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Song Z, Zhao Z, Zhu S, Jin Q, Zhang S, Wang Z, Shen B, Wang Z, Zhao Z. Arylsulfatase D is a prognostic biomarker that promotes glioma cells progression through JAK2/STAT3 pathway and M2 macrophage infiltration. Front Oncol 2023; 13:1228426. [PMID: 37766864 PMCID: PMC10521731 DOI: 10.3389/fonc.2023.1228426] [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: 05/24/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Background Arylsulfatase D (ARSD) belongs to the sulfatase family and plays a crucial role in maintaining the proper structure of bone and cartilage matrix. Although several researches have revealed the functions of ARSD in tumor progression, the prognostic value of ARSD in glioma and the related mechanisms have not been fully investigated. Methods We performed a pan-cancer analysis of ARSD, and investigated the relationship between expression of ARSD and overall survival (OS) in multiple glioma datasets. ROC curves and nomograms were created to investigate the predictive capacity of ARSD. Immune and analysis were conducted to investigate the mechanisms underlying the roles of ARSD in glioma. Glioma tissue samples were collected to verify the expression of ARSD in glioma, while the functions of ARSD were explored using cell experiment. M2 macrophage infiltration assay was used to determine the relation between ARSD and tumor immune microenvironment. Results Survival analysis indicated that individuals with high ARSD expression in glioma had a shorter survival time. Cox analysis showed that ARSD had a good ability for predicting prognosis in glioma. Immune analysis suggested that ARSD could regulate immune cell infiltration and affect the Cancer-Immunity Cycle to create an immunosuppressive environment. Combined with cell experiment and bioinformatic analysis, we found that ARSD can promote glioma progression through regulation of JAK2/STAT3 pathway and M2 macrophage infiltration. Conclusion Our study found that ARSD can promote glioma development by regulating immune microenvironment and JAK2/STAT3 signaling pathway, which provided a potential therapy target for glioma treatment.
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Affiliation(s)
- Zihan Song
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zijun Zhao
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Siyu Zhu
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Qianxu Jin
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shiyang Zhang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zairan Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowei Shen
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zijian Wang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Bossi LE, Palumbo C, Trojani A, Melluso A, Di Camillo B, Beghini A, Sarnataro LM, Cairoli R. A Nine-Gene Expression Signature Distinguished a Patient with Chronic Lymphocytic Leukemia Who Underwent Prolonged Periodic Fasting. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1405. [PMID: 37629695 PMCID: PMC10456711 DOI: 10.3390/medicina59081405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: This study aimed to investigate the causes of continuous deep fluctuations in the absolute lymphocyte count (ALC) in an untreated patient with Chronic Lymphocytic Leukemia (CLL), who has had a favorable prognosis since the time of diagnosis. Up until now, the patient has voluntarily chosen to adopt a predominantly vegetarian and fruitarian diet, along with prolonged periods of total fasting (ranging from 4 to 39 days) each year. Materials and Methods: For this purpose, we decided to analyze the whole transcriptome profiling of peripheral blood (PB) CD19+ cells from the patient (#1) at different time-points vs. the same cells of five other untreated CLL patients who followed a varied diet. Consequently, the CLL patients were categorized as follows: the 1st group comprised patient #1 at 20 different time-points (16 time-points during nutrition and 4 time-points during fasting), whereas the 2nd group included only one time point for each of the patients (#2, #3, #4, #5, and #6) as they followed a varied diet. We performed microarray experiments using a powerful tool, the Affymetrix Human Clariom™ D Pico Assay, to generate high-fidelity biomarker signatures. Statistical analysis was employed to identify differentially expressed genes and to perform sample clustering. Results: The lymphocytosis trend in patient #1 showed recurring fluctuations since the time of diagnosis. Interestingly, we observed that approximately 4-6 weeks after the conclusion of fasting periods, the absolute lymphocyte count was reduced by about half. The gene expression profiling analysis revealed that nine genes were statistically differently expressed between the 1st group and the 2nd group. Specifically, IGLC3, RPS26, CHPT1, and PCDH9 were under expressed in the 1st group compared to the 2nd group of CLL patients. Conversely, IGHV3-43, IGKV3D-20, PLEKHA1, CYBB, and GABRB2 were over-expressed in the 1st group when compared to the 2nd group of CLL patients. Furthermore, clustering analysis validated that all the samples from patient #1 clustered together, showing clear separation from the samples of the other CLL patients. Conclusions: This study unveiled a small gene expression signature consisting of nine genes that distinguished an untreated CLL patient who followed prolonged periods of total fasting, maintaining a gradual growth trend of lymphocytosis, compared to five untreated CLL patients with a varied diet. Future investigations focusing on patient #1 could potentially shed light on the role of prolonged periodic fasting and the implication of this specific gene signature in sustaining the lymphocytosis trend and the favorable course of the disease.
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Affiliation(s)
- Luca Emanuele Bossi
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Cassandra Palumbo
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Alessandra Trojani
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Agostina Melluso
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35020 Padua, Italy;
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padua, Italy
| | | | - Luca Maria Sarnataro
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
| | - Roberto Cairoli
- Department of Hematology and Oncology ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (A.T.); (A.M.); (L.M.S.); (R.C.)
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3
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Liang X, Meng Y, Li C, Liu L, Wang Y, Pu L, Hu L, Li Q, Zhai Z. Super-Enhancer–Associated nine-gene prognostic score model for prediction of survival in chronic lymphocytic leukemia patients. Front Genet 2022; 13:1001364. [PMID: 36186463 PMCID: PMC9521409 DOI: 10.3389/fgene.2022.1001364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a type of highly heterogeneous mature B-cell malignancy with various disease courses. Although a multitude of prognostic markers in CLL have been reported, insights into the role of super-enhancer (SE)–related risk indicators in the occurrence and development of CLL are still lacking. A super-enhancer (SE) is a cluster of enhancers involved in cell differentiation and tumorigenesis, and is one of the promising therapeutic targets for cancer therapy in recent years. In our study, the CLL-related super-enhancers in the training database were processed by LASSO-penalized Cox regression analysis to screen a nine-gene prognostic model including TCF7, VEGFA, MNT, GMIP, SLAMF1, TNFRSF25, GRWD1, SLC6AC, and LAG3. The SE-related risk score was further constructed and it was found that the predictive performance with overall survival and time-to-treatment (TTT) was satisfactory. Moreover, a high correlation was found between the risk score and already known prognostic markers of CLL. In the meantime, we noticed that the expressions of TCF7, GMIP, SLAMF1, TNFRSF25, and LAG3 in CLL were different from those of healthy donors (p < 0.01). Moreover, the risk score and LAG3 level of matched pairs before and after treatment samples varied significantly. Finally, an interactive nomogram consisting of the nine-gene risk group and four clinical traits was established. The inhibitors of mTOR and cyclin-dependent kinases (CDKs) were considered effective in patients in the high-risk group according to the pRRophetic algorithm. Collectively, the SE-associated nine-gene prognostic model developed here may be used to predict the prognosis and assist in the risk stratification and treatment of CLL patients in the future.
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Lin Y, Li C, Xiong W, Fan L, Pan H, Li Y. ARSD, a novel ERα downstream target gene, inhibits proliferation and migration of breast cancer cells via activating Hippo/YAP pathway. Cell Death Dis 2021; 12:1042. [PMID: 34725332 PMCID: PMC8560752 DOI: 10.1038/s41419-021-04338-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 02/05/2023]
Abstract
Advanced breast cancer (BC), especially basal like triple-negative BC (TNBC), is a highly malignant tumor without viable treatment option, highlighting the urgent need to seek novel therapeutic targets. Arylsulfatase D (ARSD), localized at Xp22.3, is a female-biased gene due to its escaping from X chromosome inactivation (XCI). Unfortunately, no systematic investigation of ARSD on BC has been reported. In this study, we observed that ARSD expression was positively related to ERα status either in BC cells or tissue specimens, which were associated with good prognosis. Furthermore, we found a set of hormone-responsive lineage-specific transcription factors, FOXA1, GATA3, ERα, directly drove high expression of ARSD through chromatin looping in luminal subtype BC cells. Opposingly, ARSD still subjected to XCI in TNBC cells mediated by Xist, CpG islands methylation, and inhibitory histone modification. Unexpectedly, we also found that ectopic ARSD overexpression could inhibit proliferation and migration of TNBC cells by activating Hippo/YAP pathway, indicating that ARSD may be a molecule brake on ERα signaling pathway, which restricted ERα to be an uncontrolled active status. Combined with other peoples' researches that Hippo signaling maintained ER expression and ER + BC growth, we believed that there should exist a regulative feedback loop formation among ERα, ARSD, and Hippo/YAP pathway. Collectively, our findings will help filling the knowledge gap about the influence of ARSD on BC and providing evidence that ARSD may serve as a potential marker to predict prognosis and as a therapeutic target.
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Affiliation(s)
- Yun Lin
- Central laboratory, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515041, China
| | - Chun Li
- Faculty of Health science, Hull York Medical School, University of Hull, Hull, UK, HU6 7RX
| | - Wei Xiong
- Central laboratory, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515041, China
| | - Liping Fan
- Central laboratory, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515041, China
| | - Hongchao Pan
- Central laboratory, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515041, China.
| | - Yaochen Li
- Central laboratory, Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515041, China.
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5
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Eagle GL, Herbert JMJ, Zhuang J, Oates M, Khan UT, Kitteringham NR, Clarke K, Park BK, Pettitt AR, Jenkins RE, Falciani F. Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells. Sci Rep 2021; 11:2932. [PMID: 33536534 PMCID: PMC7858606 DOI: 10.1038/s41598-021-82609-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.
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Affiliation(s)
- Gina L Eagle
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John M J Herbert
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - Jianguo Zhuang
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Melanie Oates
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Umair T Khan
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Neil R Kitteringham
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Kim Clarke
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Rosalind E Jenkins
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK.
| | - Francesco Falciani
- Computational Biology Facility, University of Liverpool, Liverpool, UK. .,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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6
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Guo C, Gao YY, Ju QQ, Zhang CX, Gong M, Li ZL. HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. J Transl Med 2021; 19:42. [PMID: 33485349 PMCID: PMC7825181 DOI: 10.1186/s12967-021-02708-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/16/2021] [Indexed: 11/16/2022] Open
Abstract
Background IGHV mutation status is a crucial prognostic biomarker for CLL. In the present study, we investigated the transcriptomic signatures associating with IGHV mutation status and CLL prognosis. Methods The co-expression modules and hub genes correlating with IGHV status, were identified using the GSE28654, by ‘WGCNA’ package and R software (version 4.0.2). The over-representation analysis was performed to reveal enriched cell pathways for genes of correlating modules. Then 9 external cohorts were used to validate the correlation of hub genes expression with IGHV status or clinical features (treatment response, transformation to Richter syndrome, etc.). Moreover, to elucidate the significance of hub genes on disease course and prognosis of CLL patients, the Kaplan–Meier analysis for the OS and TTFT of were performed between subgroups dichotomized by the median expression value of individual hub genes. Results 2 co-expression modules and 9 hub genes ((FCRL1/FCRL2/HELQ/EGR3LPL/LDOC1/ZNF667/SOWAHC/SEPTIN10) correlating with IGHV status were identified by WGCNA, and validated by external datasets. The modules were found to be enriched in NF-kappaB, HIF-1 and other important pathways, involving cell proliferation and apoptosis. The expression of hub genes was revealed to be significantly different, not only between CLL and normal B cell, but also between various types of lymphoid neoplasms. HELQ expression was found to be related with response of immunochemotherapy treatment significantly (p = 0.0413), while HELQ and ZNF667 were expressed differently between stable CLL and Richter syndrome patients (p < 0.0001 and p = 0.0278, respectively). By survival analysis of subgroups, EGR3 expression was indicated to be significantly associated with TTFT by 2 independent cohorts (GSE39671, p = 0.0311; GSE22762, p = 0.0135). While the expression of HELQ and EGR3 was found to be associated with OS (p = 0.0291 and 0.0114 respectively).The Kras, Hedgehog and IL6-JAK-STAT3 pathways were found to be associating with the expression of hub genes, resulting from GSEA. Conclusions The expression of HELQ and EGR3 were correlated with IGHV mutation status in CLL patients. Additionally, the expression of HELQ/EGR3 were prognostic markers for CLL associating with targetable cell signaling pathways.
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Affiliation(s)
- Chao Guo
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ya-Yue Gao
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Qian-Qian Ju
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Chun-Xia Zhang
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ming Gong
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Zhen-Ling Li
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China.
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7
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Winham SJ, Larson NB, Armasu SM, Fogarty ZC, Larson MC, McCauley BM, Wang C, Lawrenson K, Gayther S, Cunningham JM, Fridley BL, Goode EL. Molecular signatures of X chromosome inactivation and associations with clinical outcomes in epithelial ovarian cancer. Hum Mol Genet 2019; 28:1331-1342. [PMID: 30576442 DOI: 10.1093/hmg/ddy444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/12/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
X chromosome inactivation (XCI) is a key epigenetic gene expression regulatory process, which may play a role in women's cancer. In particular tissues, some genes are known to escape XCI, yet patterns of XCI in ovarian cancer (OC) and their clinical associations are largely unknown. To examine XCI in OC, we integrated germline genotype with tumor copy number, gene expression and DNA methylation information from 99 OC patients. Approximately 10% of genes showed different XCI status (either escaping or being subject to XCI) compared with the studies of other tissues. Many of these genes are known oncogenes or tumor suppressors (e.g. DDX3X, TRAPPC2 and TCEANC). We also observed strong association between cis promoter DNA methylation and allele-specific expression imbalance (P = 2.0 × 10-10). Cluster analyses of the integrated data identified two molecular subgroups of OC patients representing those with regulated (N = 47) and dysregulated (N = 52) XCI. This XCI cluster membership was associated with expression of X inactive specific transcript (P = 0.002), a known driver of XCI, as well as age, grade, stage, tumor histology and extent of residual disease following surgical debulking. Patients with dysregulated XCI (N = 52) had shorter time to recurrence (HR = 2.34, P = 0.001) and overall survival time (HR = 1.87, P = 0.02) than those with regulated XCI, although results were attenuated after covariate adjustment. Similar findings were observed when restricted to high-grade serous tumors. We found evidence of a unique OC XCI profile, suggesting that XCI may play an important role in OC biology. Additional studies to examine somatic changes with paired tumor-normal tissue are needed.
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Affiliation(s)
- Stacey J Winham
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicholas B Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Sebastian M Armasu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zachary C Fogarty
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brian M McCauley
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Chen Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kate Lawrenson
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Ellen L Goode
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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Gradin R, Lindstedt M, Johansson H. Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects. PLoS One 2019; 14:e0212669. [PMID: 30794641 PMCID: PMC6386283 DOI: 10.1371/journal.pone.0212669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
Many biological data acquisition platforms suffer from inadvertent inclusion of biologically irrelevant variance in analyzed data, collectively termed batch effects. Batch effects can lead to difficulties in downstream analysis by lowering the power to detect biologically interesting differences and can in certain instances lead to false discoveries. They are especially troublesome in predictive modelling where samples in training sets and test sets are often completely correlated with batches. In this article, we present BARA, a normalization method for adjusting batch effects in predictive modelling. BARA utilizes a few reference samples to adjust for batch effects in a compressed data space spanned by the training set. We evaluate BARA using a collection of publicly available datasets and three different prediction models, and compare its performance to already existing methods developed for similar purposes. The results show that data normalized with BARA generates high and consistent prediction performances. Further, they suggest that BARA produces reliable performances independent of the examined classifiers. We therefore conclude that BARA has great potential to facilitate the development of predictive assays where test sets and training sets are correlated with batch.
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Affiliation(s)
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University, Lund, Sweden
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9
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Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol 2018; 14:e8124. [PMID: 29925568 PMCID: PMC6010767 DOI: 10.15252/msb.20178124] [Citation(s) in RCA: 503] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
Multi-omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities. The learnt factors enable a variety of downstream analyses, including identification of sample subgroups, data imputation and the detection of outlier samples. We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profiled for somatic mutations, RNA expression, DNA methylation and ex vivo drug responses. MOFA identified major dimensions of disease heterogeneity, including immunoglobulin heavy-chain variable region status, trisomy of chromosome 12 and previously underappreciated drivers, such as response to oxidative stress. In a second application, we used MOFA to analyse single-cell multi-omics data, identifying coordinated transcriptional and epigenetic changes along cell differentiation.
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Affiliation(s)
- Ricard Argelaguet
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Britta Velten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Damien Arnol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | | | - Thorsten Zenz
- Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (dkfz) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Germany & Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Florian Buettner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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10
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Inhibition of maternal embryonic leucine zipper kinase with OTSSP167 displays potent anti-leukemic effects in chronic lymphocytic leukemia. Oncogene 2018; 37:5520-5533. [PMID: 29895969 DOI: 10.1038/s41388-018-0333-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 11/08/2022]
Abstract
TP53 pathway defects contributed to therapy resistance and adverse clinical outcome in chronic lymphocytic leukemia (CLL), which represents an unmet clinical need with few therapeutic options. Maternal embryonic leucine zipper kinase (MELK) is a novel oncogene, which plays crucial roles in mitotic progression and stem cell maintenance. OTSSP167, an orally administrated inhibitor targeting MELK, is currently in a phase I/II clinical trial in patients with advanced breast cancer and acute myeloid leukemia. Yet, no investigation has been elucidated to date regarding the oncogenic role of MELK and effects of OTSSP167 in chronic lymphocytic leukemia (CLL). Previous studies confirmed MELK inhibition abrogated cancer cell survival via p53 signaling pathway. Thus, we aimed to determine the biological function of MELK and therapeutic potential of OTSSP167 in CLL. Herein, MELK over-expression was observed in CLL cells, and correlated with higher WBC count, advanced stage, elevated LDH, increased β2-MG level, unmutated IGHV, positive ZAP-70, deletion of 17p13 and inferior prognosis of CLL patients. In accordance with functional enrichment analyses in gene expression profiling, CLL cells with depletion or inhibition of MELK exhibited impaired cell proliferation, enhanced fast-onset apoptosis, induced G2/M arrest, attenuated cell chemotaxis and promoted sensitivity to fludarabine and ibrutinib. However, gain-of-function assay showed increased cell proliferation and cell chemotaxis. In addition, OTSSP167 treatment reduced phosphorylation of AKT and ERK1/2. It decreased FoxM1 phosphorylation, expression of FoxM1, cyclin B1 and CDK1, while up-regulating p53 and p21 expression. Taken together, MELK served as a candidate of therapeutic target in CLL. OTSSP167 exhibits potent anti-tumor activities in CLL cells, highlighting a novel molecule-based strategy for leukemic interventions.
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11
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Nørgaard CH, Jakobsen LH, Gentles AJ, Dybkær K, El-Galaly TC, Bødker JS, Schmitz A, Johansen P, Herold T, Spiekermann K, Brown JR, Klitgaard JL, Johnsen HE, Bøgsted M. Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow - A proof of concept study. PLoS One 2018; 13:e0193249. [PMID: 29513759 PMCID: PMC5841735 DOI: 10.1371/journal.pone.0193249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 11/26/2022] Open
Abstract
Diagnostic and prognostic evaluation of chronic lymphocytic leukemia (CLL) involves blood cell counts, immunophenotyping, IgVH mutation status, and cytogenetic analyses. We generated B-cell associated gene-signatures (BAGS) based on six naturally occurring B-cell subsets within normal bone marrow. Our hypothesis is that by segregating CLL according to BAGS, we can identify subtypes with prognostic implications in support of pathogenetic value of BAGS. Microarray-based gene-expression samples from eight independent CLL cohorts (1,024 untreated patients) were BAGS-stratified into pre-BI, pre-BII, immature, naïve, memory, or plasma cell subtypes; the majority falling within the memory (24.5-45.8%) or naïve (14.5-32.3%) categories. For a subset of CLL patients (n = 296), time to treatment (TTT) was shorter amongst early differentiation subtypes (pre-BI/pre-BII/immature) compared to late subtypes (memory/plasma cell, HR: 0.53 [0.35-0.78]). Particularly, pre-BII subtype patients had the shortest TTT among all subtypes. Correlates derived for BAGS subtype and IgVH mutation (n = 405) revealed an elevated mutation frequency in late vs. early subtypes (71% vs. 45%, P < .001). Predictions for BAGS subtype resistance towards rituximab and cyclophosphamide varied for rituximab, whereas all subtypes were sensitive to cyclophosphamide. This study supports our hypothesis that BAGS-subtyping may be of tangible prognostic and pathogenetic value for CLL patients.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Agents, Immunological/therapeutic use
- B-Lymphocyte Subsets/metabolism
- Bone Marrow/metabolism
- Cyclophosphamide/therapeutic use
- Drug Resistance, Neoplasm/physiology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Microarray Analysis
- Middle Aged
- Prognosis
- Proof of Concept Study
- Retrospective Studies
- Rituximab/therapeutic use
- Survival Analysis
- Time-to-Treatment
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Affiliation(s)
| | - Lasse Hjort Jakobsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Andrew J. Gentles
- Departments of Medicine and Biomedical Data Science, Stanford, California, United States of America
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Preben Johansen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Tobias Herold
- Department of Internal Medicine 3, University of Munich, Munich, Germany
| | | | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Josephine L. Klitgaard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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12
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Holmes RS. Comparative and evolutionary studies of mammalian arylsulfatase and sterylsulfatase genes and proteins encoded on the X-chromosome. Comput Biol Chem 2017; 68:71-77. [DOI: 10.1016/j.compbiolchem.2017.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/22/2016] [Accepted: 02/22/2017] [Indexed: 12/09/2022]
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13
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Heo SG, Koh Y, Kim JK, Jung J, Kim HL, Yoon SS, Park JW. Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia. BMC MEDICAL GENETICS 2017; 18:23. [PMID: 28249600 PMCID: PMC5333433 DOI: 10.1186/s12881-017-0382-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 02/15/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a biologically and clinically heterogeneous cancer of the bone marrow that is characterized by the rapid growth of abnormal myeloid cells. METHODS We performed a mutational analysis to identify AML somatic mutations using the whole-exome sequencing data of 36 tumor-normal sample pairs from Korean patients with de novo AML. We explored the functional impact of the genes identified in the mutational analyses through an integrated Gene Ontology (GO) and pathway analysis. RESULTS A total of 11 genes, including NEFH (p = 6.27 × 10-13 and q = 1.18 × 10-8) and TMPRSS13 (p = 1.40 × 10-10 and q = 1.32 × 10-6), also demonstrated q values less than 0.1 in 36 Korean AML patients. Five out of the 11 novel genes have previously been reported to be associated with other cancers. Two gene mutations, CEBPA (p = 5.22 × 10-5) and ATXN3 (p = 9.75 × 10-4), showed statistical significance exclusively in the M2 and M3 subtypes of the French-American-British classifications, respectively. A total of 501 genes harbored 478 missense, 22 nonsense, 93 frameshift indels, and/or three stop codon deletions and these gene mutations significantly enriched GO terms for signal transduction (GO:0007165, p = 1.77 × 10-3), plasma membrane (GO:0005886, p = 3.07 × 10-4), and scaffold protein binding (GO:0097110, p = 8.65 × 10-4). The mitogen-activated protein kinase (hsa04010, 7.67 × 10-4) was the most enriched Kyoto Encyclopedia of Genes and Genomes pathway. CONCLUSIONS Morphological AML subtypes may in part reflect subtype specific patterns of genomic alterations. Following validation, future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile.
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Affiliation(s)
- Seong Gu Heo
- Department of Medical Genetics, College of Medicine, Hallym University, 1 Hallymdaehak-gil, Chuncheon, Gangwon-do, 24252, Republic of Korea.,Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jong Kwang Kim
- Omics Core Lab., National Cancer Center, Goyang, Republic of Korea.,The Catholic University, Seoul, Republic of Korea
| | | | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ji Wan Park
- Department of Medical Genetics, College of Medicine, Hallym University, 1 Hallymdaehak-gil, Chuncheon, Gangwon-do, 24252, Republic of Korea.
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14
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Gu Y, Zhou X, Hu F, Yu Y, Xie T, Huang Y, Zhao X, Zhang X. Differential DNA methylome profiling of nonfunctioning pituitary adenomas suggesting tumour invasion is correlated with cell adhesion. J Neurooncol 2016; 129:23-31. [DOI: 10.1007/s11060-016-2139-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
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15
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Morabito F, Cutrona G, Mosca L, D'Anca M, Matis S, Gentile M, Vigna E, Colombo M, Recchia AG, Bossio S, De Stefano L, Maura F, Manzoni M, Ilariucci F, Consoli U, Vincelli I, Musolino C, Cortelezzi A, Molica S, Ferrarini M, Neri A. Surrogate molecular markers for IGHV mutational status in chronic lymphocytic leukemia for predicting time to first treatment. Leuk Res 2015; 39:840-5. [PMID: 26038121 DOI: 10.1016/j.leukres.2015.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
Abstract
ZAP-70 is a marker of clinical outcome in chronic lymphocytic leukemia (CLL), however its assessment suffers from a lack of standardization consensus. To identify novel markers able to surrogate IGHV mutational status, CD19(+)CD5(+)-B-lymphocytes from 216 patients enrolled in a prospective study (ClinicalTrial.gov Identifier:NCT00917540), underwent gene expression profiling. Samples were split into CLL-Training (n=102) and CLL-Validation (n=114) sets, and an independent supervised analysis for IGHV mutational status was performed considering all genes with gene expression equal or above that of ZAP-70. Thirty-one genes (23 up- and 8 down-regulated) and 23 genes (18 up- and 5 down-regulated) satisfied these criteria in the CLL-Training and CLL-Validation sets, respectively, and 20 common genes (15 up and 5 down) were found to be differentially regulated in both sets. Two (SNORA70F, NRIP1) of the down-regulated and 6 (SEPT10, ZNF667, TGFBR3, MBOAT1, LPL, CRY1) of the up-regulated genes were significantly associated with a reduced risk of disease progression in both sets. Forcing the afore-mentioned genes in a Cox multivariate model together with IGHV mutational status, only CRY1 (HR=2.3, 95% CI: 1.1-4.9, P=.027) and MBOAT1 (HR=2.1, 95% CI: 1.1-3.7, P=.018) retained their independent prognostic impact, supporting the hypothesis that these genes may potentially act as surrogates for predicting IGHV mutational status.
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Affiliation(s)
- Fortunato Morabito
- Hematology Unit, AO, Cosenza, Italy; Biotecnology Research Unit, Aprigliano, Cosenza, Italy.
| | - Giovanna Cutrona
- SS di Diagnostica Molecolare IRCCS S. Martino-IST, Genova, Italy
| | - Laura Mosca
- Department of Clinical and Community Science, University of Milan, Milano, Italy
| | - Marianna D'Anca
- Department of Clinical and Community Science, University of Milan, Milano, Italy
| | - Serena Matis
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | | | | | - Monica Colombo
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | | | | | | | - Francesco Maura
- Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | - Martina Manzoni
- Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | | | - Ugo Consoli
- Hematology-Oncology Unit, Garibaldi-Nesima Hospital, Catania, Italy
| | | | | | - Agostino Cortelezzi
- Department of Clinical and Community Science, University of Milan, Milano, Italy; Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | | | - Manlio Ferrarini
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | - Antonino Neri
- Department of Clinical and Community Science, University of Milan, Milano, Italy; Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
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16
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Shortt K, Chaudhary S, Grigoryev D, Heruth DP, Venkitachalam L, Zhang LQ, Ye SQ. Identification of novel single nucleotide polymorphisms associated with acute respiratory distress syndrome by exome-seq. PLoS One 2014; 9:e111953. [PMID: 25372662 PMCID: PMC4221189 DOI: 10.1371/journal.pone.0111953] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/29/2014] [Indexed: 12/26/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a lung condition characterized by impaired gas exchange with systemic release of inflammatory mediators, causing pulmonary inflammation, vascular leak and hypoxemia. Existing biomarkers have limited effectiveness as diagnostic and therapeutic targets. To identify disease-associating variants in ARDS patients, whole-exome sequencing was performed on 96 ARDS patients, detecting 1,382,399 SNPs. By comparing these exome data to those of the 1000 Genomes Project, we identified a number of single nucleotide polymorphisms (SNP) which are potentially associated with ARDS. 50,190SNPs were found in all case subgroups and controls, of which89 SNPs were associated with susceptibility. We validated three SNPs (rs78142040, rs9605146 and rs3848719) in additional ARDS patients to substantiate their associations with susceptibility, severity and outcome of ARDS. rs78142040 (C>T) occurs within a histone mark (intron 6) of the Arylsulfatase D gene. rs9605146 (G>A) causes a deleterious coding change (proline to leucine) in the XK, Kell blood group complex subunit-related family, member 3 gene. rs3848719 (G>A) is a synonymous SNP in the Zinc-Finger/Leucine-Zipper Co-Transducer NIF1 gene. rs78142040, rs9605146, and rs3848719 are associated significantly with susceptibility to ARDS. rs3848719 is associated with APACHE II score quartile. rs78142040 is associated with 60-day mortality in the overall ARDS patient population. Exome-seq is a powerful tool to identify potential new biomarkers for ARDS. We selectively validated three SNPs which have not been previously associated with ARDS and represent potential new genetic biomarkers for ARDS. Additional validation in larger patient populations and further exploration of underlying molecular mechanisms are warranted.
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Affiliation(s)
- Katherine Shortt
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Suman Chaudhary
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Dmitry Grigoryev
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Daniel P. Heruth
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Lakshmi Venkitachalam
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Li Q. Zhang
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Shui Q. Ye
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- * E-mail:
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17
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Porpaczy E, Tauber S, Bilban M, Kostner G, Gruber M, Eder S, Heintel D, Le T, Fleiss K, Skrabs C, Shehata M, Jäger U, Vanura K. Lipoprotein lipase in chronic lymphocytic leukaemia - strong biomarker with lack of functional significance. Leuk Res 2013; 37:631-6. [PMID: 23478142 DOI: 10.1016/j.leukres.2013.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/05/2013] [Accepted: 02/09/2013] [Indexed: 12/31/2022]
Abstract
In chronic lymphocytic leukaemia (CLL), lipoprotein lipase (LPL) mRNA overexpression is an established poor prognostic marker, its function, however, is poorly understood. Measuring extracellular LPL enzymatic activity and protein, we found no difference between levels in CLL patients and those of controls, both before and after heparin treatment in vivo and in vitro. Investigating LPL knock down effects, we determined five potential downstream targets, of which one gene, STXBP3, reportedly is involved in fatty acid metabolism. While possibly reflecting an epigenetic switch towards an incorrect transcriptional program, LPL overexpression by itself does not appear to significantly influence CLL cell survival.
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Affiliation(s)
- Edit Porpaczy
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Austria
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