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Gossmann A, Cao S, Brzyski D, Zhao LJ, Deng HW, Wang YP. A Sparse Regression Method for Group-Wise Feature Selection with False Discovery Rate Control. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1066-1078. [PMID: 29990279 PMCID: PMC6326365 DOI: 10.1109/tcbb.2017.2780106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The method of Sorted L-One Penalized Estimation, or SLOPE, is a sparse regression method recently introduced by Bogdan et. al. [1] . It can be used to identify significant predictor variables in a linear model that may have more unknown parameters than observations. When the correlations between predictor variables are small, the SLOPE method is shown to successfully control the false discovery rate (the expected proportion of the irrelevant among all selected predictors) at a user specified level. However, the requirement for nearly uncorrelated predictors is too restrictive for genomic data, as demonstrated in our recent study [2] by an application of SLOPE to realistic simulated DNA sequence data. A possible solution is to divide the predictor variables into nearly uncorrelated groups, and to modify the procedure to select entire groups with an overall significant group effect, rather than individual predictors. Following this motivation, we extend SLOPE in the spirit of Group LASSO to Group SLOPE, a method that can handle group structures between the predictor variables, which are ubiquitous in real genomic data. Our theoretical results show that Group SLOPE controls the group-wise false discovery rate (gFDR), when groups are orthogonal to each other. For use in non-orthogonal settings, we propose two types of Monte Carlo based heuristics, which lead to gFDR control with Group SLOPE in simulations based on real SNP data. As an illustration of the merits of this method, an application of Group SLOPE to a dataset from the Framingham Heart Study results in the identification of some known DNA sequence regions associated with bone health, as well as some new candidate regions. The novel methods are implemented in the R package grpSLOPEMC , which is publicly available at https://github.com/agisga/grpSLOPEMC.
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Conditional deletion of CD98hc inhibits osteoclast development. Biochem Biophys Rep 2015; 5:203-210. [PMID: 28955825 PMCID: PMC5600448 DOI: 10.1016/j.bbrep.2015.11.023] [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: 03/31/2015] [Revised: 10/31/2015] [Accepted: 11/30/2015] [Indexed: 11/22/2022] Open
Abstract
The CD98 heavy chain (CD98hc) regulates virus-induced cell fusion and monocyte fusion, and is involved in amino acid transportation. Here, we examined the role that CD98hc plays in the formation of osteoclasts using CD98hcflox/floxLysM-cre peritoneal macrophages (CD98hc-defect macrophages). Peritoneal macrophages were stimulated with co-cultured with osteoblasts in the presence of 1,25(OH)2 vitamin D3, and thereafter stained with tartrate-resistant acid phosphatase staining solution. The multinucleated osteoclast formation was severely impaired in the peritoneal macrophages isolated from the CD98hc-defect mice compared with those from wild-type mice. CD98hc mediates integrin signaling and amino acid transport through the CD98 light chain (CD98lc). In integrin signaling, suppression of the M-CSF-RANKL-induced phosphorylation of ERK, Akt, JNK and p130Cas were observed at the triggering phase in the CD98h-defect peritoneal macrophages. Moreover, we showed that the general control non-derepressible (GCN) pathway, which was activated by amino acid starvation, was induced by the CD98hc-defect peritoneal macrophages stimulated with RANKL. These results indicate that CD98 plays two important roles in osteoclast formation through integrin signaling and amino acid transport. The osteoclastogenesis was severely impaired in the CD98hc-defect macrophages. CD98hc-defect peritoneal macrophages fall into amino acid starvation, resulting in inducing the general control non-derepressible (GCN) pathway in the osteoclastogenesis.
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Carneiro BA, Altman JK, Kaplan JB, Ossenkoppele G, Swords R, Platanias LC, Giles FJ. Targeted therapy of acute myeloid leukemia. Expert Rev Anticancer Ther 2015; 15:399-413. [PMID: 25623136 DOI: 10.1586/14737140.2015.1004316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in the understanding of the genetic underpinnings of acute myeloid leukemia are rapidly being translated into novel treatment strategies. Genomic profiling has highlighted the importance of the epigenetic machinery for leukemogenesis by identifying recurrent somatic mutations involving chromatin-modifier proteins. These genetic alterations function as dynamic regulators of gene expression and involve DNA-methyltransferase 3A, methyltransferase DOT1L, enhancer of zeste homologue 2, isocitrate dehydrogenases 1 and 2 and bromodomain-containing proteins. New therapeutic targets are also emerging from further delineation of cell signaling networks in acute myeloid leukemia blasts mediated by PIM kinases, polo-like kinase 1, cell surface protein CD98 and nucleocytoplasmic shuttling receptors, among others. Early results of targeted therapies directed at these molecular mechanisms are discussed in this review and their potential to improve the outcomes of patients by allowing the use of more effective and less toxic treatments.
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Affiliation(s)
- Benedito A Carneiro
- Northwestern Developmental Therapeutics Institute, Northwestern University Feinberg School of Medicine, 645 N Michigan Ave. Suite 1006, Chicago, IL 60611, USA
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Inder KL, Ruelcke JE, Petelin L, Moon H, Choi E, Rae J, Blumenthal A, Hutmacher D, Saunders NA, Stow JL, Parton RG, Hill MM. Cavin-1/PTRF alters prostate cancer cell-derived extracellular vesicle content and internalization to attenuate extracellular vesicle-mediated osteoclastogenesis and osteoblast proliferation. J Extracell Vesicles 2014; 3:23784. [PMID: 25018864 PMCID: PMC4072912 DOI: 10.3402/jev.v3.23784] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/22/2014] [Accepted: 05/26/2014] [Indexed: 12/15/2022] Open
Abstract
Background Tumour-derived extracellular vesicles (EVs) play a role in tumour progression; however, the spectrum of molecular mechanisms regulating EV secretion and cargo selection remain to be fully elucidated. We have reported that cavin-1 expression in prostate cancer PC3 cells reduced the abundance of a subset of EV proteins, concomitant with reduced xenograft tumour growth and metastasis. Methods We examined the functional outcomes and mechanisms of cavin-1 expression on PC3-derived EVs (PC3-EVs). Results PC3-EVs were internalized by osteoclast precursor RAW264.7 cells and primary human osteoblasts (hOBs) in vitro, stimulating osteoclastogenesis 37-fold and hOB proliferation 1.5-fold, respectively. Strikin
gly, EVs derived from cavin-1-expressing PC3 cells (cavin-1-PC3-EVs) failed to induce multinucleate osteoblasts or hOB proliferation. Cavin-1 was not detected in EVs, indicating an indirect mechanism of action. EV morphology, size and quantity were also not affected by cavin-1 expression, suggesting that cavin-1 modulated EV cargo recruitment rather than release. While cavin-1-EVs had no osteoclastogenic function, they were internalized by RAW264.7 cells but at a reduced efficiency compared to control EVs. EV surface proteins are required for internalization of PC3-EVs by RAW264.7 cells, as proteinase K treatment abolished uptake of both control and cavin-1-PC3-EVs. Removal of sialic acid modifications by neuraminidase treatment increased the amount of control PC3-EVs internalized by RAW264.7 cells, without affecting cavin-1-PC3-EVs. This suggests that cavin-1 expression altered the glycosylation modifications on PC3-EV surface. Finally, cavin-1 expression did not affect EV in vivo tissue targeting as both control and cavin-1-PC3-EVs were predominantly retained in the lung and bone 24 hours after injection into mice. Discussion Taken together, our results reveal a novel pathway for EV cargo sorting, and highlight the potential of utilizing cavin-1-mediated pathways to attenuate metastatic prostate cancer.
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Affiliation(s)
- Kerry L Inder
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Jayde E Ruelcke
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Lara Petelin
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Hyeongsun Moon
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Eunju Choi
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - James Rae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia ; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Dietmar Hutmacher
- Institute for Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Nicholas A Saunders
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia ; Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
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Cantor JM, Ginsberg MH. CD98 at the crossroads of adaptive immunity and cancer. J Cell Sci 2012; 125:1373-82. [PMID: 22499670 DOI: 10.1242/jcs.096040] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adaptive immunity, a vertebrate specialization, adds memory and exquisite specificity to the basic innate immune responses present in invertebrates while conserving metabolic resources. In adaptive immunity, antigenic challenge requires extremely rapid proliferation of rare antigen-specific lymphocytes to produce large, clonally expanded effector populations that neutralize pathogens. Rapid proliferation and resulting clonal expansion are dependent on CD98, a protein whose well-conserved orthologs appear restricted to vertebrates. Thus, CD98 supports lymphocyte clonal expansion to enable protective adaptive immunity, an advantage that could account for the presence of CD98 in vertebrates. CD98 supports lymphocyte clonal expansion by amplifying integrin signals that enable proliferation and prevent apoptosis. These integrin-dependent signals can also provoke cancer development and invasion, anchorage-independence and the rapid proliferation of tumor cells. CD98 is highly expressed in many cancers and contributes to formation of tumors in experimental models. Strikingly, vertebrates, which possess highly conserved CD98 proteins, CD98-binding integrins and adaptive immunity, also display propensity towards invasive and metastatic tumors. In this Commentary, we review the roles of CD98 in lymphocyte biology and cancer. We suggest that the CD98 amplification of integrin signaling in adaptive immunity provides survival benefits to vertebrates, which, in turn, bear the price of increased susceptibility to cancer.
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Affiliation(s)
- Joseph M Cantor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Yuasa K, Avnet S, Salerno M, Mori K, Ishikawa H, Sudo A, Baldini N, Uchida A, Ito Y. Spontaneous formation of multinucleated giant cells with bone resorbing activity by long culture of human peripheral blood CD14-positive monocytes in vitro. CELL COMMUNICATION & ADHESION 2010; 17:13-22. [PMID: 20298143 DOI: 10.3109/15419061003678810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Several reports indicate that multinucleated giant cells that derived from human peripheral blood CD14-positive monocytes have osteoclastic properties, and although the mechanism is not completely understood, the authors have previously demonstrated that spontaneous osteoclastogenesis from monocytes can occur. Here, the authors investigated the effect of detachment and long-term cultures in this process. When monocytes were incubated for 2 weeks, spontaneous formation of polykaryocytes was rarely observed. In addition, when monocytes precultured for 2 weeks were detached by a cell scraper and further subcultured, almost all cells died. Surprisingly, when monocytes were incubated for 8 weeks without any pro-osteoclastogenic factors and without detachment, the authors observed the spontaneous formation of tartrate-resistant acid phosphatase (TRAP)-positive polykaryocytes that were able of lacunae resorption. These findings indicate that cell adhesion is a prerequisite for differentiation and survival of CD14-positive monocytes, and that a long incubation period spontaneously induces multinucleation and bone-resorbing activity of monocytes, even in the absence of osteoclastogenesis-stimulating factors.
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Affiliation(s)
- Kimitaka Yuasa
- Department of Orthopaedic Surgery, Mie University Graduate School of Medicine, Tsu City, Mie Prefecture, Japan.
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Helming L, Gordon S. The molecular basis of macrophage fusion. Immunobiology 2007; 212:785-93. [PMID: 18086379 DOI: 10.1016/j.imbio.2007.09.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 09/28/2007] [Indexed: 10/22/2022]
Abstract
Multinucleated giant cells (MGCs), characteristic of granulomatous infections as well as multinucleated osteoclasts originate from fusion of macrophages. While intracellular and viral membrane fusion have been studied in detail, much less is known about the machinery which mediates cell-to-cell fusion, in particular macrophage polykaryon formation. Several molecules have been implicated in this process which may involve the action of multiple glycoproteins mediating membrane attachment and fusion. Macrophage fusion can be induced by soluble mediators such as cytokines and growth factors, even though several other stimuli may be involved, especially for the induction of granuloma-associated giant cells. The function of MGCs during granulomatous diseases is currently unknown. However, a better understanding of the mechanistic basis of macrophage fusion may lead to a better understanding of the function of MGCs found in granulomas.
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Affiliation(s)
- Laura Helming
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Yuasa K, Mori K, Ishikawa H, Sudo A, Uchida A, Ito Y. Characterization of two types of osteoclasts from human peripheral blood monocytes. Biochem Biophys Res Commun 2007; 356:354-60. [PMID: 17368425 DOI: 10.1016/j.bbrc.2007.02.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
The two osteoclastogenesis pathways, receptor activator nuclear factor (NF)-kappaB ligand (RANKL)-mediated and fusion regulatory protein-1 (FRP-1)-mediated osteoclastogenesis, have recently been reported. There were significant differences in differentiation and activation mechanisms between the two pathways. When monocytes were cultured with FRP-1 without adding M-CSF, essential for the RANKL system, TRAP-positive polykaryocyte formation occurred. FRP-1-mediated osteoclasts formed larger pits on mineralized calcium phosphate plates than RANKL+M-CSF-mediated osteoclasts did. Lacunae on dentin surfaces induced by FRP-1-mediated osteoclasts were inclined to be single and isolated. However, osteoclasts induced by RANKL+M-CSF made many connected pits on dentin surfaces as if they crawled on there. Interestingly, FRP-1 osteoclastogenesis was enhanced by M-CSF/IL-1alpha, while chemotactic behavior to the dentin slices was not effected. There were differences in pH and concentration of HCO3- at culture endpoint and in adherent feature to dentin surfaces. Our findings indicate there are two types of osteoclasts with distinct properties.
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Affiliation(s)
- Kimitaka Yuasa
- Department of Microbiology, Mie University Graduate School of Medicine, Japan.
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Lee L, Liu J, Manuel J, Gorczynski RM. A role for the immunomodulatory molecules CD200 and CD200R in regulating bone formation. Immunol Lett 2006; 105:150-8. [PMID: 16530849 DOI: 10.1016/j.imlet.2006.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 12/12/2005] [Accepted: 02/06/2006] [Indexed: 01/07/2023]
Abstract
Altered osteoprotogerin (OPG) and OPG ligand (RANKL) ratios are known to regulate bone metabolism. We investigated whether CD200:CD200R interaction would alter OPG:RANKL ratios, and thus modulate bone differentiation in cultures derived from neonatal calvariae, a source of osteoblast precursors (OBp), or bone marrow-derived myeloid cells as a source of osteoclast precursors (OCp). We characterized cells in cultures using real-time PCR to measure expression of a number of mRNAs characteristic of cells differentiating towards the osteoblast or osteoclast lineage, and enumerated bone nodule formation and osteoclasts directly. CD200Fc or anti-CD200 mAbs were included as modulating agents. In addition, calvariae from transgenic mice overexpressing CD200 under control of a doxycycline-inducible promoter were used as a source of OBp endogenously overexpressing CD200. Our data show that increased endogenous expression of CD200 on OBp, or addition of CD200Fc into cultures, led to increased OPG:RANKL ratios and increased bone nodule growth, while anti-CD200 abolished this effect.
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Affiliation(s)
- L Lee
- The Toronto Hospital, University Health Network, Toronto, Canada
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Chillarón J, Roca R, Valencia A, Zorzano A, Palacín M. Heteromeric amino acid transporters: biochemistry, genetics, and physiology. Am J Physiol Renal Physiol 2001; 281:F995-1018. [PMID: 11704550 DOI: 10.1152/ajprenal.2001.281.6.f995] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The heteromeric amino acid transporters (HATs) are composed of two polypeptides: a heavy subunit (HSHAT) and a light subunit (LSHAT) linked by a disulfide bridge. HSHATs are N-glycosylated type II membrane glycoproteins, whereas LSHATs are nonglycosylated polytopic membrane proteins. The HSHATs have been known since 1992, and the LSHATs have been described in the last three years. HATs represent several of the classic mammalian amino acid transport systems (e.g., L isoforms, y(+)L isoforms, asc, x(c)(-), and b(0,+)). Members of the HAT family are the molecular bases of inherited primary aminoacidurias cystinuria and lysinuric protein intolerance. In addition to the role in amino acid transport, one HSHAT [the heavy subunit of the cell-surface antigen 4F2 (also named CD98)] is involved in other cell functions that might be related to integrin activation. This review covers the biochemistry, human genetics, and cell physiology of HATs, including the multifunctional character of CD98.
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Affiliation(s)
- J Chillarón
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona E-08028, Spain
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