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Liu Y, Zhang H, Zhao S, Zhang Y. A retrospective analysis of the clinicopathological features and prognostic value of MAPK12 protein expression in diffuse large B-cell lymphoma. Clin Transl Oncol 2024:10.1007/s12094-024-03515-3. [PMID: 38773060 DOI: 10.1007/s12094-024-03515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/03/2024] [Indexed: 05/23/2024]
Abstract
PURPOSE Mitogen-activated protein kinase 12 (MAPK12), also known as p38γ, is a member of the p38 MAPK family and plays a crucial role in tumor occurrence and invasion. However, there is still uncertainty regarding MAPK12 involvement in diffuse large B-cell lymphoma (DLBCL). METHODS Our study investigated the expression of MAPK12 mRNA in various types of cancer using bioinformatic analysis. Furthermore, we performed immunohistochemistry (IHC) to detect the expression of MAPK12 in patients with DLBCL and compared clinical indicators and survival rates. RESULTS We found that the high expression rate of MAPK12 was 43.1% in DLBCL patients. Several clinical indicators, including IPI scores, Hans classifications, LDH levels, and Ki-67 expression were closely associated with MAPK12 expression. Survival analysis revealed that higher expression of MAPK12 was significantly correlated with shorter progression-free survival (PFS) and overall survival (OS) in DLBCL patients. In addition, both univariate and multivariate analyses revealed IPI score, MAPK12 expression, and rituximab use as the independent OS risk factors (P < 0.05). To explore the functional role of MAPK12 in DLBCL, weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) were used to confirm the involvement of MAPK12 in the regulation of type II interferon production, positive regulation of lymphocyte proliferation, and other related biological processes. CONCLUSION DLBCL patients have poor prognoses when MAPK12 levels are high, which is expected to be a therapeutic target and prognostic factor.
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Affiliation(s)
- Yue Liu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Han Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shu Zhao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Yue Zhang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China.
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJF, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun JH, DeMeo D, Levy D, Johnson AD, Mathias RA, Taub MA, Arnett D, North KE, Raffield LM, Carson AP, Doyle MF, Rich SS, Rotter JI, Guo X, Cox NJ, Roden DM, Franceschini N, Desai P, Reiner AP, Auer PL, Scheet PA, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. Nat Commun 2024; 15:3800. [PMID: 38714703 PMCID: PMC11076528 DOI: 10.1038/s41467-024-48190-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/23/2024] [Indexed: 05/10/2024] Open
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
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Affiliation(s)
- Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Yasminka A Jakubek
- Internal Medicine, Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Adrienne M Stilp
- Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Braxton D Mitchell
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz, Aurora, CO, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ali Shojaie
- Biostatistics, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Donna Arnett
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Margaret F Doyle
- Department of Pathology & Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Weill Cornell Medical College, New York, NY, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Insitute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul A Scheet
- Dept of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA.
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Watanabe F, Sato S, Hirose T, Endo M, Endo A, Ito H, Ohba K, Mori T, Takahashi K. NRIP1 regulates cell proliferation in lung adenocarcinoma cells. J Biochem 2024; 175:323-333. [PMID: 38102728 DOI: 10.1093/jb/mvad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Nuclear receptor interacting protein 1 (NRIP1) is a transcription cofactor that regulates the activity of nuclear receptors and transcription factors. Functional expression of NRIP1 has been identified in multiple cancers. However, the expression and function of NRIP1 in lung adenocarcinoma have remained unclear. Thus, we aimed to clarify the NRIP1 expression and its functions in lung adenocarcinoma cells. NRIP1 and Ki-67 were immunostained in the tissue microarray section consisting of 64 lung adenocarcinoma cases, and the association of NRIP1 immunoreactivity with clinical phenotypes was examined. Survival analysis was performed in lung adenocarcinoma data from The Cancer Genome Atlas (TCGA). Human A549 lung adenocarcinoma cell line with an NRIP1-silencing technique was used in vitro study. Forty-three of 64 cases were immunostained with NRIP1. Ki-67-positive cases were more frequent in NRIP1-positive cases as opposed to NRIP1-negative cases. Higher NRIP1 mRNA expression was associated with poor prognosis in the TCGA lung adenocarcinoma data. NRIP1 was mainly located in the nucleus of A549 cells. NRIP1 silencing significantly reduced the number of living cells, suppressed cell proliferation, and induced apoptosis. These results suggest that NRIP1 participates in the progression and development of lung adenocarcinoma. Targeting NRIP1 may be a possible therapeutic strategy against lung adenocarcinoma.
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Affiliation(s)
- Fumihiko Watanabe
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, 1, Hikarigaoka, Fukushima, 960-1295 Fukushima, Japan
| | - Shigemitsu Sato
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
- Division of Integrative Renal Replacement Therapy, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
| | - Takuo Hirose
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
- Division of Integrative Renal Replacement Therapy, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
- Division of Nephrology and Endocrinology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
| | - Moe Endo
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
| | - Akari Endo
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
- Division of Nephrology and Endocrinology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
| | - Hiroki Ito
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
- Division of Nephrology and Endocrinology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
| | - Koji Ohba
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
| | - Takefumi Mori
- Division of Integrative Renal Replacement Therapy, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
- Division of Nephrology and Endocrinology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino, 983-8536 Sendai, Japan
| | - Kazuhiro Takahashi
- Department of Endocrinology and Applied Medical Science, Tohoku University Graduate School of Medicine, 2-1, Seiryo, Aoba, 980-8575 Sendai, Japan
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Zhang M, Li X, Herman JG, Gao A, Wang Q, Yao Y, Shen F, He K, Guo M. Methylation of NRIP3 Is a Synthetic Lethal Marker for Combined PI3K and ATR/ATM Inhibitors in Colorectal Cancer. Clin Transl Gastroenterol 2024; 15:e00682. [PMID: 38235705 PMCID: PMC10962901 DOI: 10.14309/ctg.0000000000000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
INTRODUCTION The aim of this study was to investigate the epigenetic regulation and underlying mechanism of NRIP3 in colorectal cancer (CRC). METHODS Eight cell lines (SW480, SW620, DKO, LOVO, HT29, HCT116, DLD1, and RKO), 187 resected margin samples from colorectal cancer tissue, 146 cases with colorectal adenomatous polyps, and 308 colorectal cancer samples were used. Methylation-specific PCR, Western blotting, RNA interference assay, and a xenograft mouse model were used. RESULTS NRIP3 exhibited methylation in 2.7% (5/187) of resected margin samples from colorectal cancer tissue, 32.2% (47/146) of colorectal adenomatous polyps, and 50.6% (156/308) of CRC samples, and the expression of NRIP3 was regulated by promoter region methylation. The methylation of NRIP3 was found to be significantly associated with late onset (at age 50 years or older), poor tumor differentiation, lymph node metastasis, and poor 5-year overall survival in CRC (all P < 0.05). In addition, NRIP3 methylation was an independent poor prognostic marker ( P < 0.05). NRIP3 inhibited cell proliferation, colony formation, invasion, and migration, while induced G1/S arrest. NRIP3 suppressed CRC growth by inhibiting PI3K-AKT signaling both in vitro and in vivo . Methylation of NRIP3 sensitized CRC cells to combined PI3K and ATR/ATM inhibitors. DISCUSSION NRIP3 was frequently methylated in both colorectal adenomatous polyps and CRC. The methylation of NRIP3 may potentially serve as an early detection, late-onset, and poor prognostic marker in CRC. NRIP3 is a potential tumor suppressor. NRIP3 methylation is a potential synthetic lethal marker for combined PI3K and ATR/ATM inhibitors.
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Affiliation(s)
- Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoyun Li
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - James G. Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qian Wang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Shen
- Department of Gastroenterology, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Kunlun He
- Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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Huang HY, Wang Y, Herold T, Gale RP, Wang JZ, Li L, Lin HX, Liang Y. A survival prediction model and nomogram based on immune-related gene expression in chronic lymphocytic leukemia cells. Front Med (Lausanne) 2022; 9:1026812. [PMID: 36600891 PMCID: PMC9806429 DOI: 10.3389/fmed.2022.1026812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction There are many different chronic lymphoblastic leukemia (CLL) survival prediction models and scores. But none provide information on expression of immune-related genes in the CLL cells. Methods We interrogated data from the Gene Expression Omnibus database (GEO, GSE22762; Number = 151; training) and International Cancer Genome Consortium database (ICGC, CLLE-ES; Number = 491; validation) to develop an immune risk score (IRS) using Least absolute shrinkage and selection operator (LASSO) Cox regression analyses based on expression of immune-related genes in CLL cells. The accuracy of the predicted nomogram we developed using the IRS, Binet stage, and del(17p) cytogenetic data was subsequently assessed using calibration curves. Results A survival model based on expression of 5 immune-related genes was constructed. Areas under the curve (AUC) for 1-year survivals were 0.90 (95% confidence interval, 0.78, 0.99) and 0.75 (0.54, 0.87) in the training and validation datasets, respectively. 5-year survivals of low- and high-risk subjects were 89% (83, 95%) vs. 6% (0, 17%; p < 0.001) and 98% (95, 100%) vs. 92% (88, 96%; p < 0.001) in two datasets. The IRS was an independent survival predictor of both datasets. A calibration curve showed good performance of the nomogram. In vitro, the high expression of CDKN2A and SREBF2 in the bone marrow of patients with CLL was verified by immunohistochemistry analysis (IHC), which were associated with poor prognosis and may play an important role in the complex bone marrow immune environment. Conclusion The IRS is an accurate independent survival predictor with a high C-statistic. A combined nomogram had good survival prediction accuracy in calibration curves. These data demonstrate the potential impact of immune related genes on survival in CLL.
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Affiliation(s)
- Han-ying Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Robert Peter Gale
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China,Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Jing-zi Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huan-xin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China,Huan-xin Lin,
| | - Yang Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China,Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China,*Correspondence: Yang Liang,
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Kerbs P, Vosberg S, Krebs S, Graf A, Blum H, Swoboda A, Batcha AMN, Mansmann U, Metzler D, Heckman CA, Herold T, Greif PA. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica 2022; 107:100-111. [PMID: 34134471 PMCID: PMC8719081 DOI: 10.3324/haematol.2021.278436] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022] Open
Abstract
Identification of fusion genes in clinical routine is mostly based on cytogenetics and targeted molecular genetics, such as metaphase karyotyping, fluorescence in situ hybridization and reverse-transcriptase polymerase chain reaction. However, sequencing technologies are becoming more important in clinical routine as processing time and costs per sample decrease. To evaluate the performance of fusion gene detection by RNAsequencing compared to standard diagnostic techniques, we analyzed 806 RNA-sequencing samples from patients with acute myeloid leukemia using two state-of-the-art software tools, namely Arriba and FusionCatcher. RNA-sequencing detected 90% of fusion events that were reported by routine with high evidence, while samples in which RNA-sequencing failed to detect fusion genes had overall lower and inhomogeneous sequence coverage. Based on properties of known and unknown fusion events, we developed a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Thereby, we detected known recurrent fusion events in 26 cases that were not reported by routine and found discrepancies in evidence for known fusion events between routine and RNA-sequencing in three cases. Moreover, we identified 157 fusion genes as novel robust candidates and comparison to entries from ChimerDB or Mitelman Database showed novel recurrence of fusion genes in 14 cases. Finally, we detected the novel recurrent fusion gene NRIP1- MIR99AHG resulting from inv(21)(q11.2;q21.1) in nine patients (1.1%) and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients (0.25%). We demonstrated that NRIP1-MIR99AHG results in overexpression of the 3' region of MIR99AHG and the disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. Interestingly, upregulation of MIR99AHG and deregulation of the miRNA cluster, residing in the MIR99AHG locus, are known mechanisms of leukemogenesis in acute megakaryoblastic leukemia. Our findings demonstrate that RNA-sequencing has a strong potential to improve the systematic detection of fusion genes in clinical applications and provides a valuable tool for fusion discovery.
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Affiliation(s)
- Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Anja Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Aarif M N Batcha
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Ulrich Mansmann
- Department of Medical Data Processing, Biometry and Epidemiology, LMU Munich, Munich, Germany
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich; and; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, Boorgula MP, Blackwell TW, Brody JA, Broome J, Chami N, Chen MH, Conomos MP, Cox C, Curran JE, Daya M, Ekunwe L, Glahn DC, Heard-Costa N, Highland HM, Hobbs BD, Ilboudo Y, Jain D, Lange LA, Miller-Fleming TW, Min N, Moon JY, Preuss MH, Rosen J, Ryan K, Smith AV, Sun Q, Surendran P, de Vries PS, Walter K, Wang Z, Wheeler M, Yanek LR, Zhong X, Abecasis GR, Almasy L, Barnes KC, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Chavan S, Cho MH, Choquet H, Correa A, Cox N, DeMeo DL, Faraday N, Fornage M, Gerszten RE, Hou L, Johnson AD, Jorgenson E, Kaplan R, Kooperberg C, Kundu K, Laurie CA, Lettre G, Lewis JP, Li B, Li Y, Lloyd-Jones DM, Loos RJF, Manichaikul A, Meyers DA, Mitchell BD, Morrison AC, Ngo D, Nickerson DA, Nongmaithem S, North KE, O'Connell JR, Ortega VE, Pankratz N, Perry JA, Psaty BM, Rich SS, Soranzo N, Rotter JI, Silverman EK, Smith NL, Tang H, Tracy RP, Thornton TA, Vasan RS, Zein J, Mathias RA, Reiner AP, Auer PL. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:1836-1851. [PMID: 34582791 PMCID: PMC8546043 DOI: 10.1016/j.ajhg.2021.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.
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MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/metabolism
- Asthma/pathology
- Biomarkers/metabolism
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/metabolism
- Dermatitis, Atopic/pathology
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Humans
- Leukocytes/pathology
- National Heart, Lung, and Blood Institute (U.S.)
- Phenotype
- Polymorphism, Single Nucleotide
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Pulmonary Disease, Chronic Obstructive/epidemiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/pathology
- Quantitative Trait Loci
- United Kingdom/epidemiology
- United States/epidemiology
- Whole Genome Sequencing
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Affiliation(s)
- Anna V Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Linda M Polfus
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Corey Cox
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02155, USA
| | - Nancy Heard-Costa
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yann Ilboudo
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jonathon Rosen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lifang Hou
- Institute for Public Health and Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Guillaume Lettre
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, and Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald M Lloyd-Jones
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Debby Ngo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Suraj Nongmaithem
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge CB1 8RN, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Department of Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA; Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Ramachandran S Vasan
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P Reiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI 53205, USA.
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8
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Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D. Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia. Nat Commun 2021; 12:5395. [PMID: 34518531 PMCID: PMC8438057 DOI: 10.1038/s41467-021-25403-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the genomic landscape of chronic lymphocytic leukemia (CLL) grows increasingly detailed, providing challenges in contextualizing the accumulated information. To define the underlying networks, we here perform a multi-platform molecular characterization. We identify major subgroups characterized by genomic instability (GI) or activation of epithelial-mesenchymal-transition (EMT)-like programs, which subdivide into non-inflammatory and inflammatory subtypes. GI CLL exhibit disruption of genome integrity, DNA-damage response and are associated with mutagenesis mediated through activation-induced cytidine deaminase or defective mismatch repair. TP53 wild-type and mutated/deleted cases constitute a transcriptionally uniform entity in GI CLL and show similarly poor progression-free survival at relapse. EMT-like CLL exhibit high genomic stability, reduced benefit from the addition of rituximab and EMT-like differentiation is inhibited by induction of DNA damage. This work extends the perspective on CLL biology and risk categories in TP53 wild-type CLL. Furthermore, molecular targets identified within each subgroup provide opportunities for new treatment approaches.
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Affiliation(s)
| | - Andrejs Braun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Sandra Robrecht
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Julia Krzykalla
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam Giza
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Gulnara Akylzhanova
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Annika Scheffold
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Harvey E Johnston
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Ru-Fang Yeh
- Biostatistics, Genentech Inc., South San Francisco, CA, USA
| | - Tetyana Klymenko
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eugen Tausch
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Barbara Eichhorst
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Lars Bullinger
- Medical Clinic for Hematology, Oncology and Tumor Biology, Charité University Hospital, Berlin, Germany
| | - Kirsten Fischer
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Martin Weisser
- Roche Pharma Research and Early Development, Penzberg, Germany
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | - John Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lekh N Dahal
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
- Department of Pharmacology and Therapeutics, Faculty of Life and Health Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mathew J Carter
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- Cancer Genomics and Evolutionary Dynamics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Donna S Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark S Cragg
- Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, Cancer Research UK Centre and Experimental Cancer Medicine Centre, University of Southampton, Southampton, UK
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Michael Hallek
- Department I for Internal Medicine and Centre for Integrated Oncology, University of Cologne, Cologne, Germany
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Daniel Mertens
- Department of Internal Medicine III, University of Ulm, Ulm, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Flindris S, Katsoulas N, Goussia A, Lazaris AC, Navrozoglou I, Paschopoulos M, Thymara I. The Expression of NRIP1 and LCOR in Endometrioid Endometrial Cancer. In Vivo 2021; 35:2631-2640. [PMID: 34410950 DOI: 10.21873/invivo.12545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/15/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND The aim of the study was to analyze the expression of nuclear receptor interacting protein 1 (NRIP1) and its partner ligand-dependent nuclear receptor co-repressor (LCOR) in endometrioid endometrial cancer and to investigate their association with estrogen receptor (ER), progesterone receptor (PR), Ki-67, clinicopathological parameters and patient survival. MATERIALS AND METHODS Immunohistochemical evaluation was carried out to investigate the subcellular expression of NRIP1 and LCOR in endometrioid endometrial cancer samples. Statistical analysis was used to identify the correlations of NRIP1 and LCOR expression with clinicopathological variables and to estimate the survival rates. RESULTS Endometrial cancer tissues exhibited higher expression of NRIP1 and LCOR in comparison with the normal tissues. Cytoplasmic LCOR expression was positively associated with ER and PR expression, while cytoplasmic NRIP1 expression was positively associated with ER expression. Moreover, cytoplasmic expression of NRIP1 was positively associated with Ki-67. CONCLUSION Our study demonstrated that high cytoplasmic expression of LCOR may predict a longer overall survival of patients with endometrioid endometrial cancer. Patients with tumors expressing low levels of LCOR showed a worse survival compared to those expressing high levels.
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Affiliation(s)
- Stefanos Flindris
- Department of Obstetrics and Gynecology, University Hospital of Ioannina, Ioannina, Greece;
| | - Nikolaos Katsoulas
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Laiko General Hospital of Athens, Athens, Greece
| | - Anna Goussia
- Department of Pathology, University Hospital of Ioannina, Ioannina, Greece
| | - Andreas Christos Lazaris
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Laiko General Hospital of Athens, Athens, Greece
| | - Iordanis Navrozoglou
- Department of Obstetrics and Gynecology, University Hospital of Ioannina, Ioannina, Greece
| | - Minas Paschopoulos
- Department of Obstetrics and Gynecology, University Hospital of Ioannina, Ioannina, Greece
| | - Irene Thymara
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Laiko General Hospital of Athens, Athens, Greece
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10
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Zhang Q, Yuan J, Liu Y, Liu X, Lv T, Zhou K, Song Y. KIAA0101 knockdown inhibits cell proliferation and induces cell cycle arrest and cell apoptosis in chronic lymphocytic leukemia cells. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:487. [PMID: 33850884 PMCID: PMC8039647 DOI: 10.21037/atm-21-626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with intense cytogenetic aberrations. Importantly, our recent report indicated that thyroid hormone receptor interactor 13 (TRIP13) is a potential new therapeutic target in CLL. In this study, we predicted 20 TRIP13-related genes and found that KIAA0101 is a novel gene that regulates cell proliferation and the cell cycle of CLL cells. Methods CD19+ B cells were isolated from the peripheral blood of 26 CLL patients and 6 healthy donors through magnetic cell sorting. Cell proliferation was assessed by the CCK-8 assay. The mRNA and protein levels of genes were examined through RT-qPCR and western blot assays, respectively. Cell cycle and cell apoptosis were measured through Annexin V-based flow cytometry and the caspase 3/7 activity assay. Potential targets of KIAA0101 were identified through microarray analysis. 20 TRIP13 related genes was predicted by Ingenuity Pathway Analysis (IPA). KIAA0101-regulated functions and molecular pathways were predicted through IPA. Results KIAA0101 knockdown had the strongest inhibitory effect on CLL cell proliferation among the 20 TRIP13-related genes. KIAA0101 was highly expressed in CD19+ B cells of CLL patients. KIAA0101 knockdown induced cell cycle arrest and cell apoptosis, and inhibited FOXO1, MYD88, and TLR4 expression in CLL cells. Conclusions Taken together, we demonstrated that KIAA0101 plays a critical role in cell proliferation and the cell cycle of human CLL cells. KIAA0101 knockdown induced cell apoptosis, and reduced FOXO1, MYD88, and TLR4 expression, and may therefore be used as a therapeutic target of CLL.
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Affiliation(s)
- Qing Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jingjing Yuan
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yanyan Liu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xingchen Liu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Tianxin Lv
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Keshu Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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11
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Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020; 370:370/6518/eaba7721. [PMID: 33184181 DOI: 10.1126/science.aba7721] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
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Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul D Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
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12
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Sixou S, Müller K, Jalaguier S, Kuhn C, Harbeck N, Mayr D, Engel J, Jeschke U, Ditsch N, Cavaillès V. Importance of RIP140 and LCoR Sub-Cellular Localization for Their Association With Breast Cancer Aggressiveness and Patient Survival. Transl Oncol 2018; 11:1090-1096. [PMID: 30007204 PMCID: PMC6070698 DOI: 10.1016/j.tranon.2018.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/29/2022] Open
Abstract
New markers are needed to improve diagnosis and to personalize treatments for patients with breast cancer (BC). Receptor-interacting protein of 140 kDa (RIP140) and ligand-dependent corepressor (LCoR), two transcriptional co-regulators of estrogen receptors, strongly interact in BC cells. Although their role in cancer progression has been outlined in the last few years, their function in BC has not been elucidated yet. In this study, we investigated RIP140 and LCoR localization (cytoplasm vs nucleus) in BC samples from a well-characterized cohort of patients (n = 320). RIP140 and LCoR were expressed in more than 80% of tumors, (predominantly in the cytoplasm), and the two markers were highly correlated. Expression of RIP140 and LCoR in the nucleus was negatively correlated with tumor size. Conversely, RIP140 and LCoR cytoplasmic expression strongly correlated with expression of two tumor aggressiveness markers: N-cadherin and CD133 (epithelial mesenchymal transition and cancer stem cell markers, respectively). Finally, high RIP140 nuclear expression was significantly correlated with longer overall survival, whereas high total or cytoplasmic expression of RIP140 was associated with shorter disease-free survival. Our study strongly suggests that the role of RIP140 and LCoR in BC progression could vary according to their prevalent sub-cellular localization, with opposite prognostic values for nuclear and cytoplasmic expression. The involvement in BC progression/invasiveness of cytoplasmic RIP140 could be balanced by the anti-tumor action of nuclear RIP140, thus explaining the previous contradictory findings about its role in BC.
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Affiliation(s)
- Sophie Sixou
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Campus Innenstadt, Klinikum der Ludwig-Maximilians-Universität, Maistrasse 11, D-80337 München, Germany; Université Paul Sabatier Toulouse III, Faculté des Sciences Pharmaceutiques, F-31062 Toulouse cedex 09, France.
| | - Katharina Müller
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Campus Innenstadt, Klinikum der Ludwig-Maximilians-Universität, Maistrasse 11, D-80337 München, Germany.
| | - Stéphan Jalaguier
- IRCM - Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université Montpellier, Parc Euromédecine, 208 rue des Apothicaires, F-34298 Montpellier Cedex 5, France.
| | - Christina Kuhn
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Campus Innenstadt, Klinikum der Ludwig-Maximilians-Universität, Maistrasse 11, D-80337 München, Germany.
| | - Nadia Harbeck
- Brustzentrum der Universität München, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Klinikum der Ludwig-Maximilians-Universität, Maistrasse 11, D-80337 München, Germany.
| | - Doris Mayr
- Department of Pathology, Campus Innenstadt, Ludwig-Maximilians-University Hospital, Thalkirchner Str. 36, D-80337 Munich, Germany.
| | - Jutta Engel
- Tumorregister München (TRM) des Tumorzentrums München (TZM) am Klinikum der Universität München (KUM), Marchionistraße 15, 81377 Munich, Germany.
| | - Udo Jeschke
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Campus Innenstadt, Klinikum der Ludwig-Maximilians-Universität, Maistrasse 11, D-80337 München, Germany.
| | - Nina Ditsch
- Department of Obstetrics and Gynaecology, Campus Großhadern, Ludwig-Maximilians-University Hospital, Marchionistraße 15, 81377 Munich, Germany.
| | - Vincent Cavaillès
- IRCM - Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université Montpellier, Parc Euromédecine, 208 rue des Apothicaires, F-34298 Montpellier Cedex 5, France.
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13
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Chen CP, Chen M, Wu CH, Lin CJ, Chern SR, Wu PS, Chen YN, Chen SW, Chang SP, Chen LF, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of mosaicism for a small supernumerary marker chromosome derived from chromosome 21q11.2-q21.1 and a literature review. Taiwan J Obstet Gynecol 2018; 56:554-557. [PMID: 28805618 DOI: 10.1016/j.tjog.2017.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2017] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis and molecular cytogenetic characterization of mosaicism for a small supernumerary marker chromosome (sSMC) derived from chromosome 21q11.2-q21.1, and we review the literature of an sSMC(21) with a duplication of 21q11.2-q21.1. CASE REPORT A 40-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XX,+mar [18]/46,XX [4]. The parental karyotypes were normal. Prenatal ultrasound findings were unremarkable. aCGH analysis of cultured amniocytes revealed a 2.855-Mb duplication of 21q11.2-q21.1 encompassing the genes of LIPI, ABCC13 and NRIP1. Metaphase fluorescence in situ hybridization analysis on cultured amniocytes revealed a result of 47,XX,+mar .ish der(13/21) (D13/21Z1+) [10]. Spectral karyotyping analysis determined the origin of chromosome 21 in the sSMC. A female fetus was delivered with no phenotypic features of Down syndrome and no structural abnormalities. We discuss the genotype-phenotype correlation of LIPI, ABCC13 and NRIP1, and review the literature of an sSMC(21) associated with dup(21)(q11.2q21.1). CONCLUSION aCGH is useful for identification of the nature and genetic component of a prenatally detected sSMC.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Ming Chen
- Department of Medical Research, Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan; Department of Genomic Medicine, Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan; Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - Chia-Hsun Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Ju Lin
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Yen-Ni Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shun-Ping Chang
- Department of Medical Research, Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan; Department of Genomic Medicine, Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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14
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Zhou K, Zhang W, Zhang Q, Gui R, Zhao H, Chai X, Li Y, Wei X, Song Y. Loss of thyroid hormone receptor interactor 13 inhibits cell proliferation and survival in human chronic lymphocytic leukemia. Oncotarget 2018; 8:25469-25481. [PMID: 28424416 PMCID: PMC5421944 DOI: 10.18632/oncotarget.16038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/07/2017] [Indexed: 12/13/2022] Open
Abstract
Background The genetic regulation of apoptosis and cell proliferation plays a role in the growth of chronic lymphocytic leukemia (CLL), the most common form of leukemia in the Western hemisphere. Although thyroid hormone receptor interactors (TRIPs) are known to play roles in cell cycle, the potential involvement of the novel family member TRIP13 in CLL has not yet been investigated. Methods Quantitative PCR (qPCR) was used to detect expression of TRIP13 in 36 CLL patients and 33 healthy donors CD19+ B cells. Loss-of-function (siRNA) assays were used to alter TRIP13 expression levels. The effect of TRIP13 on cell proliferation and apoptosis was measured by MTT, Annexin V-based flow cytometry and Caspase 3/7 activity assay. Affymetrix GeneChip and Ingenuity Pathway Analysis (IPA) were used to describe an overview of TRIP13 potential biological function and downstream pathways. Dual-luciferase reporter assay was performed to assess the promoting effect of c-MYC on TRIP13 transcription. RESULTS The qPCR data showed that TRIP13 is significantly over-expressed in CLL patients. Microarray analyses indicated that the biological function of TRIP13 in CLL is majorly cell apoptosis and cell proliferation associated. TRIP13 siRNA expressing cells exhibited a slower cell proliferation rate and underwent apoptosis compared with control cells. TRIP13 knockdown induced CLL cells apoptosis through PUMA independent of p53. TRIP13 up-regulation is induced by c-MYC dependent transcriptional activation. Conclusion Overall, our data suggest the bio-function of TRIP13 in CLL cell for the first time, and that this gene might be a therapeutic target for CLL.
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Affiliation(s)
- Keshu Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Wentao Zhang
- Armed Police Forces Hospital of Henan, People's Republic of China
| | - Qing Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Huifang Zhao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Xiaofei Chai
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Yufu Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Xudong Wei
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, People's Republic of China
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15
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Bird RP. The Emerging Role of Vitamin B6 in Inflammation and Carcinogenesis. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 83:151-194. [PMID: 29477221 DOI: 10.1016/bs.afnr.2017.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vitamin B6 serves as a coenzyme catalyzing more than 150 enzymes regulating metabolism and synthesis of proteins, carbohydrates, lipids, heme, and important bioactive metabolites. For several years vitamin B6 and its vitamers (B6) were recognized as antioxidant and antiinflammatory and in modulating immunity and gene expression. During the last 10 years, there were growing reports implicating B6 in inflammation and inflammation-related chronic illnesses including cancer. It is unclear if the deficiency of B6 or additional intake of B6, above the current requirement, should be the focus. Whether the current recommended daily intake for B6 is adequate should be revisited, since B6 is important to human health beyond its role as a coenzyme and its status is affected by many factors including but not limited to age, obesity, and inflammation associated with chronic illnesses. A link between inflammation B6 status and carcinogenesis is not yet completely understood. B6-mediated synthesis of H2S, a gasotransmitter, and taurine in health and disease, especially in maintaining mitochondrial integrity and biogenesis and inflammation, remains an important area to be explored. Recent developments in the molecular role of B6 and its direct interaction with inflammasomes, and nuclear receptor corepressor and coactivator, receptor-interacting protein 140, provide a strong impetus to further explore the multifaceted role of B6 in carcinogenesis and human health.
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Affiliation(s)
- Ranjana P Bird
- School of Health Sciences, University of Northern British Columbia, Prince George, BC, Canada.
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16
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Nautiyal J. Transcriptional coregulator RIP140: an essential regulator of physiology. J Mol Endocrinol 2017; 58:R147-R158. [PMID: 28073818 DOI: 10.1530/jme-16-0156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 01/10/2017] [Indexed: 12/26/2022]
Abstract
Transcriptional coregulators drive gene regulatory decisions in the transcriptional space. Although transcription factors including all nuclear receptors provide a docking platform for coregulators to bind, these proteins bring enzymatic capabilities to the gene regulatory sites. RIP140 is a transcriptional coregulator essential for several physiological processes, and aberrations in its function may lead to diseased states. Unlike several other coregulators that are known either for their coactivating or corepressing roles, in gene regulation, RIP140 is capable of acting both as a coactivator and a corepressor. The role of RIP140 in female reproductive axis and recent findings of its role in carcinogenesis and adipose biology have been summarised.
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Affiliation(s)
- Jaya Nautiyal
- Institute of Reproductive and Developmental BiologyFaculty of Medicine, Imperial College London, London, UK
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17
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Kakehashi A, Stefanov VE, Ishii N, Okuno T, Fujii H, Kawai K, Kawada N, Wanibuchi H. Proteome Characteristics of Non-Alcoholic Steatohepatitis Liver Tissue and Associated Hepatocellular Carcinomas. Int J Mol Sci 2017; 18:ijms18020434. [PMID: 28218651 PMCID: PMC5343968 DOI: 10.3390/ijms18020434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 12/18/2022] Open
Abstract
To uncover mechanisms of nonalcoholic steatohepatitis (NASH) associated hepatocarcinogenesis, we compared the proteomes of human NASH-associated liver biopsies, resected hepatocellular carcinomas (HCCs) and HCCs of HCV⁺ patients with normal liver tissue of patients with gastrointestinal tumor metastasis, in formalin-fixed paraffin-embedded samples obtained after surgery in our hospital during the period from 2006 to 2011. In addition, proteome analysis of liver tumors in male STAM NASH-model mice was performed. Similar changes in the proteome spectrum such as overexpression of enzymes involved in lipid, cholesterol and bile acid biosynthesis and examples associated with suppression of fatty acid oxidation and catabolism, alcohol metabolism, mitochondrial function as well as low expression levels of cytokeratins 8 and 18 were observed in both human NASH biopsies and NASH HCCs, but not HCV⁺ HCCs. Alterations in downstream protein expression pointed to significant activation of transforming growth factor β, SMAD family member 3, β-catenin, Nrf2, SREBP-LXRα and nuclear receptor-interacting protein 1 (NRIP1), and inhibition of PPARs and p53 in human NASH biopsies and/or HCCs, suggesting their involvement in accumulation of lipids, development of fibrosis, oxidative stress, cell proliferation and suppression of apoptosis in NASH hepatocarcinogenesis. In STAM mice, PPARs inhibition was not obvious, while expression of cytokeratins 8 and 18 was elevated, indicative of essential differences between human and mouse NASH pathogenesis.
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Affiliation(s)
- Anna Kakehashi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, Asahi-machi 1-4-3, Abeno-ku, Osaka 545-8585, Japan.
| | - Vasily E Stefanov
- Department of Biochemistry, Saint Petersburg State University, Saint Petersburg 199034, Russia.
| | - Naomi Ishii
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, Asahi-machi 1-4-3, Abeno-ku, Osaka 545-8585, Japan.
| | - Takahiro Okuno
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, Asahi-machi 1-4-3, Abeno-ku, Osaka 545-8585, Japan.
| | - Hideki Fujii
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Kazuaki Kawai
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu 807-8555, Japan.
| | - Norifumi Kawada
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Hideki Wanibuchi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine, Asahi-machi 1-4-3, Abeno-ku, Osaka 545-8585, Japan.
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18
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Piao H, Chu X, Lv W, Zhao Y. Involvement of receptor-interacting protein 140 in estrogen-mediated osteoclasts differentiation, apoptosis, and bone resorption. J Physiol Sci 2017; 67:141-150. [PMID: 27016936 PMCID: PMC10716944 DOI: 10.1007/s12576-016-0447-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/10/2016] [Indexed: 01/28/2023]
Abstract
Estrogen withdrawal following menopause results in an increase of osteoclasts formation and bone resorption, which is one of the most important mechanisms of postmenopausal osteoporosis. Recently, growing evidence has suggested that receptor-interacting protein 140 was implicated in estrogen-regulated metabolic disease, including fat metabolism and lipid metabolism. However, little is known regarding the role of receptor-interacting protein 140 in the regulation of bone metabolic by estrogen. In the present study, Western blotting disclosed that estrogen brings a significant increasing expression of receptor-interacting protein 140 in osteoclasts, but not in osteoblasts and bone marrow mesenchymal stem cells. Furthermore, analysis of TRAP staining and bone resorption assay showed that depletion of receptor-interacting protein 140 could significantly alleviate the inhibitory effects of estrogen on osteoclasts formation and bone resorption activity. Moreover, estrogen could induce osteoclasts apoptosis by increasing receptor-interacting protein 140 expression through the Fas/FasL pathway. Taken together, receptor-interacting protein 140 might be a critical player in estrogen-mediated osteoclastogenesis and bone resorption.
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Affiliation(s)
| | - Xiaojie Chu
- Daqing Oilfield General Hospital, Daqing, China
| | - Wentao Lv
- Department of Pharmacy and Laboratory Medicine, Daqing Medical College, Daqing, China
| | - Yan Zhao
- Daqing Oilfield General Hospital, Daqing, China.
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19
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Abstract
NOP14, which is functionally conserved among eukaryotes, has been implicated in cancer development. Here, we show that NOP14 is poorly expressed in breast cancer cells and invasive breast cancer tissues. In vivo and in vitro studies indicated that NOP14 suppressed the tumorigenesis and metastasis of breast cancer cells. Further investigations revealed that NOP14 enhanced ERα expression and inhibited the Wnt/β-catenin pathway by up-regulating NRIP1 expression. Survival analysis indicated that low NOP14 expression was significantly associated with poor overall survival (P = 0.0006) and disease-free survival (P = 0.0007), suggesting that NOP14 is a potential prognostic factor in breast cancer. Taken together, our findings reveal that NOP14 may suppress breast cancer progression and provide new insights into the development of targeted therapeutic agents for breast cancer.
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20
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Crisan M, Solaimani Kartalaei P, Neagu A, Karkanpouna S, Yamada-Inagawa T, Purini C, Vink CS, van der Linden R, van Ijcken W, Chuva de Sousa Lopes SM, Monteiro R, Mummery C, Dzierzak E. BMP and Hedgehog Regulate Distinct AGM Hematopoietic Stem Cells Ex Vivo. Stem Cell Reports 2016; 6:383-95. [PMID: 26923823 PMCID: PMC4788785 DOI: 10.1016/j.stemcr.2016.01.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
Hematopoietic stem cells (HSC), the self-renewing cells of the adult blood differentiation hierarchy, are generated during embryonic stages. The first HSCs are produced in the aorta-gonad-mesonephros (AGM) region of the embryo through endothelial to a hematopoietic transition. BMP4 and Hedgehog affect their production and expansion, but it is unknown whether they act to affect the same HSCs. In this study using the BRE GFP reporter mouse strain that identifies BMP/Smad-activated cells, we find that the AGM harbors two types of adult-repopulating HSCs upon explant culture: One type is BMP-activated and the other is a non-BMP-activated HSC type that is indirectly controlled by Hedgehog signaling through the VEGF pathway. Transcriptomic analyses demonstrate that the two HSC types express distinct but overlapping genetic programs. These results revealing the bifurcation in HSC types at early embryonic stages in the AGM explant model suggest that their development is dependent upon the signaling molecules in the microenvironment. AGM explants contain two HSC types, BMP-activated and non-BMP-activated Non-BMP-activated HSCs are dependent on Hedgehog/VEGF Changes in the microenvironment ex vivo contribute to novel HSC composition
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Affiliation(s)
- Mihaela Crisan
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands; BHF Centre for Cardiovascular Science, Scottish Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Parham Solaimani Kartalaei
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands; Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Alex Neagu
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands
| | - Sofia Karkanpouna
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands
| | - Tomoko Yamada-Inagawa
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands
| | - Caterina Purini
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands
| | - Chris S Vink
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands; Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Reinier van der Linden
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands
| | - Wilfred van Ijcken
- Center for Biomics, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | | | - Rui Monteiro
- Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Christine Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Elaine Dzierzak
- Department of Cell Biology, Erasmus Medical Center, Erasmus MC Stem Cell Institute, 3000 CA Rotterdam, the Netherlands; Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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