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Liu Y, Gao Y, Fang R, Cao H, Sa J, Wang J, Liu H, Wang T, Cui Y. Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach. Brief Bioinform 2021; 22:6346804. [PMID: 34373892 DOI: 10.1093/bib/bbab305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/01/2021] [Accepted: 07/17/2021] [Indexed: 11/12/2022] Open
Abstract
Genes do not function independently; rather, they interact with each other to fulfill their joint tasks. Identification of gene-gene interactions has been critically important in elucidating the molecular mechanisms responsible for the variation of a phenotype. Regression models are commonly used to model the interaction between two genes with a linear product term. The interaction effect of two genes can be linear or nonlinear, depending on the true nature of the data. When nonlinear interactions exist, the linear interaction model may not be able to detect such interactions; hence, it suffers from substantial power loss. While the true interaction mechanism (linear or nonlinear) is generally unknown in practice, it is critical to develop statistical methods that can be flexible to capture the underlying interaction mechanism without assuming a specific model assumption. In this study, we develop a mixed kernel function which combines both linear and Gaussian kernels with different weights to capture the linear or nonlinear interaction of two genes. Instead of optimizing the weight function, we propose a grid search strategy and use a Cauchy transformation of the P-values obtained under different weights to aggregate the P-values. We further extend the two-gene interaction model to a high-dimensional setup using a de-biased LASSO algorithm. Extensive simulation studies are conducted to verify the performance of the proposed method. Application to two case studies further demonstrates the utility of the model. Our method provides a flexible and computationally efficient tool for disentangling complex gene-gene interactions associated with complex traits.
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Affiliation(s)
- Yan Liu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Yuzhao Gao
- School of Statistics, Shanxi University of Finance and Economics, Taiyuan, PR China
| | - Ruiling Fang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Hongyan Cao
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Jian Sa
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Hongqi Liu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Tong Wang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, PR China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
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2
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Abstract
Phospholipase C γ1 (PLCγ1) is a member of the PLC family that functions as signal transducer by hydrolyzing membrane lipid to generate second messengers. The unique protein structure of PLCγ1 confers a critical role as a direct effector of VEGFR2 and signaling mediated by other receptor tyrosine kinases. The distinct vascular phenotypes in PLCγ1-deficient animal models and the gain-of-function mutations of PLCγ1 found in human endothelial cancers point to a major physiological role of PLCγ1 in the endothelial system. In this review, we discuss aspects of physiological and molecular function centering around PLCγ1 in the context of endothelial cells and provide a perspective for future investigation.
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Affiliation(s)
- Dongying Chen
- Yale Cardiovascular Research Center, Departments of Internal Medicine and Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Michael Simons
- Yale Cardiovascular Research Center, Departments of Internal Medicine and Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA.
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3
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Su Y, Fan Z, Wu X, Li Y, Wang F, Zhang C, Wang J, Du J, Wang S. Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs. BMC Genomics 2016; 17:134. [PMID: 26911717 PMCID: PMC4766650 DOI: 10.1186/s12864-016-2485-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/17/2016] [Indexed: 12/28/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification critical to the regulation of gene expression during development. To date, little is known about the role of DNA methylation in tooth development in large animal models. Thus, we carried out a comparative genomic analysis of genome-wide DNA methylation profiles in E50 and E60 tooth germ from miniature pigs using methylated DNA immunoprecipitation-sequencing (MeDIP-seq). Results We observed different DNA methylation patterns during the different developmental stages of pig tooth germ. A total of 2469 differentially methylated genes were identified. Functional analysis identified several signaling pathways and 104 genes that may be potential key regulators of pig tooth development from E50 to E60. Conclusions The present study provided a comprehensive analysis of the global DNA methylation pattern of tooth germ in miniature pigs and identified candidate genes that potentially regulate tooth development from E50 to E60. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2485-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Su
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Xiaoshan Wu
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Yang Li
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Fu Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Chunmei Zhang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Jinsong Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China. .,Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
| | - Jie Du
- Department of Physiology and Pathophysiology, Beijing An Zhen Hospital the Key Laboratory of Remodeling-Related Cardiovascular Diseases, School of Basic Medical Sciences, Capital Medical University, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
| | - Songlin Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China. .,Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
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4
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Dahéron L, Zenz T, Siracusa LD, Brenner C, Calabretta B. Molecular cloning of Ian4: a BCR/ABL-induced gene that encodes an outer membrane mitochondrial protein with GTP-binding activity. Nucleic Acids Res 2001; 29:1308-16. [PMID: 11238997 PMCID: PMC29751 DOI: 10.1093/nar/29.6.1308] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Using the representation difference analysis technique, we have identified a novel gene, Ian4, which is preferentially expressed in hematopoietic precursor 32D cells transfected with wild-type versus mutant forms of the Bcr/Abl oncogene. Ian4 expression was undetectable in 32D cells transfected with v-src, oncogenic Ha-ras or v-Abl. Murine Ian4 maps to chromosome 6, 25 cM from the centromere. The Ian4 mRNA contains two open reading frames (ORFs) separated by 5 nt. The first ORF has the potential to encode for a polypeptide of 67 amino acids without apparent homology to known proteins. The second ORF encodes a protein of 301 amino acids with a GTP/ATP-binding site in the N-terminus and a hydrophobic domain in the extreme C-terminus. The IAN-4 protein resides in the mitochondrial outer membrane and the last 20 amino acids are necessary for this localization. The IAN-4 protein has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Line
- Chromosome Mapping
- Cloning, Molecular
- Crosses, Genetic
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Female
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/physiology
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Gene Expression Regulation
- Haplotypes
- Humans
- Intracellular Membranes/metabolism
- K562 Cells
- Male
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Microscopy, Confocal
- Mitochondria/metabolism
- Molecular Sequence Data
- RNA/genetics
- RNA/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tumor Cells, Cultured
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Affiliation(s)
- L Dahéron
- Thomas Jefferson University, Department of Microbiology and Immunology, Kimmel Cancer Institute, Philadelphia, PA 19107, USA
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5
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Bagella L, Stiegler P, De Luca A, Siracusa LD, Giordano A. Genomic organization, promoter analysis, and chromosomal mapping of the mouse gene encoding Cdk9. J Cell Biochem 2000. [DOI: 10.1002/(sici)1097-4644(20000701)78:1<170::aid-jcb16>3.0.co;2-a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Ghiselli G, Siracusa LD, Iozzo RV. Complete cDNA cloning, genomic organization, chromosomal assignment, functional characterization of the promoter, and expression of the murine Bamacan gene. J Biol Chem 1999; 274:17384-93. [PMID: 10358101 DOI: 10.1074/jbc.274.24.17384] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bamacan is a chondroitin sulfate proteoglycan that abounds in basement membranes. To gain insights into the bamacan gene regulation and transcriptional control, we examined the genomic organization and identified the promoter region of the mouse bamacan gene. Secondary structure analysis of the protein reveals a sequential organization of three globular regions interconnected by two alpha-helix coiled-coils. The N- and the C-terminal ends carry a P-loop and a DA box motif that can act cooperatively to bind ATP. These features as well as the high sequence homology with members of the SMC (structural maintenance of chromosome) protein family led us to conclude that bamacan is a member of this protein family. The gene comprises 31 exons and is driven by a promoter that is highly enriched in GC sequences and lacks TATA and CAAT boxes. The promoter is highly functional in transient cell transfection assays, and step-wise 5' deletions identify a strong enhancer element between -659 and -481 base pairs that includes Jun/Fos proto-oncogene-binding elements. Using backcrossing experiments we mapped the Bam gene to distal chromosome 19, a locus syntenic to human chromosome 10q25. Bamacan is differentially expressed in mouse tissues with the highest levels in testes and brain. Notably, bamacan mRNA levels are low in normal cells and markedly reduced during quiescence but are highly increased when cells resume growth upon serum stimulation. In contrast, in all transformed cells tested, bamacan is constitutively overexpressed, and its levels do not change with cell cycle progression. These results suggest that bamacan is involved in the control of cell growth and transformation.
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Affiliation(s)
- G Ghiselli
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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7
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Kamat A, Carpenter G. Phospholipase C-gamma1: regulation of enzyme function and role in growth factor-dependent signal transduction. Cytokine Growth Factor Rev 1997; 8:109-17. [PMID: 9244406 DOI: 10.1016/s1359-6101(97)00003-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Phospholipase C(gamma)1 (PLC-gamma1), a tyrosine kinase substrate, is a multi-domain molecule that modulates the intracellular levels of the second messenger molecules: Ca2+ and diacylglycerol. Although a wide variety of growth factor receptor tyrosine kinases phosphorylate and activate PLC-gamma1, the biological role and necessity of this signal transduction element in mitogenesis has remained unclear. Recent results, however, point to a more essential role than was suggested by initial studies. Also, biochemical studies have indicated a putative means for the intramolecular repression of PLC-gamma1 activity and provide a means for interpreting activation signals through a derepression mechanism.
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Affiliation(s)
- A Kamat
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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8
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Ji QS, Winnier GE, Niswender KD, Horstman D, Wisdom R, Magnuson MA, Carpenter G. Essential role of the tyrosine kinase substrate phospholipase C-gamma1 in mammalian growth and development. Proc Natl Acad Sci U S A 1997; 94:2999-3003. [PMID: 9096335 PMCID: PMC20311 DOI: 10.1073/pnas.94.7.2999] [Citation(s) in RCA: 200] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The activation of many tyrosine kinases leads to the phosphorylation and activation of phospholipase C-gamma1 (PLC-gamma1). To examine the biological function of this protein, homologous recombination has been used to selectively disrupt the Plcg1 gene in mice. Homozygous disruption of Plcg1 results in embryonic lethality at approximately embryonic day (E) 9.0. Histological analysis indicates that Plcg1 (-/-) embryos appear normal at E 8.5 but fail to continue normal development and growth beyond E 8.5-E9.0. These results clearly demonstrate that PLC-gamma1 with, by inference, its capacity to mobilize second messenger molecules is an essential signal transducing molecule whose absence is not compensated by other signaling pathways or other genes encoding PLC isozymes.
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Affiliation(s)
- Q S Ji
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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9
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Becker-Follmann J, Gaa A, Baùsch E, Natt E, Scherer G, von Deimling O. High-resolution mapping of a linkage group on mouse chromosome 8 conserved on human chromosome 16Q. Mamm Genome 1997; 8:172-7. [PMID: 9069116 DOI: 10.1007/s003359900384] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have performed a high-resolution linkage analysis for the conserved segment on distal mouse Chromosome (Chr) 8 that is homologous to human Chr 16q. The interspecific backcross used involved M. m. molossinus and an M. m. domesticus line congenic for an M. spretus segment from Chr 8 flanked by phenotypic markers Os (oligosyndactyly) and e, a coat colormarker. From a total of 682 N2 progeny, the 191 animals revealing a recombination event between these phenotypic markers were typed for 23 internal loci. The following locus order with distances in cM was obtained: (centromere)-Os-4.1-Mmp2-0.2-Ces1,Es1, Es22-1.2-Mt1,D8Mit15-2.2-Got2, D8Mit11-3.7-Es30-0.3-Es2, Es7-0.9-Ctra1,Lcat-0.3-Cdh1, Cadp, Nmor1, D8Mit12-0.2-Mov34-2.5-Hp,Tat-0.2-Zfp4-1.6-Zfp1,+ ++Ctrb-10.9-e. In a separate interspecific cross involving 62 meioses, Dpep1 was mapped together with Aprt and Cdh3 at 12.9 cM distal to Hp, Tat, to the vicinity of e. Our data give locus order for markers not previously resolved, add Mmp2 and Dpep1 as new markers on mouse Chr 8, and indicate that Ctra1 is the mouse homolog for human CTRL. Comparison of the order of 17 mouse loci with that of their human homologs reveals that locus order is well conserved and that the conserved segment in the human apparently spans the whole long arm of Chr 16.
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Affiliation(s)
- J Becker-Follmann
- Institute of Human Genetics, University of Freiburg, Breisacherstr. 33, D-79106 Freiburg, Germany
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10
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Lyu MS, Park DJ, Rhee SG, Kozak CA. Genetic mapping of the human and mouse phospholipase C genes. Mamm Genome 1996; 7:501-4. [PMID: 8672127 DOI: 10.1007/s003359900151] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
To determine chromosome positions for 10 mouse phospholipase C (PLC) genes, we typed the progeny of two sets of genetic crosses for inheritance of restriction enzyme polymorphisms of each PLC. Four mouse chromosomes, Chr 1, 11, 12, and 19, contained single PLC genes. Four PLC loci, Plcb1, Plcb2, Plcb4, and Plcg1, mapped to three sites on distal mouse Chr 2. Two PLC genes, Plcd1 and Plcg2, mapped to distinct sites on Chr 8. We mapped the human homologs of eight of these genes to six chromosomes by analysis of human x rodent somatic cell hybrids. The map locations of seven of these genes were consistent with previously defined regions of conserved synteny; Plcd1 defines a new region of homology between human Chr 3 and mouse Chr 8.
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Affiliation(s)
- M S Lyu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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11
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MacPhee M, Chepenik KP, Liddell RA, Nelson KK, Siracusa LD, Buchberg AM. The secretory phospholipase A2 gene is a candidate for the Mom1 locus, a major modifier of ApcMin-induced intestinal neoplasia. Cell 1995; 81:957-66. [PMID: 7781071 DOI: 10.1016/0092-8674(95)90015-2] [Citation(s) in RCA: 441] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mutations in the APC gene are responsible for various familial and sporadic colorectal cancers. Min mice carry a dominant mutation in the homolog of the Apc gene and develop multiple adenomas throughout their small and large intestine. Quantitative trait loci studies have identified a locus, Mom1, which maps to the distal region of chromosome 4, that dramatically modifies Min-induced tumor number. We report here the identification of a candidate gene for Mom1. The gene for secretory type II phospholipase A2 (Pla2s) maps to the same region that contains Mom1 and displays 100% concordance between allele type and tumor susceptibility. Expression and sequence analysis revealed that Mom1 susceptible strains are most likely null for Pla2s activity. Our results indicate that Pla2s acts as a novel gene that modifies polyp number by altering the cellular microenvironment within the intestinal crypt.
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Affiliation(s)
- M MacPhee
- Department of Microbiology and Immunology, Jefferson Cancer Center, Jefferson Medical College, Philadelphia, Pennsylvania 19107, USA
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