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Zhang H, Ren Y, Wang F, Tu X, Tong Z, Liu L, Zheng Y, Zhao P, Cheng J, Li J, Fang W, Liu X. The long-term effectiveness and mechanism of oncolytic virotherapy combined with anti-PD-L1 antibody in colorectal cancer patient. Cancer Gene Ther 2024:10.1038/s41417-024-00807-2. [PMID: 39068234 DOI: 10.1038/s41417-024-00807-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
Colorectal cancer (CRC) is known to be resistant to immunotherapy. In our phase-I clinical trial, one patient achieved a 313-day prolonged response during the combined treatment of oncolytic virotherapy and immunotherapy. To gain a deeper understanding of the potential molecular mechanisms, we performed a comprehensive multi-omics analysis on this patient and three non-responders. Our investigation unveiled that, initially, the tumor microenvironment (TME) of this responder presented minimal infiltration of T cells and natural killer cells, along with a relatively higher presence of macrophages compared to non-responders. Remarkably, during treatment, there was a progressive increase in CD4+ T cells, CD8+ T cells, and B cells in the responder's tumor tissue. This was accompanied by a significant upregulation of transcription factors associated with T-cell activation and cytotoxicity, including GATA3, EOMES, and RUNX3. Furthermore, dynamic monitoring of peripheral blood samples from the responder revealed a rapid decrease in circulating tumor DNA (ctDNA), suggesting its potential as an early blood biomarker of treatment efficacy. Collectively, our findings demonstrate the effectiveness of combined oncolytic virotherapy and immunotherapy in certain CRC patients and provide molecular evidence that virotherapy can potentially transform a "cold" TME into a "hot" one, thereby improving sensitivity to immunotherapy.
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Affiliation(s)
- Hangyu Zhang
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Yiqing Ren
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Feiyu Wang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaoxuan Tu
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Zhou Tong
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Lulu Liu
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Yi Zheng
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Peng Zhao
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Jianwen Li
- Geneplus-Shenzhen, Shenzhen, P. R. China.
| | - Weijia Fang
- Department of Medical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China.
| | - Xia Liu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, P. R. China.
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Zhao B, Wang Z, Liu D, Zhang S. Genetically predicted serum testosterone and risk of gynecological disorders: a Mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1161356. [PMID: 38075074 PMCID: PMC10710168 DOI: 10.3389/fendo.2023.1161356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Background Testosterone plays a key role in women, but the associations of serum testosterone level with gynecological disorders risk are inconclusive in observational studies. Methods We leveraged public genome-wide association studies to analyze the effects of four testosterone related exposure factors on nine gynecological diseases. Causal estimates were calculated by inverse variance-weighted (IVW), MR-Egger and weighted median methods. The heterogeneity test was performed on the obtained data through Cochrane's Q value, and the horizontal pleiotropy test was performed on the data through MR-Egger intercept and MR-PRESSO methods. "mRnd" online analysis tool was used to evaluate the statistical power of MR estimates. Results The results showed that total testosterone and bioavailable testosterone were protective factors for ovarian cancer (odds ratio (OR) = 0.885, P = 0.012; OR = 0.871, P = 0.005) and endometriosis (OR = 0.805, P = 0.020; OR = 0.842, P = 0.028) but were risk factors for endometrial cancer (OR = 1.549, P < 0.001; OR = 1.499, P < 0.001) and polycystic ovary syndrome (PCOS) (OR = 1.606, P = 0.019; OR = 1.637, P = 0.017). dehydroepiandrosterone sulfate (DHEAS) is a protective factor against endometriosis (OR = 0.840, P = 0.016) and premature ovarian failure (POF) (OR = 0.461, P = 0.046) and a risk factor for endometrial cancer (OR= 1.788, P < 0.001) and PCOS (OR= 1.970, P = 0.014). sex hormone-binding globulin (SHBG) is a protective factor against endometrial cancer (OR = 0.823, P < 0.001) and PCOS (OR = 0.715, P = 0.031). Conclusion Our analysis suggested causal associations between serum testosterone level and ovarian cancer, endometrial cancer, endometriosis, PCOS, POF.
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Affiliation(s)
| | | | | | - Songling Zhang
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, China
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Kabir M, Padilha EC, Shah P, Huang R, Sakamuru S, Gonzalez E, Ye L, Hu X, Henderson MJ, Xia M, Xu X. Identification of Selective CYP3A7 and CYP3A4 Substrates and Inhibitors Using a High-Throughput Screening Platform. Front Pharmacol 2022; 13:899536. [PMID: 35847040 PMCID: PMC9283723 DOI: 10.3389/fphar.2022.899536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
Cytochrome P450 (CYP) 3A7 is one of the major xenobiotic metabolizing enzymes in human embryonic, fetal, and newborn liver. CYP3A7 expression has also been observed in a subset of the adult population, including pregnant women, as well as in various cancer patients. The characterization of CYP3A7 is not as extensive as other CYPs, and health authorities have yet to provide guidance towards DDI assessment. To identify potential CYP3A7-specific molecules, we used a P450-Glo CYP3A7 enzyme assay to screen a library of ∼5,000 compounds, including FDA-approved drugs and drug-like molecules, and compared these screening data with that from a P450-Glo CYP3A4 assay. Additionally, a subset of 1,000 randomly selected compounds were tested in a metabolic stability assay. By combining the data from the qHTS P450-Glo and metabolic stability assays, we identified several chemical features important for CYP3A7 selectivity. Halometasone was chosen for further evaluation as a potential CYP3A7-selective inhibitor using molecular docking. From the metabolic stability assay, we identified twenty-two CYP3A7-selective substrates over CYP3A4 in supersome setting. Our data shows that CYP3A7 has ligand promiscuity, much like CYP3A4. Furthermore, we have established a large, high-quality dataset that can be used in predictive modeling for future drug metabolism and interaction studies.
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Affiliation(s)
- Md Kabir
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Department of Pharmacology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elias C. Padilha
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Pranav Shah
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Srilatha Sakamuru
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Eric Gonzalez
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
| | - Lin Ye
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Xin Hu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Mark J. Henderson
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Menghang Xia
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
| | - Xin Xu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
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Haas CB, Hsu L, Lampe JW, Wernli KJ, Lindström S. Cross-ancestry Genome-wide Association Studies of Sex Hormone Concentrations in Pre- and Postmenopausal Women. Endocrinology 2022; 163:6534466. [PMID: 35192695 PMCID: PMC8962449 DOI: 10.1210/endocr/bqac020] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Concentrations of circulating sex hormones have been associated with a variety of diseases in women and are strongly influenced by menopausal status. We investigated the genetic architectures of circulating concentrations of estradiol, testosterone, and SHBG by menopausal status in women of European and African ancestry. METHODS Using data on 229 966 women from the UK Biobank, we conducted genome-wide association studies (GWASs) of circulating concentrations of estradiol, testosterone, and SHBG in premenopausal and postmenopausal women. We tested for evidence of heterogeneity of genetic effects by menopausal status and genetic ancestry. We conducted gene-based enrichment analyses to identify tissues in which genes with GWAS-enriched signals were expressed. RESULTS We identified 4 loci (5q35.2, 12q14.3, 19q13.42, 20p12.3) that were associated with detectable concentrations of estradiol in both pre- and postmenopausal women of European ancestry. Heterogeneity analysis identified 1 locus for testosterone (7q22.1) in the CYP3A7 gene and 1 locus that was strongly associated with concentrations of SHBG in premenopausal women only (10q15.1) near the AKR1C4 gene. Gene-based analysis of testosterone revealed evidence of enrichment of GWAS signals in genes expressed in adipose tissue for postmenopausal women. We did not find any evidence of ancestry-specific genetic effects for concentrations of estradiol, testosterone, or SHBG. CONCLUSIONS We identified specific loci that showed genome-wide significant evidence of heterogeneity by menopausal status for testosterone and SHBG. We also observed support for a more prominent role of genetic variants located near genes expressed in adipose tissue in determining testosterone concentrations among postmenopausal women.
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Affiliation(s)
- Cameron B Haas
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Correspondence: Cameron B. Haas, PhD, MPH, Hans Rosling Population Health Building, 3980 15th Ave NE, Box 351619, Seattle, WA 98195, USA.
| | - Li Hsu
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Johanna W Lampe
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, USA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Qi G, Han C, Zhou Y, Wang X. Allele and genotype frequencies of CYP3A4, CYP3A5, CYP3A7, and GSTP1 gene polymorphisms among mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations. Clin Exp Pharmacol Physiol 2021; 49:219-227. [PMID: 34689350 DOI: 10.1111/1440-1681.13604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 01/06/2023]
Abstract
Over 50% prescribed drugs are metabolised by cytochrome P450 3A (CYP3A) and glutathione S-transferase pi (GSTP1) adds a glutathione to the oxidative products by CYP3A, which increases the hydrophilic property of metabolites and facilitates the excretion. Single nucleotide polymorphisms (SNPs) of CYP3A and GSTP1 show a diverse allele and genotype frequencies distribution among the world populations. The present study aimed to investigate the genotype and allele frequency distribution patterns of CYP3A4, CYP3A5, CYP3A7 and GSTP1 polymorphisms among healthy participants in mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations. Blood samples were collected from 842 unrelated healthy subjects (323 Tibetan, 134 Mongolian, 162 Uyghur, and 223 Han) for genotyping analysis. Variant allele frequencies of CYP3A4 rs2242480, CYP3A5 rs776746, CYP3A7 rs2257401, and GSTP1 Ile105Val were observed in Han (0.253, 0.686, 0.312 and 0.188), Tibetan (0.186, 0.819, 0.192 and 0.173), Mongolian (0.198, 0.784, 0.228 and 0.235) and Uyghur (0.179, 0.858, 0.182 and 0.250) respectively. The allele frequency of CYP3A7*1C in Uyghur (0.019) was higher than that in Tibetan (0.002, p < 0.01). There was a strong linkage disequilibrium between CYP3A4 rs2242480, CYP3A5 rs776746, and CYP3A7 rs2257401 among the four ethnic groups. The results might be useful for the precise medication in the Chinese populations.
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Affiliation(s)
- Guangzhao Qi
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Pharmacology, Basic Medical School, Peking University, Beijing, China
| | - Chao Han
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yubing Zhou
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xin Wang
- Department of Pharmacology, Basic Medical School, Peking University, Beijing, China
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OpenCYP: An open source database exploring human variability in activities and frequencies of polymophisms for major cytochrome P-450 isoforms across world populations. Toxicol Lett 2021; 350:267-282. [PMID: 34352333 DOI: 10.1016/j.toxlet.2021.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022]
Abstract
The open source database "OpenCYP database" has been developed based on the results of extensive literature searches from the peer-reviewed literature. OpenCYP provides data on human variability on baseline of activities and polymophism frequencies for selected cytochrome P-450 isoforms (CYP1A2, CYP2A6, CYP2D6, CYP3A4/3A5 and CYP3A7) in healthy adult populations from world populations. CYP enzymatic activities were generally expressed as the metabolic ratio (MR) between an unchanged probe drug and its metabolite(s) in urine or plasma measured in healthy adults. Data on other age groups were very limited and fragmented, constituting an important data gap. Quantitative comparisons were often hampered by the different experimental conditions used. However, variability was quite limited for CYP1A2, using caffeine as a probe substrate, with a symmetrical distribution of metabolic activity values. For CYP3A4, human variability was dependent on the probe substrate itself with low variability when data considering the dextromethorphan/demethilathed metabolite MR were used and large variability when the urinary 6β-hydroxycortisol/cortisol ratio was used. The largest variability in CYP activity was shown for CYP2D6 activity, after oral dosing of dextromethorphan, for which genetic polymorphisms are well characterised and constitute a significant source of variability. It is foreseen that the OpenCYP database can contribute to promising tools to support the further development of QIVIVE and PBK models for human risk assessment of chemicals particularly when combined with information on isoform-specific content in cells using proteomic approaches.
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Long L, Pang XX, Zeng FM, Zhan XH, Xie YH, Pan F, Wang W, Liao LD, Xu XE, Li B, Wang LD, Chang ZJ, Li EM, Xu LY. Promotion of rs3746804 (p. L267P) polymorphism to intracellular SLC52A3a trafficking and riboflavin transportation in esophageal cancer cells. Amino Acids 2021; 53:1197-1209. [PMID: 34223992 DOI: 10.1007/s00726-021-03025-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 06/21/2021] [Indexed: 02/05/2023]
Abstract
Riboflavin is an essential micronutrient for normal cellular growth and function. Lack of dietary riboflavin is associated with an increased risk for esophageal squamous cell carcinoma (ESCC). Previous studies have identified that the human riboflavin transporter SLC52A3a isoform (encoded by SLC52A3) plays a prominent role in esophageal cancer cell riboflavin transportation. Furthermore, SLC52A3 gene single nucleotide polymorphisms rs3746804 (T>C, L267P) and rs3746803 (C >T, T278M) are associated with ESCC risk. However, whether SLC52A3a (p.L267P) and (p.T278M) act in riboflavin transportation in esophageal cancer cell remains inconclusive. Here, we constructed the full-length SLC52A3a protein fused to green fluorescent protein (GFP-SLC52A3a-WT and mutants L267P, T278M, and L267P/T278M). It was confirmed by immunofluorescence-based confocal microscopy that SLC52A3a-WT, L267P, T278M, and L267P/T278M expressed in cell membrane, as well as in a variety of intracellular punctate structures. The live cell confocal imaging showed that SLC52A3a-L267P and L267P/T278M increased the intracellular trafficking of SLC52A3a in ESCC cells. Fluorescence recovery after photobleaching of GFP-tagged SLC52A3a meant that intracellular trafficking of SLC52A3a-L267P and L267P/T278M was rapid dynamics process, leading to its stronger ability to transport riboflavin. Taken together, the above results indicated that the rs3746804 (p.L267P) polymorphism promoted intracellular trafficking of SLC52A3a and riboflavin transportation in ESCC cells.
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Affiliation(s)
- Lin Long
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Xiao-Xiao Pang
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, Guangdong, China
| | - Fa-Min Zeng
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Xiu-Hui Zhan
- Research Center of Translational Medicine, Department of Spine Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ying-Hua Xie
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Feng Pan
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Wei Wang
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Lian-Di Liao
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Xiu-E Xu
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China
| | - Bin Li
- State Key Laboratory of Luminescence and Applications, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Science, Changchun, China
| | - Li-Dong Wang
- Henan Key Laboratory for Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-Jie Chang
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing, China
| | - En-Min Li
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China.
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou, 515041, Guangdong, China.
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Iwata H, Umeyama Y, Liu Y, Zhang Z, Schnell P, Mori Y, Fletcher O, Marshall JC, Johnson JG, Wood LS, Toi M, Finn RS, Turner NC, Bartlett CH, Cristofanilli M. Evaluation of the Association of Polymorphisms With Palbociclib-Induced Neutropenia: Pharmacogenetic Analysis of PALOMA-2/-3. Oncologist 2021; 26:e1143-e1155. [PMID: 33955129 PMCID: PMC8265363 DOI: 10.1002/onco.13811] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/20/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The most frequently reported treatment-related adverse event in clinical trials with the cyclin-dependent kinase 4/6 (CDK4/6) inhibitor palbociclib is neutropenia. Allelic variants in ABCB1 and ERCC1 might be associated with early occurrence (i.e., end of week 2 treatment) of grade 3/4 neutropenia. Pharmacogenetic analyses were performed to uncover associations between single nucleotide polymorphisms (SNPs) in these genes, patient baseline characteristics, and early occurrence of grade 3/4 neutropenia. MATERIALS AND METHODS ABCB1 (rs1045642, rs1128503) and ERCC1 (rs3212986, rs11615) were analyzed in germline DNA from palbociclib-treated patients from PALOMA-2 (n = 584) and PALOMA-3 (n = 442). SNP, race, and cycle 1 day 15 (C1D15) absolute neutrophil count (ANC) data were available for 652 patients. Univariate and multivariable analyses evaluated associations between SNPs, patient baseline characteristics, and early occurrence of grade 3/4 neutropenia. Analyses were stratified by Asian (n = 122) and non-Asian (n = 530) ethnicity. Median progression-free survival (mPFS) was estimated using the Kaplan-Meier method. The effect of genetic variants on palbociclib pharmacokinetics was analyzed. RESULTS ABCB1 and ERCC1_rs11615 SNP frequencies differed between Asian and non-Asian patients. Multivariable analysis showed that low baseline ANC was a strong independent risk factor for C1D15 grade 3/4 neutropenia regardless of race (Asians: odds ratio [OR], 6.033, 95% confidence interval [CI], 2.615-13.922, p < .0001; Non-Asians: OR, 6.884, 95% CI, 4.138-11.451, p < .0001). ABCB1_rs1128503 (C/C vs. T/T: OR, 0.57, 95% CI, 0.311-1.047, p = .070) and ERCC1_rs11615 (A/A vs. G/G: OR, 1.75, 95% CI, 0.901-3.397, p = .098) were potential independent risk factors for C1D15 grade 3/4 neutropenia in non-Asian patients. Palbociclib mPFS was consistent across genetic variants; exposure was not associated with ABCB1 genotype. CONCLUSION This is the first comprehensive assessment of pharmacogenetic data in relationship to exposure to a CDK4/6 inhibitor. Pharmacogenetic testing may inform about potentially increased likelihood of patients developing severe neutropenia (NCT01740427, NCT01942135). IMPLICATIONS FOR PRACTICE Palbociclib plus endocrine therapy improves hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer outcomes, but is commonly associated with neutropenia. Genetic variants in ABCB1 may influence palbociclib exposure, and in ERCC1 are associated with chemotherapy-induced severe neutropenia. Here, the associations of single nucleotide polymorphisms in these genes and baseline characteristics with neutropenia were assessed. Low baseline absolute neutrophil count was a strong risk factor (p < .0001) for grade 3/4 neutropenia. There was a trend indicating that ABCB1_rs1128503 and ERCC1_rs11615 were potential risk factors (p < .10) for grade 3/4 neutropenia in non-Asian patients. Pharmacogenetic testing could inform clinicians about the likelihood of severe neutropenia with palbociclib.
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Affiliation(s)
| | | | - Yuan Liu
- Pfizer Inc, San Diego, California, USA
| | - Zhe Zhang
- Pfizer Inc, San Diego, California, USA
| | | | | | - Olivia Fletcher
- Breast Cancer Now Toby Robins Research Centre, The Institute for Cancer Research, London, United Kingdom
| | | | | | | | - Masakazu Toi
- Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Richard S Finn
- David Geffen School of Medicine, University of California Los Angeles, Santa Monica, California, USA
| | - Nicholas C Turner
- Breast Cancer Now Toby Robins Research Centre, The Institute for Cancer Research, London, United Kingdom.,Royal Marsden Hospital, London, United Kingdom
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Structural Basis for the Diminished Ligand Binding and Catalytic Ability of Human Fetal-Specific CYP3A7. Int J Mol Sci 2021; 22:ijms22115831. [PMID: 34072457 PMCID: PMC8198134 DOI: 10.3390/ijms22115831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3A4, the ligand binding and catalytic capacity of CYP3A7 are substantially reduced. To better understand the structural basis for these functional differences, the 2.15 Å crystal structure of CYP3A7 has been solved. Comparative analysis of CYP3A enzymes shows that decreased structural plasticity rather than the active site microenvironment defines the ligand binding ability of CYP3A7. In particular, a rotameric switch in the gatekeeping amino acid F304 triggers local and long-range rearrangements that transmit to the F-G fragment and alter its interactions with the I-E-D-helical core, resulting in a more rigid structure. Elongation of the β3-β4 strands, H-bond linkage in the substrate channel, and steric constraints in the C-terminal loop further increase the active site rigidity and limit conformational ensemble. Collectively, these structural distinctions lower protein plasticity and change the heme environment, which, in turn, could impede the spin-state transition essential for optimal reactivity and oxidation of substrates.
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Ma C, Storer CE, Chandran U, LaFramboise WA, Petrosko P, Frank M, Hartman DJ, Pantanowitz L, Haritunians T, Head RD, Liu TC. Crohn's disease-associated ATG16L1 T300A genotype is associated with improved survival in gastric cancer. EBioMedicine 2021; 67:103347. [PMID: 33906066 PMCID: PMC8099593 DOI: 10.1016/j.ebiom.2021.103347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A non-synonymous single nucleotide polymorphism of the ATG16L1 gene, T300A, is a major Crohn's disease (CD) susceptibility allele, and is known to be associated with increased apoptosis induction in the small intestinal crypt base in CD subjects and mouse models. We hypothesized that ATG16L1 T300A genotype also correlates with increased tumor apoptosis and therefore could lead to superior clinical outcome in cancer subjects. METHODS T300A genotyping by Taqman assay was performed for gastric carcinoma subjects who underwent resection from two academic medical centers. Transcriptomic analysis was performed by RNA-seq on formalin-fixed paraffin-embedded cancerous tissue. Tumor apoptosis and autophagy were determined by cleaved caspase-3 and p62 immunohistochemistry, respectively. The subjects' genotypes were correlated with demographics, various histopathologic features, transcriptome, and clinical outcome. FINDINGS Of the 220 genotyped subjects, 163 (74%) subjects carried the T300A allele(s), including 55 (25%) homozygous and 108 (49%) heterozygous subjects. The T300A/T300A subjects had superior overall survival than the other groups. Their tumors were associated with increased CD-like lymphoid aggregates and increased tumor apoptosis without concurrent increase in tumor mitosis or defective autophagy. Transcriptomic analysis showed upregulation of WNT/β-catenin signaling and downregulation of PPAR, EGFR, and inflammatory chemokine pathways in tumors of T300A/T300A subjects. INTERPRETATION Gastric carcinoma of subjects with the T300A/T300A genotype is associated with repressed EGFR and PPAR pathways, increased tumor apoptosis, and improved overall survival. Genotyping gastric cancer subjects may provide additional insight for clinical stratification.
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Affiliation(s)
- Changqing Ma
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States.
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, United States
| | - William A LaFramboise
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Patricia Petrosko
- UPMC Hillman Cancer Center, Cancer Genomics Facility, Pittsburgh, PA 15232, United States
| | - Madison Frank
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, A-610, Pittsburgh, PA 15213, United States
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Ta-Chiang Liu
- Departments of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, Saint Louis, MO 63110, United States.
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Zhang J, Yang M, Luan P, Jia W, Liu Q, Ma Z, Dang J, Lu H, Ma Q, Wang Y, Mu C, Huo Z. Associations Between Cytochrome P450 (CYP) Gene Single-Nucleotide Polymorphisms and Second-to-Fourth Digit Ratio in Chinese University Students. Med Sci Monit 2021; 27:e930591. [PMID: 33723203 PMCID: PMC7980499 DOI: 10.12659/msm.930591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/22/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cytochrome P450 (CYP) genes are necessary for the production or metabolism of fetal sex hormones during pregnancy. The second-to-fourth digit ratio (2D: 4D) is formed in the early stage of human fetal development and considered an indicator reflecting prenatal sex steroids levels. We explored the association between 2D: 4D and single-nucleotide polymorphisms (SNPs) of CYP. MATERIAL AND METHODS Correlation analysis between 2D: 4D and 8 SNPs, rs2687133 (CPY3A7), rs7173655 (CYP11A1), rs1004467, rs17115149, and rs2486758 (CYP17A1), and rs4646, rs2255192, rs4275794 (CYP19A1), was performed using data from 426 female and 412 male Chinese university students. SNP genotyping was conducted using PCR. Digit lengths were photographed and measured by image processing software. RESULTS rs2486758 (CYP17A1) correlated with left hand 2D: 4D in men (P=0.026), and rs1004467 (CYP17A1) correlated with right hand 2D: 4D in men (P=0.008) and the whole population (P=0.032). In men, allele G rs1004467 decreased right hand 2D: 4D, while allele C of rs2486758 increased left hand 2D: 4D. In women, left hand 2D: 4D was higher in genotypes with allele A of SNP rs4646 (CYP19A1) under the dominant genetic model; female DR-L was higher in genotypes with allele T of rs17115149 (CYP11A1). SNPs rs2687133 (CYP3A7) and rs1004467 (CYP17A1) were significantly correlated with right hand 2D: 4D (P=0.0107). CONCLUSIONS SNPs rs1004467 and rs2486758 of CYP17A1 are significant in the relationship between 2D: 4D and CYP gene polymorphisms under different conditions. SNP interactions between CYP genes probably impact 2D: 4D. The correlation between 2D: 4D and some sex hormone-related diseases may be due to the effect of CYP variants on the 2 phenotypes.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
- Ningxia Key Laboratory of Cerebrocranial Diseases, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Mengyi Yang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Pengfei Luan
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Wei Jia
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Qiujun Liu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Zhanbing Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Jie Dang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Hong Lu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Qian Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Yanfeng Wang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Chunlan Mu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
| | - Zhenghao Huo
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education/Key Laboratory of Reproduction and Genetics/Basic Medical College, Ningxia Medical University, Yinchuan, Ningxia, P.R. China
- Department of Biology, Gansu Medical College, Pingliang, Gansu, P.R. China
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12
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Johnson N, Maguire S, Morra A, Kapoor PM, Tomczyk K, Jones ME, Schoemaker MJ, Gilham C, Bolla MK, Wang Q, Dennis J, Ahearn TU, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Augustinsson A, Baynes C, Freeman LEB, Beckmann MW, Benitez J, Bermisheva M, Blomqvist C, Boeckx B, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Burwinkel B, Campa D, Canzian F, Castelao JE, Chanock SJ, Chenevix-Trench G, Clarke CL, Conroy DM, Couch FJ, Cox A, Cross SS, Czene K, Dörk T, Eliassen AH, Engel C, Evans DG, Fasching PA, Figueroa J, Floris G, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, Gaudet MM, Giles GG, Goldberg MS, González-Neira A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hart SN, Hooning MJ, Hopper JL, Howell A, Hunter DJ, Jager A, Jakubowska A, John EM, Kaaks R, Keeman R, Khusnutdinova E, Kitahara CM, Kosma VM, Koutros S, Kraft P, Kristensen VN, Kurian AW, Lambrechts D, Le Marchand L, Linet M, Lubiński J, Mannermaa A, Manoukian S, Margolin S, Martens JWM, Mavroudis D, Mayes R, Meindl A, Milne RL, Neuhausen SL, Nevanlinna H, Newman WG, Nielsen SF, Nordestgaard BG, Obi N, Olshan AF, Olson JE, Olsson H, Orban E, Park-Simon TW, Peterlongo P, Plaseska-Karanfilska D, Pylkäs K, Rennert G, Rennert HS, Ruddy KJ, Saloustros E, Sandler DP, Sawyer EJ, Schmutzler RK, Scott C, Shu XO, Simard J, Smichkoska S, Sohn C, Southey MC, Spinelli JJ, Stone J, Tamimi RM, Taylor JA, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Vachon CM, van Veen EM, Wang SS, Weinberg CR, Wendt C, Wildiers H, Winqvist R, Wolk A, Zheng W, Ziogas A, Dunning AM, Pharoah PDP, Easton DF, Howie AF, Peto J, Dos-Santos-Silva I, Swerdlow AJ, Chang-Claude J, Schmidt MK, Orr N, Fletcher O. CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers. Br J Cancer 2021; 124:842-854. [PMID: 33495599 PMCID: PMC7884683 DOI: 10.1038/s41416-020-01185-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/21/2020] [Accepted: 11/05/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. METHODS We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. RESULTS For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (-49.2%, 95% CI -56.1% to -41.1%, P = 3.1 × 10-18); in follow-up analyses, rs45446698-C was also associated with lower progesterone (-26.7%, 95% CI -39.4% to -11.6%, P = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82-0.91, P = 6.9 × 10-8). CONCLUSIONS The CYP3A7*1C allele is associated with reduced risk of hormone receptor-positive breast cancer possibly mediated via an effect on the metabolism of endogenous sex hormones in premenopausal women.
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Affiliation(s)
- Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Sarah Maguire
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Ireland, UK
| | - Anna Morra
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Gilham
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Annelie Augustinsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Javier Benitez
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Don M Conroy
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Giuseppe Floris
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, QC, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, QC, Canada
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pascal Guénel
- Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, INSERM, University Paris-Saclay, Villejuif, France
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Esther M John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Veli-Matti Kosma
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Allison W Kurian
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Martha Linet
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Rebecca Mayes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Campus Großhadern, Munich, Germany
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sune F Nielsen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadia Obi
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Ester Orban
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', MASA, Skopje, Republic of North Macedonia
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Hedy S Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | | | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Snezhana Smichkoska
- Ss. Cyril and Methodius University in Skopje, Medical Faculty, University Clinic of Radiotherapy and Oncology, Skopje, Republic of North Macedonia
| | - Christof Sohn
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, INSERM, University Paris-Saclay, Villejuif, France
| | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Elke M van Veen
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sophia S Wang
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Hans Wildiers
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - A Forbes Howie
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Ireland, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
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13
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Carr DF, Turner RM, Pirmohamed M. Pharmacogenomics of anticancer drugs: Personalising the choice and dose to manage drug response. Br J Clin Pharmacol 2020; 87:237-255. [PMID: 32501544 DOI: 10.1111/bcp.14407] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
The field of pharmacogenomics has made great strides in oncology over the last 20 years and indeed a significant number of pre-emptive genetic tests are now routinely undertaken prior to anticancer drug administration. Many of these gene-drug interactions are the fruits of candidate gene and genome-wide association studies, which have largely focused on common genetic variants (allele frequency>1%). Examples where there is clinical utility include genotyping or phenotyping for G6PD to prevent rasburicase-induced RBC haemolysis, and TPMT to prevent thiopurine-induced bone marrow suppression. Other associations such as CYP2D6 status in determining the efficacy of tamoxifen are more controversial because of contradictory evidence from different sources, which has led to variability in the implementation of testing. As genomic technology becomes ever cheaper and more accessible, we must look to the additional data our genome can provide to explain interindividual variability in anticancer drug response. Clearly genes do not act on their own and it is therefore important to investigate genetic factors in conjunction with clinical factors, interacting concomitant drug therapies and other factors such as the microbiome, which can all affect drug disposition. Taking account of all of these factors, in conjunction with the somatic genome, is more likely to provide better predictive accuracy in determining anticancer drug response, both efficacy and safety. This review summarises the existing knowledge related to the pharmacogenomics of anticancer drugs and discusses areas of opportunity for further advances in personalisation of therapy in order to improve both drug safety and efficacy.
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Affiliation(s)
- Daniel F Carr
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Richard M Turner
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
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14
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Turner RM, Fontana V, Zhang JE, Carr D, Yin P, FitzGerald R, Morris AP, Pirmohamed M. A Genome-wide Association Study of Circulating Levels of Atorvastatin and Its Major Metabolites. Clin Pharmacol Ther 2020; 108:287-297. [PMID: 32128760 DOI: 10.1002/cpt.1820] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/28/2020] [Indexed: 01/03/2023]
Abstract
Atorvastatin (ATV) is frequently prescribed and generally well tolerated, but can lead to myotoxicity, especially at higher doses. A genome-wide association study of circulating levels of ATV, 2-hydroxy (2-OH) ATV, ATV lactone (ATV L), and 2-OH ATV L was performed in 590 patients who had been hospitalized with a non-ST elevation acute coronary syndrome 1 month earlier and were on high-dose ATV (80 mg or 40 mg daily). The UGT1A locus (lead single nucleotide polymorphism, rs887829) was strongly associated with both increased 2-OH ATV/ATV (P = 7.25 × 10-16 ) and 2-OH ATV L/ATV L (P = 3.95 × 10-15 ) metabolic ratios. Moreover, rs45446698, which tags CYP3A7*1C, was nominally associated with increased 2-OH ATV/ATV (P = 6.18 × 10-7 ), and SLCO1B1 rs4149056 with increased ATV (P = 2.21 × 10-6 ) and 2-OH ATV (P = 1.09 × 10-6 ) levels. In a subset of these patients whose levels of ATV and metabolites had also been measured at 12 months after hospitalization (n = 149), all of these associations remained, except for 2-OH ATV and rs4149056 (P = 0.057). Clinically, rs4149056 was associated with increased muscular symptoms (odds ratio (OR) 3.97; 95% confidence interval (CI) 1.29-12.27; P = 0.016) and ATV intolerance (OR 1.55; 95% CI 1.09-2.19; P = 0.014) in patients (n = 870) primarily discharged on high-dose ATV. In summary, both novel and recognized genetic associations have been identified with circulating levels of ATV and its major metabolites. Further study is warranted to determine the clinical utility of genotyping rs4149056 in patients on high-dose ATV.
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Affiliation(s)
- Richard M Turner
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Vanessa Fontana
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Jieying E Zhang
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Daniel Carr
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Peng Yin
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Chinese Academy of Sciences, Shenzhen Institutes of Advanced Technology, Shenzhen, China
| | - Richard FitzGerald
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
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15
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Cohen M, Lamparello AJ, Schimunek L, El-Dehaibi F, Namas RA, Xu Y, Kaynar AM, Billiar TR, Vodovotz Y. Quality Control Measures and Validation in Gene Association Studies: Lessons for Acute Illness. Shock 2020; 53:256-268. [PMID: 31365490 PMCID: PMC6989353 DOI: 10.1097/shk.0000000000001409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Acute illness is a complex constellation of responses involving dysregulated inflammatory and immune responses, which are ultimately associated with multiple organ dysfunction. Gene association studies have associated single-nucleotide polymorphisms (SNPs) with clinical and pharmacological outcomes in a variety of disease states, including acute illness. With approximately 4 to 5 million SNPs in the human genome and recent studies suggesting that a large portion of SNP studies are not reproducible, we suggest that the ultimate clinical utility of SNPs in acute illness depends on validation and quality control measures. To investigate this issue, in December 2018 and January 2019 we searched the literature for peer-reviewed studies reporting data on associations between SNPs and clinical outcomes and between SNPs and pharmaceuticals (i.e., pharmacogenomics) published between January 2011 to February 2019. We review key methodologies and results from a variety of clinical and pharmacological gene association studies, including trauma and sepsis studies, as illustrative examples on current SNP association studies. In this review article, we have found three key points which strengthen the potential accuracy of SNP association studies in acute illness and other diseases: providing evidence of following a protocol quality control method such as the one in Nature Protocols or the OncoArray QC Guidelines; enrolling enough patients to have large cohort groups; and validating the SNPs using an independent technique such as a second study using the same SNPs with new patient cohorts. Our survey suggests the need to standardize validation methods and SNP quality control measures in medicine in general, and specifically in the context of complex disease states such as acute illness.
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Affiliation(s)
- Maria Cohen
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh PA 15213
| | | | - Lukas Schimunek
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | - Fayten El-Dehaibi
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | - Rami A. Namas
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh PA 15213
| | - A Murat Kaynar
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh PA 15213
- Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Laboratory, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15261
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219
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16
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Wu Y, Feng W, Liu R, Xia T, Liu S. Graphene Oxide Causes Disordered Zonation Due to Differential Intralobular Localization in the Liver. ACS NANO 2020; 14:877-890. [PMID: 31891481 DOI: 10.1021/acsnano.9b08127] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The liver is the primary organ to sequester nanodrugs, representing a substantial hurdle for drug delivery and raising toxicity concerns. However, the mechanistic details underlying the liver sequestration and effects on the liver are still elusive. The difficulty in studying the liver lies in its complexity, which is structured with stringently organized anatomical units called lobules. Graphene oxide (GO) has attracted attention for its applications in biomedicine, especially as a nanocarrier; however, its sequestration and effects in the liver, the major enrichment and metabolic organ, are less understood. Herein, we unveiled the differential distribution of GO in lobules in the liver, with a higher amount surrounding portal triad zones than the central vein zones. Strikingly, liver zonation patterns also changed, as reflected by changes in vital zonated genes involved in hepatocyte integrity and metabolism, leading to compromised hepatic functions. RNA-Seq and DNA methylation sequencing analyses unraveled that GO-induced changes in liver functional zonation could be ascribed to dysregulation of key signaling pathways governing liver zonation at not only mRNA transcriptions but also DNA methylation imprinting patterns, partially through TET-dependent signaling. Together, this study reveals the differential GO distribution pattern in liver lobules and pinpoints the genetic and epigenetic mechanisms in GO-induced liver zonation alterations.
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Affiliation(s)
- Yakun Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Wenya Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Rui Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tian Xia
- Division of Nanomedicine, Department of Medicine, California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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17
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Influence of Genetic Variants on Steady-State Etonogestrel Concentrations Among Contraceptive Implant Users. Obstet Gynecol 2020; 133:783-794. [PMID: 30870275 DOI: 10.1097/aog.0000000000003189] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To identify genetic variants that influence steady-state etonogestrel concentrations among contraceptive implant users. METHODS We enrolled healthy, reproductive-age women in our pharmacogenomic study using etonogestrel implants for 12-36 months without concomitant use of hepatic enzyme inducers or inhibitors. We collected participant characteristics, measured serum etonogestrel concentrations, and genotyped each participant for 120 single nucleotide variants in 14 genes encoding proteins involved in steroid hormone (ie, estrogens, progestins) metabolism, regulation, or function. We performed generalized linear modeling to identify genetic variants associated with steady-state etonogestrel concentrations. RESULTS We enrolled 350 women, who had a median serum etonogestrel concentration of 137.4 pg/mL (range 55.8-695.1). Our final generalized linear model contained three genetic variants associated with serum etonogestrel concentrations: NR1I2(PXR) rs2461817 (β=13.36, P=.005), PGR rs537681 (β=-29.77, P=.007), and CYP3A7*1C (β=-35.06, P=.025). Variant allele frequencies were 69.4%, 84.9%, and 5.1%, respectively. Our linear model also contained two nongenetic factors associated with etonogestrel concentrations: body mass index (BMI) (β=-3.08, P=7.0×10) and duration of implant use (β=-1.60, P=5.8×10); R for the model =0.17. CONCLUSION Only BMI and duration of implant use remained significantly associated with steady-state etonogestrel concentrations. Of the three novel genetic associations found, one variant associated with increased etonogestrel metabolism (CYP3A7*1C) causes adult expression of fetal CYP3A7 proteins and can consequently alter steroid hormone metabolism. Women with this variant may potentially have increased metabolism of all steroid hormones, as 27.8% (5/18) of CYP3A7*1C carriers had serum etonogestrel concentrations that fell below the threshold for consistent ovulatory suppression (less than 90 pg/mL). More pharmacogenomic investigations are needed to advance our understanding of how genetic variation can influence the effectiveness and safety of hormonal contraception, and lay the groundwork for personalized medicine approaches in women's health. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov, NCT03092037.
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18
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Li H, Lampe JN. Neonatal cytochrome P450 CYP3A7: A comprehensive review of its role in development, disease, and xenobiotic metabolism. Arch Biochem Biophys 2019; 673:108078. [PMID: 31445893 DOI: 10.1016/j.abb.2019.108078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/14/2022]
Abstract
The human cytochrome P450 CYP3A7, once thought to be an enzyme exclusive to fetal livers, has more recently been identified in neonates and developing infants as old as 24 months post-gestational age. CYP3A7 has been demonstrated to metabolize two endogenous compounds that are known to be important in the growth and development of the fetus and neonate, namely dehydroepiandrosterone sulfate (DHEA-S) and all-trans retinoic acid (atRA). In addition, it is also known to metabolize a variety of drugs and xenobiotics, albeit generally to a lesser extent relative to CYP3A4/5. CYP3A7 is an important component in the development and protection of the fetal liver and additionally plays a role in certain disease states, such as cancer and adrenal hyperplasia. Ultimately, a full understanding of the expression, regulation, and metabolic properties of CYP3A7 is needed to provide neonates with appropriate individualized pharmacotherapy. This article summarizes the current state of knowledge of CYP3A7, including its discovery, distribution, alleles, RNA splicing, expression and regulation, metabolic properties, substrates, and inhibitors.
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Affiliation(s)
- Haixing Li
- Sino-German Joint Research Institute Nanchang University, 235 East Nanjing Road, Nanchang, 330047, Jiangxi, PR China
| | - Jed N Lampe
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
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19
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Chen YJ, Zhang J, Zhu PP, Tan XW, Lin QH, Wang WX, Yin SS, Gao LZ, Su MM, Liu CX, Xu L, Jia W, Sevrioukova IF, Lan K. Stereoselective Oxidation Kinetics of Deoxycholate in Recombinant and Microsomal CYP3A Enzymes: Deoxycholate 19-Hydroxylation Is an In Vitro Marker of CYP3A7 Activity. Drug Metab Dispos 2019; 47:574-581. [PMID: 30918015 DOI: 10.1124/dmd.119.086637] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
The primary bile acids (BAs) synthesized from cholesterol in the liver are converted to secondary BAs by gut microbiota. It was recently disclosed that the major secondary BA, deoxycholate (DCA) species, is stereoselectively oxidized to tertiary BAs exclusively by CYP3A enzymes. This work subsequently investigated the in vitro oxidation kinetics of DCA at C-1β, C-3β, C-4β, C-5β, C-6α, C-6β, and C-19 in recombinant CYP3A enzymes and naive enzymes in human liver microsomes (HLMs). The stereoselective oxidation of DCA fit well with Hill kinetics at 1-300 μM in both recombinant CYP3A enzymes and pooled HLMs. With no contributions or trace contributions from CYP3A5, CYP3A7 favors oxidation at C-19, C-4β, C-6α, C-3β, and C-1β, whereas CYP3A4 favors the oxidation at C-5β and C-6β compared with each other. Correlation between DCA oxidation and testosterone 6β-hydroxylation in 14 adult single-donor HLMs provided proof-of-concept evidence that DCA 19-hydroxylation is an in vitro marker reaction for CYP3A7 activity, whereas oxidation at other sites represents mixed indicators for CYP3A4 and CYP3A7 activities. Deactivation caused by DCA-induced cytochrome P450-cytochrome P420 conversion, as shown by the spectral titrations of isolated CYP3A proteins, was observed when DCA levels were near or higher than the critical micelle concentration (about 1500 μM). Unlike CYP3A4, CYP3A7 showed abnormally elevated activities at 500 and 750 μM, which might be associated with an altered affinity for DCA multimers. The disclosed kinetic and functional roles of CYP3A isoforms in disposing of the gut bacteria-derived DCA may help in understanding the structural and functional mechanisms of CYP3A.
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Affiliation(s)
- Yu-Jie Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Jian Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Ping-Ping Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Xian-Wen Tan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Qiu-Hong Lin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Wen-Xia Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Shan-Shan Yin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Ling-Zhi Gao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Ming-Ming Su
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Chang-Xiao Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Liang Xu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Wei Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Irina F Sevrioukova
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
| | - Ke Lan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, People's Republic of China (Y.-J.C., J.Z., P.-P.Z., X.-W.T., Q.-H.L., W.W., S.-S.Y., L.-Z.G., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.-M.S., W.J.); Department of Molecular Biology and Biochemistry, University of California, Irvine, California (I.F.S.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China (C.-X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, People's Republic of China (S.-S.Y., K.L.)
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Zhang J, Gao LZ, Chen YJ, Zhu PP, Yin SS, Su MM, Ni Y, Miao J, Wu WL, Chen H, Brouwer KLR, Liu CX, Xu L, Jia W, Lan K. Continuum of Host-Gut Microbial Co-metabolism: Host CYP3A4/3A7 are Responsible for Tertiary Oxidations of Deoxycholate Species. Drug Metab Dispos 2019; 47:283-294. [PMID: 30606729 PMCID: PMC6378331 DOI: 10.1124/dmd.118.085670] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/31/2018] [Indexed: 02/05/2023] Open
Abstract
The gut microbiota modifies endogenous primary bile acids (BAs) to produce exogenous secondary BAs, which may be further metabolized by cytochrome P450 enzymes (P450s). Our primary aim was to examine how the host adapts to the stress of microbe-derived secondary BAs by P450-mediated oxidative modifications on the steroid nucleus. Five unconjugated tri-hydroxyl BAs that were structurally and/or biologically associated with deoxycholate (DCA) were determined in human biologic samples by liquid chromatography-tandem mass spectrometry in combination with enzyme-digestion techniques. They were identified as DCA-19-ol, DCA-6β-ol, DCA-5β-ol, DCA-6α-ol, DCA-1β-ol, and DCA-4β-ol based on matching in-laboratory synthesized standards. Metabolic inhibition assays in human liver microsomes and recombinant P450 assays revealed that CYP3A4 and CYP3A7 were responsible for the regioselective oxidations of both DCA and its conjugated forms, glycodeoxycholate (GDCA) and taurodeoxycholate (TDCA). The modification of secondary BAs to tertiary BAs defines a host liver (primary BAs)-gut microbiota (secondary BAs)-host liver (tertiary BAs) axis. The regioselective oxidations of DCA, GDCA, and TDCA by CYP3A4 and CYP3A7 may help eliminate host-toxic DCA species. The 19- and 4β-hydroxylation of DCA species demonstrated outstanding CYP3A7 selectivity and may be useful as indicators of CYP3A7 activity.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Ling-Zhi Gao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Yu-Jie Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Ping-Ping Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Shan-Shan Yin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Ming-Ming Su
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Yan Ni
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Jia Miao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Wen-Lin Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Hong Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Kim L R Brouwer
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Chang-Xiao Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Liang Xu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Wei Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
| | - Ke Lan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, China (J.Z., L.Z.G., Y.J.C., P.P.Z., S.S.Y., L.X., K.L.); Metabolomics Shared Resource, University of Hawaii Cancer Center, Honolulu, Hawaii (M.M.S., Y.N., W.J.); Institute of Clinical Pharmacology, West China Hospital, Sichuan University, Chengdu, China (J.M.); Chengdu Institutes for Food and Drug Control, Chengdu, China (W.L.W., H.C.); UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina (K.L.R.B.); State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China (C.X.L.); and Chengdu Health-Balance Medical Technology Co., Ltd., Chengdu, China (S.S.Y.)
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Swart M, Stansberry WM, Pratt VM, Medeiros EB, Kiel PJ, Shen F, Schneider BP, Skaar TC. Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology. J Mol Diagn 2019; 21:491-502. [PMID: 30794985 DOI: 10.1016/j.jmoldx.2019.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 01/29/2019] [Indexed: 10/27/2022] Open
Abstract
The Clinical Laboratory Improvement Amendments of 1988 require that pharmacogenetic genotyping methods need to be established according to technical standards and laboratory practice guidelines before testing can be offered to patients. Testing methods for variants in ABCB1, CBR3, COMT, CYP3A7, C8ORF34, FCGR2A, FCGR3A, HAS3, NT5C2, NUDT15, SBF2, SEMA3C, SLC16A5, SLC28A3, SOD2, TLR4, and TPMT were validated in a Clinical Laboratory Improvement Amendments-accredited laboratory. Because no known reference materials were available, existing DNA samples were used for the analytical validation studies. Pharmacogenetic testing methods developed here were shown to be accurate and 100% analytically sensitive and specific. Other Clinical Laboratory Improvement Amendments-accredited laboratories interested in offering pharmacogenetic testing for these genetic variants, related to genotype-guided therapy for oncology, could use these publicly available samples as reference materials when developing and validating new genetic tests or refining current assays.
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Affiliation(s)
- Marelize Swart
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Wesley M Stansberry
- Department of Medicine, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Victoria M Pratt
- Department of Medicine, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Elizabeth B Medeiros
- Department of Medicine, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Patrick J Kiel
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Fei Shen
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Bryan P Schneider
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Todd C Skaar
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana
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Beaumont RN, Warrington NM, Cavadino A, Tyrrell J, Nodzenski M, Horikoshi M, Geller F, Myhre R, Richmond RC, Paternoster L, Bradfield JP, Kreiner-Møller E, Huikari V, Metrustry S, Lunetta KL, Painter JN, Hottenga JJ, Allard C, Barton SJ, Espinosa A, Marsh JA, Potter C, Zhang G, Ang W, Berry DJ, Bouchard L, Das S, Hakonarson H, Heikkinen J, Helgeland Ø, Hocher B, Hofman A, Inskip HM, Jones SE, Kogevinas M, Lind PA, Marullo L, Medland SE, Murray A, Murray JC, Njølstad PR, Nohr EA, Reichetzeder C, Ring SM, Ruth KS, Santa-Marina L, Scholtens DM, Sebert S, Sengpiel V, Tuke MA, Vaudel M, Weedon MN, Willemsen G, Wood AR, Yaghootkar H, Muglia LJ, Bartels M, Relton CL, Pennell CE, Chatzi L, Estivill X, Holloway JW, Boomsma DI, Montgomery GW, Murabito JM, Spector TD, Power C, Järvelin MR, Bisgaard H, Grant SFA, Sørensen TIA, Jaddoe VW, Jacobsson B, Melbye M, McCarthy MI, Hattersley AT, Hayes MG, Frayling TM, Hivert MF, Felix JF, Hyppönen E, Lowe WL, Evans DM, Lawlor DA, Feenstra B, Freathy RM. Genome-wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics. Hum Mol Genet 2019; 27:742-756. [PMID: 29309628 PMCID: PMC5886200 DOI: 10.1093/hmg/ddx429] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/15/2017] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86 577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother–child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P < 5 × 10−8. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate that genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.
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Affiliation(s)
- Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicole M Warrington
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Alana Cavadino
- Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK.,European Centre for Environment and Human Health, University of Exeter, The Knowledge Spa, Truro TR1 3HD, UK
| | - Michael Nodzenski
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ronny Myhre
- Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eskil Kreiner-Møller
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Ville Huikari
- Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Sarah Metrustry
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,Framingham Heart Study, Framingham, MA, USA
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Jouke-Jan Hottenga
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Sheila J Barton
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Ana Espinosa
- Pompeu Fabra University (UPF), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Julie A Marsh
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Catherine Potter
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, OH, USA.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Wei Ang
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Diane J Berry
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.,ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, QC, Canada.,Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Shikta Das
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jani Heikkinen
- FIMM Institute for Molecular Medicine Finland, Helsinki University, Helsinki FI-00014, Finland
| | - Øyvind Helgeland
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Berthold Hocher
- The First Affiliated Hospital of Jinan University, Guangzhou 510630, China.,Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Hazel M Inskip
- Medical Research Council Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Samuel E Jones
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Manolis Kogevinas
- Pompeu Fabra University (UPF), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Letizia Marullo
- Genetic Section, Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Anna Murray
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Pål R Njølstad
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway.,Department of Pediatrics, Haukeland University Hospital, Bergen 5021, Norway
| | - Ellen A Nohr
- Research Unit of Obstetrics & Gynecology, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Christoph Reichetzeder
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany.,Center for Cardiovascular Research, Charité, Berlin, Germany
| | - Susan M Ring
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Loreto Santa-Marina
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Subdirección de Salud Pública y Adicciones de Gipuzkoa, Donostia/San Sebastián, Spain.,Instituto de Investigación Sanitaria BIODONOSTIA, Donostia/San Sebastián, Spain
| | - Denise M Scholtens
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sylvain Sebert
- Institute of Health Sciences, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK
| | - Verena Sengpiel
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, Sweden
| | - Marcus A Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Marc Vaudel
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Gonneke Willemsen
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, OH, USA.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Meike Bartels
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Craig E Pennell
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Leda Chatzi
- Department of Social Medicine, University of Crete, Crete, Greece
| | - Xavier Estivill
- Pompeu Fabra University (UPF), Barcelona, Spain.,ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Dorret I Boomsma
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.,Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD 4029, Australia
| | - Joanne M Murabito
- Framingham Heart Study, Framingham, MA, USA.,Section of General Internal Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Tim D Spector
- Department of Twin Research, King's College London, St. Thomas' Hospital, London, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marjo-Ritta Järvelin
- Institute of Health Sciences, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, FI-90220 Oulu, 90029 OYS, Finland.,Department of Children and Young People and Families, National Institute for Health and Welfare, FI-90101 Oulu, Finland
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thorkild I A Sørensen
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Bo Jacobsson
- Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, Sweden
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA, USA.,Diabetes Center, Massachussetts General Hospital, Boston, MA, USA.,Department of Medicine, Universite de Sherbrooke, QC, Canada
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Elina Hyppönen
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Centre for School of Population Health Research, School of Health Sciences, and Sansom Institute, University of South Australia, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David M Evans
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia.,Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Science, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK.,Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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23
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Yu T, Wang X, Zhu G, Han C, Su H, Liao X, Yang C, Qin W, Huang K, Peng T. The prognostic value of differentially expressed CYP3A subfamily members for hepatocellular carcinoma. Cancer Manag Res 2018; 10:1713-1726. [PMID: 29983591 PMCID: PMC6025769 DOI: 10.2147/cmar.s159425] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Objective The activities of four cytochrome P3A (CYP3A) subfamily members (CYP3A4, CYP3A5, CYP3A7, and CYP3A43) are well documented in drug metabolism. However, the association between CYP3A subfamily members and hepatocellular carcinoma (HCC) remains unclear. This study investigated the prognostic value of CYP3A subfamily mRNA expression levels with HCC prognosis. Materials and methods Data from a total of 360 HCC patients were retrieved from The Cancer Genome Atlas database, and data from 231 HCC patients were retrieved from the Gene Expression Omnibus database. Kaplan–Meier analysis and Cox regression models were utilized to determine median survival, overall survival, and recurrence-free survival. Hazard ratios and 95% CI were calculated. Results Low expression of CYP3A4, CYP3A5, and CYP3A43 in the tumor tissue was associated with short median survival (crude p=0.004, 0.001, and 0.001; adjusted p=0.022, 0.005, and 0.013, respectively). Joint-effects combination analysis of CYP3A4, CYP3A5/CYP3A4, CYP3A43/CYP3A5, and CYP3A43 revealed that high expression groups of two genes (group C, group c, group 3) were associated with a reduced risk of death, as compared to low expression of two genes (group A, group a, group 1), and the adjusted p values were 0.001, 0.004, and 0.001, respectively. Joint-effects analysis of CYP3A4, CYP3A5, and CYP3A43 showed that groups III and IV had a reduced risk of death, as compared to group I (adjusted p=0.024 and 0.002, respectively). Conclusion CYP3A4, CYP3A5, and CYP3A43 mRNA expression levels are potential prognostic markers of HCC.
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Affiliation(s)
- Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China,
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24
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Ghanat Bari M, Ung CY, Zhang C, Zhu S, Li H. Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. Sci Rep 2017; 7:6993. [PMID: 28765560 PMCID: PMC5539301 DOI: 10.1038/s41598-017-07481-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/27/2017] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 108 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.
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Affiliation(s)
- Mehrab Ghanat Bari
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA.
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25
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Sood D, Johnson N, Jain P, Siskos AP, Bennett M, Gilham C, Busana MC, Peto J, Dos-Santos-Silva I, Keun HC, Fletcher O. CYP3A7*1C allele is associated with reduced levels of 2-hydroxylation pathway oestrogen metabolites. Br J Cancer 2017; 116:382-388. [PMID: 28072767 PMCID: PMC5294487 DOI: 10.1038/bjc.2016.432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 11/29/2022] Open
Abstract
Background: Endogenous sex hormones are well-established risk factors for breast cancer; the contribution of specific oestrogen metabolites (EMs) and/or ratios of specific EMs is less clear. We have previously identified a CYP3A7*1C allele that is associated with lower urinary oestrone (E1) levels in premenopausal women. The purpose of this analysis was to determine whether this allele was associated with specific pathway EMs. Methods: We measured successfully 12 EMs in mid-follicular phase urine samples from 30 CYP3A7*1C carriers and 30 non-carriers using HPLC-MS/MS. Results: In addition to having lower urinary E1 levels, CYP3A7*1C carriers had significantly lower levels of four of the 2-hydroxylation pathway EMs that we measured (2-hydroxyestrone, P=1.1 × 10−12; 2-hydroxyestradiol, P=2.7 × 10−7; 2-methoxyestrone, P=1.9 × 10−12; and 2-methoxyestradiol, P=0.0009). By contrast, 16α-hydroxylation pathway EMs were slightly higher in carriers and significantly so for 17-epiestriol (P=0.002). Conclusions: The CYP3A7*1C allele is associated with a lower urinary E1 levels, a more pronounced reduction in 2-hydroxylation pathway EMs and a lower ratio of 2-hydroxylation:16α-hydroxylation EMs in premenopausal women. To further characterise the association between parent oestrogens, EMs and subsequent risk of breast cancer, characterisation of additional genetic variants that influence oestrogen metabolism and large prospective studies of a broad spectrum of EMs will be required.
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Affiliation(s)
- Deepti Sood
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, UK
| | - Nichola Johnson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW7 3RP, UK
| | - Pooja Jain
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, UK
| | - Alexandros P Siskos
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, UK
| | - Mark Bennett
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Clare Gilham
- Department of Non-Communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Marta Cecilia Busana
- Department of Non-Communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Hector C Keun
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, UK
| | - Olivia Fletcher
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW7 3RP, UK
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