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Dalton SE, Workalemahu T, Allshouse AA, Page JM, Reddy UM, Saade GR, Pinar H, Goldenberg RL, Dudley DJ, Silver RM. Copy number variants and fetal growth in stillbirths. Am J Obstet Gynecol 2023; 228:579.e1-579.e11. [PMID: 36356697 PMCID: PMC10149588 DOI: 10.1016/j.ajog.2022.11.1274] [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: 04/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Fetal growth abnormalities are associated with a higher incidence of stillbirth, with small and large for gestational age infants incurring a 3 to 4- and 2 to 3-fold increased risk, respectively. Although clinical risk factors such as diabetes, hypertension, and placental insufficiency have been associated with fetal growth aberrations and stillbirth, the role of underlying genetic etiologies remains uncertain. OBJECTIVE This study aimed to assess the relationship between abnormal copy number variants and fetal growth abnormalities in stillbirths using chromosomal microarray. STUDY DESIGN A secondary analysis utilizing a cohort study design of stillbirths from the Stillbirth Collaborative Research Network was performed. Exposure was defined as abnormal copy number variants including aneuploidies, pathogenic copy number variants, and variants of unknown clinical significance. The outcomes were small for gestational age and large for gestational age stillbirths, defined as a birthweight <10th percentile and greater than the 90th percentile for gestational age, respectively. RESULTS Among 393 stillbirths with chromosomal microarray and birthweight data, 16% had abnormal copy number variants. The small for gestational age outcome was more common among those with abnormal copy number variants than those with a normal microarray (29.5% vs 16.5%; P=.038). This finding was consistent after adjusting for clinically important variables. In the final model, only abnormal copy number variants and maternal age remained significantly associated with small for gestational age stillbirths, with an adjusted odds ratio of 2.22 (95% confidence interval, 1.12-4.18). Although large for gestational age stillbirths were more likely to have an abnormal microarray: 6.2% vs 3.3% (P=.275), with an odds ratio of 2.35 (95% confidence interval, 0.70-7.90), this finding did not reach statistical significance. CONCLUSION Genetic abnormalities are more common in the setting of small for gestational age stillborn fetuses. Abnormal copy number variants not detectable by traditional karyotype make up approximately 50% of the genetic abnormalities in this population.
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Affiliation(s)
- Susan E Dalton
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT
| | | | | | | | | | - George R Saade
- University of Texas Medical Branch at Galveston, Galveston, TX
| | - Halit Pinar
- Brown University School of Medicine, Providence, RI
| | | | | | - Robert M Silver
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT.
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2
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Using Single-Cell RNA Sequencing and MicroRNA Targeting Data to Improve Colorectal Cancer Survival Prediction. Cells 2023; 12:cells12020228. [PMID: 36672162 PMCID: PMC9856396 DOI: 10.3390/cells12020228] [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: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer has proven to be difficult to treat as it is the second leading cause of cancer death for both men and women worldwide. Recent work has shown the importance of microRNA (miRNA) in the progression and metastasis of colorectal cancer. Here, we develop a metric based on miRNA-gene target interactions, previously validated to be associated with colorectal cancer. We use this metric with a regularized Cox model to produce a small set of top-performing genes related to colon cancer. We show that using the miRNA metric and a Cox model led to a meaningful improvement in colon cancer survival prediction and correct patient risk stratification. We show that our approach outperforms existing methods and that the top genes identified by our process are implicated in NOTCH3 signaling and general metabolism pathways, which are essential to colon cancer progression.
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3
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Kerstholt M, van de Schoor FR, Oosting M, Moorlag SJCFM, Li Y, Jaeger M, van der Heijden WA, Tunjungputri RN, dos Santos JC, Kischkel B, Vrijmoeth HD, Baarsma ME, Kullberg BJ, Lupse M, Hovius JW, van den Wijngaard CC, Netea MG, de Mast Q, Joosten LAB. Identifying platelet-derived factors as amplifiers of B. burgdorferi-induced cytokine production. Clin Exp Immunol 2022; 210:53-67. [PMID: 36001729 PMCID: PMC9585555 DOI: 10.1093/cei/uxac073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 01/25/2023] Open
Abstract
Previous studies have shown that monocytes can be 'trained' or tolerized by certain stimuli to respond stronger or weaker to a secondary stimulation. Rewiring of glucose metabolism was found to be important in inducing this phenotype. As we previously found that Borrelia burgdorferi (B. burgdorferi), the causative agent of Lyme borreliosis (LB), alters glucose metabolism in monocytes, we hypothesized that this may also induce long-term changes in innate immune responses. We found that exposure to B. burgdorferi decreased cytokine production in response to the TLR4-ligand lipopolysaccharide (LPS). In addition, B. burgdorferi exposure decreased baseline levels of glycolysis, as assessed by lactate production. Using GWAS analysis, we identified a gene, microfibril-associated protein 3-like (MFAP3L) as a factor influencing lactate production after B. burgdorferi exposure. Validation experiments proved that MFAP3L affects lactate- and cytokine production following B. burgdorferi stimulation. This is mediated by functions of MFAP3L, which includes activating ERK2 and through activation of platelet degranulation. Moreover, we showed that platelets and platelet-derived factors play important roles in B. burgdorferi-induced cytokine production. Certain platelet-derived factors, such chemokine C-X-C motif ligand 7 (CXCL7) and (C-C motif) ligand 5 (CCL5), were elevated in the circulation of LB patients in comparison to healthy individuals.
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Affiliation(s)
| | | | - Marije Oosting
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) and TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Martin Jaeger
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wouter A van der Heijden
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rahajeng N Tunjungputri
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands,Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Jéssica C dos Santos
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brenda Kischkel
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hedwig D Vrijmoeth
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - M E Baarsma
- Amsterdam Institute of Infection and Immunology, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Bart-Jan Kullberg
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihaela Lupse
- Department of Infectious Diseases, University of Medicine and Pharmacy ‘Iuliu Hatieganu’, Cluj-Napoca, Romania
| | - Joppe W Hovius
- Amsterdam Institute of Infection and Immunology, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cees C van den Wijngaard
- National Institute for Public Health and the Environment (RIVM), Center of Infectious Disease Control, Bilthoven, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands,Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Germany
| | - Quirijn de Mast
- Department of Internal Medicine and Radboudumc Center for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Correspondence: Leo A.B. Joosten, Lab Experimentele geneeskunde, Radboudumc, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, The Netherlands. E-mail:
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Mohammadi A, Sorensen GL, Pilecki B. MFAP4-Mediated Effects in Elastic Fiber Homeostasis, Integrin Signaling and Cancer, and Its Role in Teleost Fish. Cells 2022; 11:cells11132115. [PMID: 35805199 PMCID: PMC9265350 DOI: 10.3390/cells11132115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix (ECM) protein belonging to the fibrinogen-related domain superfamily. MFAP4 is highly expressed in elastin-rich tissues such as lung, blood vessels and skin. MFAP4 is involved in organization of the ECM, regulating proper elastic fiber assembly. On the other hand, during pathology MFAP4 actively contributes to disease development and progression due to its interactions with RGD-dependent integrin receptors. Both tissue expression and circulating MFAP4 levels are associated with various disorders, including liver fibrosis and cancer. In other experimental models, such as teleost fish, MFAP4 appears to participate in host defense as a macrophage-specific innate immune molecule. The aim of this review is to summarize the accumulating evidence that indicates the importance of MFAP4 in homeostasis as well as pathological conditions, discuss its known biological functions with special focus on elastic fiber assembly, integrin signaling and cancer, as well as describe the reported functions of non-mammalian MFAP4 in fish. Overall, our work provides a comprehensive overview on the role of MFAP4 in health and disease.
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Bai J, Zhu X, Zhang J, Bulin B. Screening key prognostic factors and constructing survival prognostic risk prediction model based on ceRNA network in early lung adenocarcinoma. Transl Cancer Res 2022; 10:4652-4663. [PMID: 35116321 PMCID: PMC8797449 DOI: 10.21037/tcr-20-3273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/14/2021] [Indexed: 12/25/2022]
Abstract
Background We aim to discover some prognostic factors, provide a basis for discovering molecular markers, and provide a basis for molecular features of early lung adenocarcinoma (LUAD) to predict patient prognosis. Methods Sequence data of LUAD were downloaded from The Cancer Genome Atlas (TCGA) database to screen out differentially expressed lncRNAs, miRNAs, and mRNAs (DERs). DERs were identified using R software’s limma package. The competitive endogenous RNA (ceRNA) network was constructed based on these RNAs. Univariate and multivariate Cox regression analysis on the RNAs in the ceRNA screened out independent prognostic-related RNAs to construct a prognostic risk score (PS) model. Combined with clinical data, we can calculate the survival rate of patients with early LUAD. Results There were 2,701 differentially expressed mRNAs (DEmRNAs), 47 differentially expressed lncRNAs (DElncRNAs), and 161 differentially expressed miRNAs (DEmiRNAs) identified in early LUAD. Based on these RNAs, 32 lncRNAs, 87 miRNAs, and 174 mRNAs participated in the ceRNA network. Twelve independently prognostic-related RNAs form an optimized combination. We developed a PS model based on these RNAs. Age, tumor recurrence and PS model status were independent survival prognostic clinical factors. Nomogram was established to predict the 3-year and 5-year survival rates. Conclusions We successfully constructed a ceRNA regulatory network based on the DERs in early LUAD. It can help us clarify the molecular mechanism of early LUAD. Simultaneously, the prognostic-related RNAs in early LUAD were also screened out. This network could provide new bases for diagnoses and prognoses of patients with LUAD.
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Affiliation(s)
- Juncheng Bai
- Department of Pathology, Affiliated Hospital of Inner Mongolia University for Nationalities, Tongliao, China
| | - Xiaochun Zhu
- Department of Pathology, Affiliated Hospital of Inner Mongolia University for Nationalities, Tongliao, China
| | - Jintao Zhang
- Department of Pathology, Affiliated Hospital of Inner Mongolia University for Nationalities, Tongliao, China
| | - Baila Bulin
- Drug Lab, Inner Mongolia International Mongolian Medicine Hospital, Hohhot, China
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6
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Ye J, Luo W, Luo L, Zhai L, Huang P. MicroRNA‑671‑5p inhibits cell proliferation, migration and invasion in non‑small cell lung cancer by targeting MFAP3L. Mol Med Rep 2022; 25:30. [PMID: 34841435 PMCID: PMC8669681 DOI: 10.3892/mmr.2021.12546] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNA (miR)‑671‑5p serves as a tumor suppressor in several types of cancer, including gastric and breast cancer. However, the function of miR‑671‑5p in non‑small cell lung cancer (NSCLC) has not been described in detail. The present study aimed to investigate the role of miR‑671‑5p in NSCLC. The expression levels of miR‑671‑5p were determined in NSCLC tissue samples and cell lines using reverse transcription‑quantitative PCR. Prediction of miR‑671‑5p targets was performed using the TargetScan database and verified by luciferase reporter assay and western blot analysis. Functional experiments, including Cell Counting Kit‑8, wound healing and Transwell assays, were performed in NSCLC cells. The results of the present study demonstrated that lower expression levels of miR‑671‑5p were observed in NSCLC tissues and cell lines compared with those in the corresponding controls. Low miR‑671‑5p levels were significantly associated with an advanced Tumor‑Node‑Metastasis stage and lymph node metastasis in patients with NSCLC. Microfibril‑associated protein 3‑like (MFAP3L) was confirmed to be a direct target of miR‑671‑5p. The proliferative, migratory and invasive abilities of NSCLC cells were suppressed following transfection with miR‑671‑5p mimics and promoted by the miR‑671‑5p inhibitor compared with those in the respective control groups. In addition, the effects of miR‑671‑5p on cell proliferation, migration and invasion, as well as the expression levels of proliferating cell nuclear antigen, E‑cadherin, N‑cadherin and vimentin were reversed by MFAP3L overexpression. In conclusion, targeting the miR‑671‑5p/MFAP3L signaling pathway may be a promising therapeutic strategy for NSCLC treatment.
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Affiliation(s)
- Junhui Ye
- Department of Respiratory Medicine, The People's Hospital of Sanmen, Taizhou, Zhejiang 317100, P.R. China
| | - Wujun Luo
- Department of Respiratory Medicine, The People's Hospital of Sanmen, Taizhou, Zhejiang 317100, P.R. China
| | - Lingling Luo
- Department of Respiratory Medicine, The People's Hospital of Sanmen, Taizhou, Zhejiang 317100, P.R. China
| | - Limin Zhai
- Department of Respiratory Medicine, The People's Hospital of Sanmen, Taizhou, Zhejiang 317100, P.R. China
| | - Pingping Huang
- Department of Respiratory Medicine, The People's Hospital of Sanmen, Taizhou, Zhejiang 317100, P.R. China
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7
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Powell DR, Revelli JP, Doree DD, DaCosta CM, Desai U, Shadoan MK, Rodriguez L, Mullens M, Yang QM, Ding ZM, Kirkpatrick LL, Vogel P, Zambrowicz B, Sands AT, Platt KA, Hansen GM, Brommage R. High-Throughput Screening of Mouse Gene Knockouts Identifies Established and Novel High Body Fat Phenotypes. Diabetes Metab Syndr Obes 2021; 14:3753-3785. [PMID: 34483672 PMCID: PMC8409770 DOI: 10.2147/dmso.s322083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/04/2021] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Obesity is a major public health problem. Understanding which genes contribute to obesity may better predict individual risk and allow development of new therapies. Because obesity of a mouse gene knockout (KO) line predicts an association of the orthologous human gene with obesity, we reviewed data from the Lexicon Genome5000TM high throughput phenotypic screen (HTS) of mouse gene KOs to identify KO lines with high body fat. MATERIALS AND METHODS KO lines were generated using homologous recombination or gene trapping technologies. HTS body composition analyses were performed on adult wild-type and homozygous KO littermate mice from 3758 druggable mouse genes having a human ortholog. Body composition was measured by either DXA or QMR on chow-fed cohorts from all 3758 KO lines and was measured by QMR on independent high fat diet-fed cohorts from 2488 of these KO lines. Where possible, comparisons were made to HTS data from the International Mouse Phenotyping Consortium (IMPC). RESULTS Body fat data are presented for 75 KO lines. Of 46 KO lines where independent external published and/or IMPC KO lines are reported as obese, 43 had increased body fat. For the remaining 29 novel high body fat KO lines, Ksr2 and G2e3 are supported by data from additional independent KO cohorts, 6 (Asnsd1, Srpk2, Dpp8, Cxxc4, Tenm3 and Kiss1) are supported by data from additional internal cohorts, and the remaining 21 including Tle4, Ak5, Ntm, Tusc3, Ankk1, Mfap3l, Prok2 and Prokr2 were studied with HTS cohorts only. CONCLUSION These data support the finding of high body fat in 43 independent external published and/or IMPC KO lines. A novel obese phenotype was identified in 29 additional KO lines, with 27 still lacking the external confirmation now provided for Ksr2 and G2e3 KO mice. Undoubtedly, many mammalian obesity genes remain to be identified and characterized.
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Affiliation(s)
- David R Powell
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Jean-Pierre Revelli
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Deon D Doree
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Christopher M DaCosta
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Urvi Desai
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Melanie K Shadoan
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Lawrence Rodriguez
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Michael Mullens
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Qi M Yang
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Zhi-Ming Ding
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Laura L Kirkpatrick
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Peter Vogel
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
| | - Brian Zambrowicz
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Arthur T Sands
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
- Department of Information Technology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Kenneth A Platt
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Gwenn M Hansen
- Department of Molecular Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, Tx, USA
| | - Robert Brommage
- Department of Pharmaceutical Biology, Lexicon Pharmaceuticals, Inc, The Woodlands, TX, USA
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8
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Zhu S, Ye L, Bennett S, Xu H, He D, Xu J. Molecular structure and function of microfibrillar-associated proteins in skeletal and metabolic disorders and cancers. J Cell Physiol 2020; 236:41-48. [PMID: 32572962 DOI: 10.1002/jcp.29893] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/16/2022]
Abstract
Microfibrillar-associated proteins (MFAPs) are extracellular matrix glycoproteins, which play a role in microfibril assembly, elastinogenesis, and tissue homeostasis. MFAPs consist of five subfamily members, including MFAP1, MFAP2, MFAP3, MFAP4, and MFAP5. Among these, MFAP2 and MFAP5 are most closely related, and exhibit very limited amino acid sequence homology with MFAP1, MFAP3, and MFAP4. Gene expression profiling analysis reveals that MFAP2, MFAP5, and MFAP4 are specifically expressed in osteoblastic like cells, whereas MFAP1 and MFAP3 are more ubiquitously expressed, indicative of their diverse role in the tropism of tissues. Molecular structural analysis shows that each MFAP family member has distinct features, and functional evidence reveals discrete purposes of individual MFAPs. Animal studies indicate that MFAP2-deficient mice exhibit progressive osteopenia with elevated receptor activator of NF-κB ligand (RANKL) expression, whereas MFAP5-deficient mice are neutropenic, and MFAP4-deficient mice displayed emphysema-like pathology and the impaired formation of neointimal hyperplasia. Emerging data also suggest that MFAPs are involved in cancer progression and fat metabolism. Further understanding of tissue-specific pathophysiology of MFAPs might offer potential novel therapeutic targets for related diseases, such as skeletal and metabolic disorders, and cancers.
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Affiliation(s)
- Sipin Zhu
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Lin Ye
- Department of Orthopaedic Surgery, Lishui Municipal Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, China
| | - Samuel Bennett
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Huazi Xu
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dengwei He
- Department of Orthopaedic Surgery, Lishui Municipal Central Hospital, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, China
| | - Jiake Xu
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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9
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Yang J, Song H, Chen L, Cao K, Zhang Y, Li Y, Hao X. Integrated analysis of microfibrillar-associated proteins reveals MFAP4 as a novel biomarker in human cancers. Epigenomics 2019; 11:1635-1651. [DOI: 10.2217/epi-2018-0080] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: The potential functions and underlying mechanism of microfibrillar-associated proteins (MFAPs) are explored in human cancers. Materials & methods: Here, we examined the expression profiles, prognostic values, epigenetic and genetic alterations of MFAPs in human cancers from public omics repository. Results: Among MFAPs family, MFAP4 was frequently downregulated in the most human cancers and high mRNA expression of MFAP4 significantly correlated with better overall survival in breast cancer. DNA hypermethylation in the promoter of MFAP4 decreased its mRNA expression. MFAP4 strongly associated with pathway in impairment and alteration of the elastic fibers. Conclusion: This integrated analysis provides new insights into MFAPs in human cancers and indicates that MFAP4 could be used as novel biomarker for developing therapies against human cancers.
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Affiliation(s)
- Jue Yang
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
| | - Hui Song
- The Key Laboratory of Endemic & Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang 550004, PR China
- The Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guizhou Province, Guiyang 550004, PR China
| | - Li Chen
- Guiyang University of Chinese Medicine, School of Pharmaceutical Sciences, Guiyang 550025, PR China
| | - Kun Cao
- Department of General Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, PR China
| | - Yongqiang Zhang
- Guizhou University, School of Pharmaceutical Sciences, Guiyang, 550025, PR China
| | - Yanmei Li
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
| | - Xiaojiang Hao
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
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10
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Zhang W, Le TD, Liu L, Zhou ZH, Li J. Mining heterogeneous causal effects for personalized cancer treatment. Bioinformatics 2018; 33:2372-2378. [PMID: 28369195 DOI: 10.1093/bioinformatics/btx174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/20/2017] [Indexed: 01/03/2023] Open
Abstract
Motivation Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses. Results In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients. Availability and Implementation Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree . Contact weijia.zhang@mymail.uinsa.edu.au. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Weijia Zhang
- School of Information Technology and Mathematical Sciences
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences.,Centre for Cancer Biology, University of South Australia, Adelaide 5000, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences
| | - Zhi-Hua Zhou
- National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210023, China
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences
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Zhao H, Yuan H, Hu J, Xu C, Liao G, Yin W, Xu L, Wang L, Zhang X, Shi A, Li J, Xiao Y. Optimizing prognosis-related key miRNA-target interactions responsible for cancer metastasis. Oncotarget 2017; 8:109522-109535. [PMID: 29312626 PMCID: PMC5752539 DOI: 10.18632/oncotarget.22724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence suggests that the abnormality of microRNAs (miRNAs) and their downstream targets is frequently implicated in the pathogenesis of human cancers, however, the clinical benefit of causal miRNA-target interactions has been seldom studied. Here, we proposed a computational method to optimize prognosis-related key miRNA-target interactions by combining transcriptome and clinical data from thousands of TCGA tumors across 16 cancer types. We obtained a total of 1,956 prognosis-related key miRNA-target interactions between 112 miRNAs and 1,443 their targets. Interestingly, these key target genes are specifically involved in tumor progression-related functions, such as ‘cell adhesion’ and ‘cell migration’. Furthermore, they are most significantly correlated with ‘tissue invasion and metastasis’, a hallmark of metastasis, in ten distinct types of cancer through the hallmark analysis. These results implicated that the prognosis-related key miRNA-target interactions were highly associated with cancer metastasis. Finally, we observed that the combination of these key miRNA-target interactions allowed to distinguish patients with good prognosis from those with poor prognosis both in most TCGA cancer types and independent validation sets, highlighting their roles in cancer metastasis. We provided a user-friendly database named miRNATarget (freely available at http://biocc.hrbmu.edu.cn/miRNATar/), which provides an overview of the prognosis-related key miRNA-target interactions across 16 cancer types.
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Affiliation(s)
- Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Wenkang Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Aiai Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Li
- Department of Ultrasonic Medicine, The 1st Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Chen X, Guo D, Zhu Y, Xian F, Liu S, Wu L, Lou X. Nuclear phosphoproteomics analysis reveals that CDK1/2 are involved in EGF-regulated constitutive pre-mRNA splicing in MDA-MB-468 cells. J Proteomics 2016; 141:77-84. [PMID: 27109354 DOI: 10.1016/j.jprot.2016.04.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 04/06/2016] [Accepted: 04/19/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED The epidermal growth factor (EGF) receptor (EGFR) pathway is one of the most dysregulated and extensively investigated signaling pathways in human cancers and plays important roles in the regulation of nuclear functions through both cytoplasmic and nuclear EGFR pathways. However, the current understanding of the nuclear phosphorylation responses to activated EGFR pathways remains limited. In the present study, phosphoproteomics analysis revealed the increased phosphorylation of 90 nuclear proteins, primarily involved in RNA processing, pre-mRNA splicing and cell cycle regulation, upon EGF stimulation in MDA-MB-468 cells. Cellular splicing assays of the β-globin (HBB) minigene confirmed that EGF induced constitutive pre-mRNA splicing. Further analysis of phosphoproteomics data identified multiple CDK1/2 substrates in pre-mRNA splicing-related proteins, and both CDK1/2 inhibitors and CDK1/2 knockdowns reduced EGF-regulated pre-mRNA splicing. In conclusion, the results of the present study provide evidence that CDK1/2 participate in the regulation of constitutive pre-mRNA splicing by EGF stimulation in MDA-MB-468 cells. SIGNIFICANCE In this study, we successfully carried out a survey of nuclear phosphorylation changes in response to EGF stimulation. The results from the functional category analysis and pre-mRNA splicing assay strongly indicated that EGFR activation increased constitutive pre-mRNA splicing in MDA-MB-468 cells, revealing additional role of EGFR on regulation of mRNA maturation beyond alternative pre-mRNA splicing reported by previous studies. Furthermore, we found that CDK1/2 participated in constitutive pre-mRNA splicing regulation by EGF in MDA-MB-468 cells. Our study provides new knowledge for understanding the regulation of constitutive pre-mRNA splicing by EGF stimulation.
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Affiliation(s)
- Xianwei Chen
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Dan Guo
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yinghui Zhu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Feng Xian
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lin Wu
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhang W, He J, Du Y, Gao XH, Liu Y, Liu QZ, Chang WJ, Cao GW, Fu CG. Upregulation of nemo-like kinase is an independent prognostic factor in colorectal cancer. World J Gastroenterol 2015; 21:8836-8847. [PMID: 26269673 PMCID: PMC4528026 DOI: 10.3748/wjg.v21.i29.8836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/14/2015] [Accepted: 03/27/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression and oncogenic role of nemo-like kinase (NLK) in colorectal cancer.
METHODS: Expression of NLK protein was assessed by immunohistochemistry in tissue specimens from 56 cases of normal colorectal mucosa, 51 cases of colorectal adenoma, and 712 cases of colorectal cancer. In addition, NLK expression was knocked down using a lentivirus carrying NLK small hairpin RNA in colorectal cancer cells. Cell viability methylthiazoletetrazolium assays, colony formation assays, flow cytometry cell cycle assays, Transwell migration assays, and gene expression assays were performed to explore its role on proliferation and migration of colorectal cancer.
RESULTS: Expression of NLK protein progressively increased in tissues from the normal mucosa through adenoma to various stages of colorectal cancer. Overexpression of NLK protein was associated with advanced tumor-lymph node-metastasis stages, poor differentiation, lymph node and distant metastases, and a higher recurrence rate of colorectal cancer (P < 0.05). Multivariate analyses showed that NLK expression was an independent prognostic factor to predict overall survival (hazard ratio 2.57, 95% confidence interval: 1.66-3.98; P < 0.001) and disease-free survival (hazard ratio 1.96, 95% confidence interval: 1.40-2.74: P < 0.001) of colorectal cancer patients. Furthermore, knockdown of NLK expression in colorectal cancer cell lines reduced cell viability, colony formation, and migration, and arrested tumor cells at the G0/G1 phase of the cell cycle. At the gene level, knockdown of NLK expression inhibited matrix metalloproteinase-2 expression in colorectal cancer cells.
CONCLUSION: NLK overexpression is an independent prognostic factor in colorectal cancer and knockdown of NLK expression inhibits colorectal cancer progression and metastasis.
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Mecham RP, Gibson MA. The microfibril-associated glycoproteins (MAGPs) and the microfibrillar niche. Matrix Biol 2015; 47:13-33. [PMID: 25963142 DOI: 10.1016/j.matbio.2015.05.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
The microfibril-associated glycoproteins MAGP-1 and MAGP-2 are extracellular matrix proteins that interact with fibrillin to influence microfibril function. The two proteins are related through a 60 amino acid matrix-binding domain but their sequences differ outside of this region. A distinguishing feature of both proteins is their ability to interact with TGFβ family growth factors, Notch and Notch ligands, and multiple elastic fiber proteins. MAGP-2 can also interact with αvβ3 integrins via a RGD sequence that is not found in MAGP-1. Morpholino knockdown of MAGP-1 expression in zebrafish resulted in abnormal vessel wall architecture and altered vascular network formation. In the mouse, MAGP-1 deficiency had little effect on elastic fibers in blood vessels and lung but resulted in numerous unexpected phenotypes including bone abnormalities, hematopoietic changes, increased fat deposition, diabetes, impaired wound repair, and a bleeding diathesis. Inactivation of the gene for MAGP-2 in mice produced a neutropenia yet had minimal effects on bone or adipose homeostasis. Double knockouts had phenotypes characteristic of each individual knockout as well as several additional traits only seen when both genes are inactivated. A common mechanism underlying all of the traits associated with the knockout phenotypes is altered TGFβ signaling. This review summarizes our current understanding of the function of the MAGPs and discusses ideas related to their role in growth factor regulation.
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Affiliation(s)
- Robert P Mecham
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Mark A Gibson
- School of Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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