High-risk neuroblastoma is an aggressive malignancy with high rates of treatment failure. We evaluated genetic variants associated with in vitro sensitivity to two derivatives of cyclophosphamide for association with clinical response in a separate replication cohort of neuroblastoma patients (n=2,709). Lymphoblastoid cell lines (LCLs) were exposed to increasing concentrations of 4-hydroperoxycyclophosphamide [4HC n=422] and phosphoramide mustard [PM n=428] to determine sensitivity. Genome-wide association studies (GWAS) were performed to identify single nucleotide polymorphisms (SNPs) associated with 4HC and PM sensitivity. SNPs consistently associated with LCL sensitivity were analyzed for associations with event-free survival in patients. Two linked SNPs, rs9908694 and rs1453560, were found to be associated with PM sensitivity in LCLs across populations and were associated with event-free survival in all patients (P=0.01) and within the high-risk subset (P=0.05). Our study highlights the value of cell-based models to identify candidate variants that may predict response to treatment in patients with cancer.
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Genetic variation is the major determinant of individual differences in leukocyte endothelial adhesion. PLoS One 2014; 9:e87883. [PMID: 24520339 PMCID: PMC3919726 DOI: 10.1371/journal.pone.0087883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/06/2014] [Indexed: 12/13/2022] Open
Abstract
Objective To determine the genetic contribution to leukocyte endothelial adhesion. Methods Leukocyte endothelial adhesion was assessed through a novel cell-based assay using human lymphoblastoid cell lines. A high-throughput screening method was developed to evaluate the inter-individual variability in leukocyte endothelial adhesion using lymphoblastoid cell lines derived from different donors. To assess heritability, ninety-two lymphoblastoid cell lines derived from twenty-three monozygotic twin pairs and twenty-three sibling pairs were compared. These lymphoblastoid cell lines were plated with the endothelial cell line EA.hy926 and labeled with Calcein AM dye. Fluorescence was assessed to determine endothelial cell adhesion to each lymphoblastoid cell line. Intra-pair similarity was determined for monozygotic twins and siblings using Pearson pairwise correlation coefficients. Results A leukocyte endothelial adhesion assay for lymphoblastoid cell lines was developed and optimized (CV = 8.68, Z′-factor = 0.67, SNR = 18.41). A higher adhesion correlation was found between the twins than that between the siblings. Intra-pair similarity for leukocyte endothelial adhesion in monozygotic twins was 0.60 compared to 0.25 in the siblings. The extent to which these differences are attributable to underlying genetic factors was quantified and the heritability of leukocyte endothelial adhesion was calculated to be 69.66% (p-value<0.0001). Conclusions There is a heritable component to leukocyte endothelial adhesion. Underlying genetic predisposition plays a significant role in inter-individual variability of leukocyte endothelial adhesion.
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Beam A, Motsinger-Reif A. Beyond IC 50s: Towards Robust Statistical Methods for in vitro Association Studies. ACTA ACUST UNITED AC 2014; 5:1000121. [PMID: 25110614 PMCID: PMC4125024 DOI: 10.4172/2153-0645.1000121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell line cytotoxicity assays have become increasingly popular approaches for genetic and genomic studies of differential cytotoxic response. There are an increasing number of success stories, but relatively little evaluation of the statistical approaches used in such studies. In the vast majority of these studies, concentration response is summarized using curve-fitting approaches, and then summary measure(s) are used as the phenotype in subsequent genetic association studies. The curve is usually summarized by a single parameter such as the curve's inflection point (e.g. the EC/IC50). Such modeling makes major assumptions and has statistical limitations that should be considered. In the current review, we discuss the limitations of the EC/IC50 as a phenotype in association studies, and highlight some potential limitations with a simulation experiment. Finally, we discuss some alternative analysis approaches that have been shown to be more robust.
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Affiliation(s)
- Andrew Beam
- Bioinformatics Research Center, North Carolina State University, Raleigh NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh NC, USA ; Department of Statistics, North Carolina State University, Raleigh NC, USA
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40
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Jack J, Rotroff D, Motsinger-Reif A. Lymphoblastoid cell lines models of drug response: successes and lessons from this pharmacogenomic model. Curr Mol Med 2014; 14:833-40. [PMID: 25109794 PMCID: PMC4323076 DOI: 10.2174/1566524014666140811113946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/26/2014] [Accepted: 04/23/2014] [Indexed: 12/20/2022]
Abstract
A new standard for medicine is emerging that aims to improve individual drug responses through studying associations with genetic variations. This field, pharmacogenomics, is undergoing a rapid expansion due to a variety of technological advancements that are enabling higher throughput with reductions in cost. Here we review the advantages, limitations, and opportunities for using lymphoblastoid cell lines (LCL) as a model system for human pharmacogenomic studies. There are a wide range of publicly available resources with genome-wide data available for LCLs from both related and unrelated populations, removing the cost of genotyping the data for drug response studies. Furthermore, in contrast to human clinical trials or in vivo model systems, with high-throughput in vitro screening technologies, pharmacogenomics studies can easily be scaled to accommodate large sample sizes. An important component to leveraging genome-wide data in LCL models is association mapping. Several methods are discussed herein, and include multivariate concentration response modeling, issues with multiple testing, and successful examples of the 'triangle model' to identify candidate variants. Once candidate gene variants have been determined, their biological roles can be elucidated using pathway analyses and functionally confirmed using siRNA knockdown experiments. The wealth of genomics data being produced using related and unrelated populations is creating many exciting opportunities leading to new insights into the genetic contribution and heritability of drug response.
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Affiliation(s)
| | | | - A Motsinger-Reif
- Bioinformatics Research Center, 1 Lampe Drive, CB 7566, Ricks Hall, Raleigh, NC 27695, USA.
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41
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Bolotin E, Armendariz A, Kim K, Heo SJ, Boffelli D, Tantisira K, Rotter JI, Krauss RM, Medina MW. Statin-induced changes in gene expression in EBV-transformed and native B-cells. Hum Mol Genet 2013; 23:1202-10. [PMID: 24179175 DOI: 10.1093/hmg/ddt512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human lymphoblastoid cell lines (LCLs), generated through Epstein-Barr Virus (EBV) transformation of B-lymphocytes (B-cells), are a commonly used model system for identifying genetic influences on human diseases and on drug responses. We have previously used LCLs to examine the cellular effects of genetic variants that modulate the efficacy of statins, the most prescribed class of cholesterol-lowering drugs used for the prevention and treatment of cardiovascular disease. However, statin-induced gene expression differences observed in LCLs may be influenced by their transformation, and thus differ from those observed in native B-cells. To assess this possibility, we prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24 h incubation with simvastatin (2 µm) or sham buffer. Genes involved in cholesterol metabolism were similarly regulated between the two cell types under both the statin and sham-treated conditions, and the statin-induced changes were significantly correlated. Genes whose expression differed between the native and transformed cells were primarily implicated in cell cycle, apoptosis and alternative splicing. We found that ChIP-seq signals for MYC and EBNA2 (an EBV transcriptional co-activator) were significantly enriched in the promoters of genes up-regulated in the LCLs compared with the B-cells, and could be involved in the regulation of cell cycle and alternative splicing. Taken together, the results support the use of LCLs for the study of statin effects on cholesterol metabolism, but suggest that drug effects on cell cycle, apoptosis and alternative splicing may be affected by EBV transformation. This dataset is now uploaded to GEO at the accession number GSE51444.
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Affiliation(s)
- Eugene Bolotin
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
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42
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Stark AL, Dolan ME. Lymphoblastoid cell lines in pharmacogenomics: how applicable are they to clinical outcomes? Pharmacogenomics 2013; 14:447-50. [PMID: 23556440 DOI: 10.2217/pgs.13.32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Gamazon ER, Huang RS, Dolan ME, Cox NJ, Im HK. Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Front Genet 2013; 3:202. [PMID: 23755062 PMCID: PMC3668276 DOI: 10.3389/fgene.2012.00202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/20/2012] [Indexed: 12/17/2022] Open
Abstract
Given recent advances in the generation of high-throughput data such as whole-genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs), demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we and others developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the overall significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical false discovery rate when p-values for the observed and simulated phenotypes are available.
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Affiliation(s)
- Eric R Gamazon
- Department of Medicine, University of Chicago Chicago, IL, USA
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44
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Eadon MT, Wheeler HE, Stark AL, Zhang X, Moen EL, Delaney SM, Im HK, Cunningham PN, Zhang W, Dolan ME. Genetic and epigenetic variants contributing to clofarabine cytotoxicity. Hum Mol Genet 2013; 22:4007-20. [PMID: 23720496 DOI: 10.1093/hmg/ddt240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
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Gamazon ER, Perera M. Genome-wide approaches in pharmacogenomics: heritability estimation and pharmacoethnicity as primary challenges. Pharmacogenomics 2013; 13:1101-4. [PMID: 22909197 DOI: 10.2217/pgs.12.88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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46
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Stingl (formerly Kirchheiner) J, Brockmöller J. Study Designs in Clinical Pharmacogenetic and Pharmacogenomic Research. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00009-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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47
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Zeise L, Bois FY, Chiu WA, Hattis D, Rusyn I, Guyton KZ. Addressing human variability in next-generation human health risk assessments of environmental chemicals. ENVIRONMENTAL HEALTH PERSPECTIVES 2013; 121:23-31. [PMID: 23086705 PMCID: PMC3553440 DOI: 10.1289/ehp.1205687] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/19/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Characterizing variability in the extent and nature of responses to environmental exposures is a critical aspect of human health risk assessment. OBJECTIVE Our goal was to explore how next-generation human health risk assessments may better characterize variability in the context of the conceptual framework for the source-to-outcome continuum. METHODS This review was informed by a National Research Council workshop titled "Biological Factors that Underlie Individual Susceptibility to Environmental Stressors and Their Implications for Decision-Making." We considered current experimental and in silico approaches, and emerging data streams (such as genetically defined human cells lines, genetically diverse rodent models, human omic profiling, and genome-wide association studies) that are providing new types of information and models relevant for assessing interindividual variability for application to human health risk assessments of environmental chemicals. DISCUSSION One challenge for characterizing variability is the wide range of sources of inherent biological variability (e.g., genetic and epigenetic variants) among individuals. A second challenge is that each particular pair of health outcomes and chemical exposures involves combinations of these sources, which may be further compounded by extrinsic factors (e.g., diet, psychosocial stressors, other exogenous chemical exposures). A third challenge is that different decision contexts present distinct needs regarding the identification-and extent of characterization-of interindividual variability in the human population. CONCLUSIONS Despite these inherent challenges, opportunities exist to incorporate evidence from emerging data streams for addressing interindividual variability in a range of decision-making contexts.
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Affiliation(s)
- Lauren Zeise
- Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California 94612, USA.
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48
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Mu W, Zhang W. Molecular Approaches, Models, and Techniques in Pharmacogenomic Research and Development. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00008-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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49
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Gamazon ER, Huang RS, Cox NJ. SCAN: a systems biology approach to pharmacogenomic discovery. Methods Mol Biol 2013; 1015:213-24. [PMID: 23824859 DOI: 10.1007/978-1-62703-435-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic variants identified by genome-wide scans. In particular, this public resource implements a systems biology approach to pharmacogenomic discovery.
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Affiliation(s)
- Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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50
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Brown CC, Havener TM, Medina MW, Krauss RM, McLeod HL, Motsinger‐Reif AA. Multivariate methods and software for association mapping in dose-response genome-wide association studies. BioData Min 2012; 5:21. [PMID: 23234571 PMCID: PMC3661384 DOI: 10.1186/1756-0381-5-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large sample sizes, freedom of ethical restrictions and ease of repeated measurements make cytotoxicity assays of immortalized lymphoblastoid cell lines a powerful new in vitro method in pharmacogenomics research. However, previous studies may have over-simplified the complex differences in dose-response profiles between genotypes, resulting in a loss of power. METHODS The current study investigates four previously studied methods, plus one new method based on a multivariate analysis of variance (MANOVA) design. A simulation study was performed using differences in cancer drug response between genotypes for biologically meaningful loci. These loci also showed significance in separate genome-wide association studies. This manuscript builds upon a previous study, where differences in dose-response curves between genotypes were constructed using the hill slope equation. CONCLUSION Overall, MANOVA was found to be the most powerful method for detecting real signals, and was also the most robust method for detection using alternatives generated with the previous simulation study. This method is also attractive because test statistics follow their expected distributions under the null hypothesis for both simulated and real data. The success of this method inspired the creation of the software program MAGWAS. MAGWAS is a computationally efficient, user-friendly, open source software tool that works on most platforms and performs GWASs for individuals having multivariate responses using standard file formats.
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Affiliation(s)
- Chad C Brown
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Tammy M Havener
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marisa Wong Medina
- , Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Ronald M Krauss
- , Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Howard L McLeod
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alison A Motsinger‐Reif
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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