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NELL-1 in Genome-Wide Association Studies across Human Diseases

  • Xu Cheng
    Affiliations
    State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China

    Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
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  • Jiayu Shi
    Affiliations
    Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
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  • Zhonglin Jia
    Affiliations
    State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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  • Pin Ha
    Affiliations
    Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
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  • Chia Soo
    Affiliations
    Division of Plastic and Reconstructive Surgery, Department of Orthopaedic Surgery, Orthopaedic Hospital Research Center, University of California–Los Angeles, Los Angeles, California
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  • Kang Ting
    Affiliations
    Forsyth Institute, affiliate of the Harvard School of Dental Medicine, Boston, Massachusetts
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  • Aaron W. James
    Affiliations
    Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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  • Bing Shi
    Correspondence
    Address correspondence to Bing Shi, Ph.D., M.D., No. 14, Section 3, South Renmin Rd., Wuhou District, Chengdu 610041, China; or Xinli Zhang, Ph.D., Center for the Health Sciences 30-113, University of California, Los Angeles, 10833 Le Conte Ave., Los Angeles, CA 90095.
    Affiliations
    State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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  • Xinli Zhang
    Correspondence
    Address correspondence to Bing Shi, Ph.D., M.D., No. 14, Section 3, South Renmin Rd., Wuhou District, Chengdu 610041, China; or Xinli Zhang, Ph.D., Center for the Health Sciences 30-113, University of California, Los Angeles, 10833 Le Conte Ave., Los Angeles, CA 90095.
    Affiliations
    Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
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Published:December 07, 2021DOI:https://doi.org/10.1016/j.ajpath.2021.11.006
      Neural epidermal growth factor–like (EGFL)-like protein (NELL)-1 is a potent and key osteogenic factor in the development and regeneration of skeletal tissues. Intriguingly, accumulative data from genome-wide association studies (GWASs) have started unveiling potential broader roles of NELL-1 beyond its functions in bone and cartilage. With exploration of the genetic variants of the entire genome in large-scale disease cohorts, GWASs have been used for establishing the connection between specific single-nucleotide polymorphisms of NELL1, in addition to osteoporosis, metabolic diseases, inflammatory conditions, neuropsychiatric diseases, neurodegenerative disorders, and malignant tumors. This review summarizes the findings from GWASs on the manifestation, significance level, implications on function, and correlation of specific NELL1 single-nucleotide polymorphisms in various disorders in humans. By offering a unique and comprehensive correlation between genetic variants and plausible functions of NELL1 in GWASs, this review illustrates the wide range of potential effects of a single gene on the pathogenesis of multiple disorders in humans.
      The genome-wide association study (GWAS) has been a useful method in medical and complex trait genomics for >2 decades.
      • Marigorta U.M.
      • Rodríguez J.A.
      • Gibson G.
      • Navarro A.
      Replicability and prediction: lessons and challenges from GWAS.
      By probing into large-scale genetic variants across the genomes of many individuals, GWASs can shed light on novel genotype–phenotype associations.
      • Jhamb D.
      • Magid-Slav M.
      • Hurle M.R.
      • Agarwal P.
      Pathway analysis of GWAS loci identifies novel drug targets and repurposing opportunities.
      Results from GWASs contribute to an expanded knowledge of certain diseases, including, but not limited to, their causes, pathophysiology, and clinical treatment.
      • Tam V.
      • Patel N.
      • Turcotte M.
      • Bossé Y.
      • Paré G.
      • Meyre D.
      Benefits and limitations of genome-wide association studies.
      Current interpretation of data from GWASs is typically focused on a single disease or trait and its multiple associated genes. However, studies focused on one specific gene of high frequency in multiple diseases or traits are lacking. This article reviews one specific gene, the gene that encodes neural epidermal growth factor–like (EGFL)-like protein (NELL)-1, the osteogenic capacity of which has been studied for >2 decades, by compilation of its diverging roles beyond its well-known osteochondrogenic properties.
      • Zhang X.
      • Zara J.
      • Siu R.K.
      • Ting K.
      • Soo C.
      The role of NELL-1, a growth factor associated with craniosynostosis, in promoting bone regeneration.
      ,
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      This unique perspective can illustrate the potential complex implications of the functions of a single gene on multiple systems of the body, and shed light on the importance of a comprehensive understanding of genes and diseases at a systemic level. Clearly, NELL-1 is just one key element of the functional molecules in the extremely sophisticated networks involved in multiple conditions and treatments. The potential role of NELL-1 is indeed worthy of further exploration, given the broader involvement of NELL1 in diseases and treatments revealed by GWASs.

      NELL1 Gene and the Identified Functions of the NELL-1 Protein

      NELL1 was named for its similarity to the gene NEL, which encodes EGFL protein.
      • Zhang X.
      • Zara J.
      • Siu R.K.
      • Ting K.
      • Soo C.
      The role of NELL-1, a growth factor associated with craniosynostosis, in promoting bone regeneration.
      In humans, NELL1 has been mapped to chromosome 11 at 11p15.1-p15.2, spanning around 906 kb, with 20 coding exons.
      • Zhang X.
      • Zara J.
      • Siu R.K.
      • Ting K.
      • Soo C.
      The role of NELL-1, a growth factor associated with craniosynostosis, in promoting bone regeneration.
      NELL1 is highly conserved in humans and mice, with 95% nucleotide homology.
      • Watanabe T.K.
      • Katagiri T.
      • Suzuki M.
      • Shimizu F.
      • Fujiwara T.
      • Kanemoto N.
      • Nakamura Y.
      • Hirai Y.
      • Maekawa H.
      • Takahashi E.I.
      Cloning and characterization of two novel human cDNAs (NELL1 and NELL2) encoding proteins with six EGF-like repeats.
      NELL1 encodes a cytoplasmic protein that has five EGFL repeats, in addition to a thrombospondin N-terminal domain, several von Willebrand factors, as well as histidine-rich and cysteine-rich domains.
      • Ting K.
      • Vastardis H.
      • Mulliken J.B.
      • Soo C.
      • Tieu A.
      • Do H.
      • Kwong E.
      • Bertolami C.N.
      • Kawamoto H.
      • Kuroda S.
      • Longaker M.T.
      Human NELL-1 expressed in unilateral coronal synostosis.
      NELL-1 protein has been reported to have several binding partners, such as protein kinase C (PKC)-β1, apoptosis-related protein 3, and roundabout homolog 2.
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      These binding proteins are either nonspecific or not naturally present on the cell surface.
      • Yamamoto N.
      • Kashiwagi M.
      • Ishihara M.
      • Kojima T.
      • Niimi T.
      Robo2 contains a cryptic binding site for neural EGFL-like (NELL) protein 1/2.
      ,
      • Nakamura Y.
      • Hasebe A.
      • Takahashi K.
      • Iijima M.
      • Yoshimoto N.
      • Ting K.
      • Niimi T.
      Oligomerization-induced conformational change in the c-terminal region of Nel-like molecule 1 (NELL1) protein is necessary for the efficient mediation of murine MC3T3-E1 cell adhesion and spreading.
      However, recently, the physical high-affinity ligand receptor–like binding between NELL-1 and contactin-associated protein–like protein (Cntnap)-4 was identified, indicating Cntnap-4 as a specific NELL-1 receptor.
      • Li C.
      • Zheng Z.
      • Ha P.
      • Chen X.
      • Jiang W.
      • Sun S.
      • Chen F.
      • Asatrian G.
      • Berthiaume E.A.
      • Kim J.K.
      • Chen E.C.
      • Pang S.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neurexin superfamily cell membrane receptor contactin-associated protein like-4 (Cntnap4) is involved in neural EGFL-like 1 (Nell-1)-responsive osteogenesis.
      Notably, NELL-1 protein has complex quaternary structures and several isoforms with distinct functions,
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      potentially accounting for its functional diversity.
      The functional role of NELL-1 began to be unraveled when the connection between NELL-1 expression and unilateral coronal craniosynostosis, a pathologic condition in humans, was established.
      • Ting K.
      • Vastardis H.
      • Mulliken J.B.
      • Soo C.
      • Tieu A.
      • Do H.
      • Kwong E.
      • Bertolami C.N.
      • Kawamoto H.
      • Kuroda S.
      • Longaker M.T.
      Human NELL-1 expressed in unilateral coronal synostosis.
      Since then, a myriad of animal studies have explored the functions of NELL-1, starting with disease-model simulations of human nonsyndromic CS in Nell-1–overexpression transgenic mice.
      • Zhang X.
      • Kuroda S.
      • Carpenter D.
      • Nishimura I.
      • Soo C.
      • Moats R.
      • Iida K.
      • Wisner E.
      • Hu F.
      • Miao S.
      • Beanes S.
      • Dang C.
      • Vastardis H.
      • Longaker M.
      • Tanizawa K.
      • Kanayama N.
      • Saito N.
      • Ting K.
      Craniosynostosis in transgenic mice overexpressing Nell-1.
      Continuous research efforts have attributed multiple roles to NELL-1 in physiologic and pathologic processes, which can be summarized as follows: i) NELL-1 is necessary in normal craniofacial and appendicular skeletogenesis and is a potent pro-osteogenic factor for osteochondral tissue regeneration
      • Li C.
      • Zheng Z.
      • Zhang X.
      • Asatrian G.
      • Chen E.
      • Song R.
      • Culiat C.
      • Ting K.
      • Soo C.
      Nfatc1 is a functional transcriptional factor mediating nell-1-induced Runx3 upregulation in chondrocytes.
      • Qi H.
      • Kim J.K.
      • Ha P.
      • Chen X.
      • Chen E.
      • Chen Y.
      • Li J.
      • Pan H.C.
      • Yu M.
      • Mohazeb Y.
      • Azer S.
      • Baik L.
      • Kwak J.H.
      • Ting K.
      • Zhang X.
      • Hu M.
      • Soo C.
      Inactivation of Nell-1 in chondrocytes significantly impedes appendicular skeletogenesis.
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      ; ii) NELL-1 exhibits anti-adipogenic effects when applied in bone-regeneration conditions
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      • Pakvasa M.
      • Alverdy A.
      • Mostafa S.
      • Wang E.
      • Fu L.
      • Li A.
      • Oliveira L.
      • Athiviraham A.
      • Lee M.J.
      • Wolf J.M.
      • He T.C.
      • Ameer G.A.
      • Reid R.R.
      Neural EGF-like protein 1 (NELL-1): signaling crosstalk in mesenchymal stem cells and applications in regenerative medicine.
      • James A.W.
      • Pan A.
      • Chiang M.
      • Zara J.N.
      • Zhang X.
      • Ting K.
      • Soo C.
      A new function of Nell-1 protein in repressing adipogenic differentiation.
      ; iii) NELL-1 has therapeutic potential in osteoarthritis due to its pro-osteogenic and anti-inflammatory effects
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      ,
      • Li C.
      • Zheng Z.
      • Ha P.
      • Jiang W.
      • Berthiaume E.A.
      • Lee S.
      • Mills Z.
      • Pan H.
      • Chen E.C.
      • Jiang J.
      • Culiat C.T.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neural EGFL like 1 as a potential pro-chondrogenic, anti-inflammatory dual-functional disease-modifying osteoarthritis drug.
      ; iv) NELL1 is a potential tumor-suppressing gene, on account of its involvement in promoter hypermethylation
      • Jin Z.
      • Mori Y.
      • Yang J.
      • Sato F.
      • Ito T.
      • Cheng Y.
      • Paun B.
      • Hamilton J.P.
      • Kan T.
      • Olaru A.
      • David S.
      • Agarwal R.
      • Abraham J.M.
      • Beer D.
      • Montgomery E.
      • Meltzer S.J.
      Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma.
      ,
      • Mori Y.
      • Cai K.
      • Cheng Y.
      • Wang S.
      • Paun B.
      • Hamilton J.P.
      • Jin Z.
      • Sato F.
      • Berki A.T.
      • Kan T.
      • Ito T.
      • Mantzur C.
      • Abraham J.M.
      • Meltzer S.J.
      A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer.
      ; v) NELL-1 could play an important regulatory role in the nervous system due to its newly discovered receptor, Cntnap-4, which is crucial in synapse development
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      ,
      • Li C.
      • Zheng Z.
      • Ha P.
      • Chen X.
      • Jiang W.
      • Sun S.
      • Chen F.
      • Asatrian G.
      • Berthiaume E.A.
      • Kim J.K.
      • Chen E.C.
      • Pang S.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neurexin superfamily cell membrane receptor contactin-associated protein like-4 (Cntnap4) is involved in neural EGFL-like 1 (Nell-1)-responsive osteogenesis.
      ; and vi) NELL-1 serves as a podocyte antigen marker to define a distinct type of membranous nephropathy.
      • Hanset N.
      • Aydin S.
      • Demoulin N.
      • Cosyns J.
      • Castanares-Zapatero D.
      • Crott R.
      • Cambier J.
      • Pochet J.
      • Gillerot G.
      • Reginster F.
      Podocyte antigen staining to identify distinct phenotypes and outcomes in membranous nephropathy: a retrospective multicenter cohort study.
      ,
      • Sethi S.
      • Debiec H.
      • Madden B.
      • Charlesworth M.C.
      • Morelle J.
      • Gross L.
      • Ravindran A.
      • Buob D.
      • Jadoul M.
      • Fervenza F.C.
      Neural epidermal growth factor-like 1 protein (NELL-1) associated membranous nephropathy.

      Genome-Wide Association Study of NELL1

      NELL1 gene has been a frequent hit in GWASs in a wide range of human diseases such as metabolic, neuropsychiatric, neurodegenerative, and inflammatory diseases, and cancers with susceptible gene loci spread throughout the NELL1 sequence (Figure 1).
      • Rudkowska I.
      • Guénard F.
      • Julien P.
      • Couture P.
      • Lemieux S.
      • Barbier O.
      • Calder P.C.
      • Minihane A.M.
      • Vohl M.C.
      Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation.
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      • Amre D.K.
      • MacK D.R.
      • Israel D.
      • Krupoves A.
      • Costea I.
      • Lambrette P.
      • Grimard G.
      • Dong J.
      • Levy E.
      NELL1, NCF4, and FAM92B genes are not major susceptibility genes for Crohn's disease in Canadian children and young adults.
      • Seyerle A.A.
      • Sitlani C.M.
      • Noordam R.
      • Gogarten S.M.
      • Li J.
      • Li X.
      • et al.
      Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology.
      Some of these association studies have offered novel perspectives on the genuine susceptibility gene loci.
      • Rudkowska I.
      • Guénard F.
      • Julien P.
      • Couture P.
      • Lemieux S.
      • Barbier O.
      • Calder P.C.
      • Minihane A.M.
      • Vohl M.C.
      Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation.
      ,
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      Other association studies and corresponding function studies have verified the role of NELL-1 by highlighting the potential for combating the relevant disease using therapy.
      • Amre D.K.
      • MacK D.R.
      • Israel D.
      • Krupoves A.
      • Costea I.
      • Lambrette P.
      • Grimard G.
      • Dong J.
      • Levy E.
      NELL1, NCF4, and FAM92B genes are not major susceptibility genes for Crohn's disease in Canadian children and young adults.
      ,
      • Seyerle A.A.
      • Sitlani C.M.
      • Noordam R.
      • Gogarten S.M.
      • Li J.
      • Li X.
      • et al.
      Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology.
      These gene loci are of genome-wide significance (P < 5 × 10−8),
      • Tam V.
      • Patel N.
      • Turcotte M.
      • Bossé Y.
      • Paré G.
      • Meyre D.
      Benefits and limitations of genome-wide association studies.
      suggestive significance (P < 5 × 10−5),
      • Shaffer J.R.
      • Polk D.E.
      • Wang X.
      • Feingold E.
      • Weeks D.E.
      • Lee M.K.
      • Cuenco K.T.
      • Weyant R.J.
      • Crout R.J.
      • McNeil D.W.
      • Marazita M.L.
      Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
      or nominal significance
      • Van Ingen G.
      • Li J.
      • Goedegebure A.
      • Pandey R.
      • Rose Li Y.
      • March M.E.
      • Jaddoe V.W.V.
      • Bakay M.
      • Mentch F.D.
      • Thomas K.
      • Wei Z.
      • Chang X.
      • Hain H.S.
      • Uitterlinden A.G.
      • Moll H.A.
      • Van Duijn C.M.
      • Rivadeneira F.
      • Raat H.
      • De Jong R.J.B.
      • Sleiman P.M.
      • Van Der Schroeff M.P.
      • Hakonarson H.
      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      (Table 1).
      Figure thumbnail gr1
      Figure 1NELL1-related susceptible gene loci in human disorders. Boxed region indicates the region of NELL1 gene on chromosome 11. IBD, inflammatory bowel disease; NSCLC, non–small cell lung cancer; TG, triglyceride.
      Table 1NELL1 Manifested in GWASs of Human Disorders
      Classification of disordersPublicationSample sizeEthnicityEvidence of associationSNPsLocation on NELL1
      Metabolic disease
       OsteoporosisKarasik et al (2010)
      • Karasik D.
      • Hsu Y.H.
      • Zhou Y.
      • Cupples L.A.
      • Kiel D.P.
      • Demissie S.
      Genome-wide pleiotropy of osteoporosis-related phenotypes: the Framingham study.
      Nominalrs10766761Intron 12
       ALL BMD lossInaba et al (2018)
      • Inaba H.
      • Cao X.
      • Han A.Q.
      • Panetta J.C.
      • Ness K.K.
      • Metzger M.L.
      • Rubnitz J.E.
      • Ribeiro R.C.
      • Sandlund J.T.
      • Jeha S.
      • Cheng C.
      • Pui C.H.
      • Relling M.V.
      • Kaste S.C.
      Bone mineral density in children with acute lymphoblastic leukemia.
      393AmericanSuggestivers11025915Intron 12
       TG metabolismDel-Aguila et al (2014)
      • Del-Aguila J.L.
      • Beitelshees A.L.
      • Cooper-Dehoff R.M.
      • Chapman A.B.
      • Gums J.G.
      • Bailey K.
      • Gong Y.
      • Turner S.T.
      • Johnson J.A.
      • Boerwinkle E.
      Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
      767AmericanGenome-widers12279250; rs4319515Intron 16; intron16
       TG metabolismRudkowska et al (2014)
      • Rudkowska I.
      • Guénard F.
      • Julien P.
      • Couture P.
      • Lemieux S.
      • Barbier O.
      • Calder P.C.
      • Minihane A.M.
      • Vohl M.C.
      Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation.
      141CanadianSuggestivers752088Intron 2
       TG metabolismAslibekyan et al (2013)
      • Aslibekyan S.
      • An P.
      • Frazier-Wood A.C.
      • Kabagambe E.K.
      • Irvin M.R.
      • Straka R.J.
      • Tiwari H.K.
      • Tsai M.Y.
      • Hopkins P.N.
      • Borecki I.B.
      • Ordovas J.M.
      • Arnett D.K.
      Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
      793AmericanSuggestive25 SNPs
      The specific loci of the 25 SNPs were not mentioned by the author.
      Neuropsychiatric and neurodegenerative disorder
       AutismConnolly et al (2013)
      • Connolly J.J.
      • Glessner J.T.
      • Hakonarson H.
      A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.
      2165AmericanGenome-widers1429793Intron 5
       BipolarMathieu et al (2015)
      • Mathieu F.
      • Etain B.
      • Dizier M.H.
      • Lajnef M.
      • Lathrop M.
      • Cabon C.
      • Leboyer M.
      • Henry C.
      • Bellivier F.
      Genetics of emotional reactivity in bipolar disorders.
      291FrenchSuggestivers10766743Intron 5
       MDDLin et al (2018)
      • Lin E.
      • Kuo P.H.
      • Liu Y.L.
      • Yu Y.W.Y.
      • Yang A.C.
      • Tsai S.J.
      A deep learning approach for predicting antidepressant response in major depression using clinical and genetic biomarkers.
      455TaiwaneseSuggestivers2139423Intron 2
       Multiple sclerosisTiwari et al (2015)
      • Tiwari H.
      • Patki A.
      • Cofield S.S.
      • Gustafson T.
      • Duggan D.
      • Jacobson S.
      • Wolinsky J.S.
      • Lublin F.D.
      • Cutter G.R.
      The CombiRx Investigator Group
      GWAS on relapse outcomes in CombiRx trial Poster presented at: 31st Congress of European Committee for Treatment and Research in Multiple Sclerosis (ECTRIMS), Barcelona, Spain, October 7-10.
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       Otitis mediavan Ingen et al (2016)
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      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      8790AmericanNominallyrs11026076Intron 15
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      Genome-wide association study of genetic predictors of overall survival for non-small cell lung cancer in never smokers.
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      791EuropeanSuggestivers7939346; rs10833509Intron 14
      –, not available; ALL, acute lymphoblastic leukemia; BMD, bone mineral density; GWAS, genome-wide association study; IBD, inflammatory bowel disease; MDD, major depressive disorder; NSCLC, non–small cell lung cancer; SNP, single-nucleotide polymorphism; TG, triglyceride.
      The specific loci of the 25 SNPs were not mentioned by the author.

      Metabolic Diseases

      Given the established link of NELL-1 to craniosynostosis, the functional role of NELL-1 in bone-related disease has been thoroughly investigated. Despite the large number of animal studies in which the potential role of NELL-1 in bone regeneration was verified,
      • Li C.
      • Zheng Z.
      • Ha P.
      • Chen X.
      • Jiang W.
      • Sun S.
      • Chen F.
      • Asatrian G.
      • Berthiaume E.A.
      • Kim J.K.
      • Chen E.C.
      • Pang S.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neurexin superfamily cell membrane receptor contactin-associated protein like-4 (Cntnap4) is involved in neural EGFL-like 1 (Nell-1)-responsive osteogenesis.
      • Zhang X.
      • Kuroda S.
      • Carpenter D.
      • Nishimura I.
      • Soo C.
      • Moats R.
      • Iida K.
      • Wisner E.
      • Hu F.
      • Miao S.
      • Beanes S.
      • Dang C.
      • Vastardis H.
      • Longaker M.
      • Tanizawa K.
      • Kanayama N.
      • Saito N.
      • Ting K.
      Craniosynostosis in transgenic mice overexpressing Nell-1.
      • Qi H.
      • Kim J.K.
      • Ha P.
      • Chen X.
      • Chen E.
      • Chen Y.
      • Li J.
      • Pan H.C.
      • Yu M.
      • Mohazeb Y.
      • Azer S.
      • Baik L.
      • Kwak J.H.
      • Ting K.
      • Zhang X.
      • Hu M.
      • Soo C.
      Inactivation of Nell-1 in chondrocytes significantly impedes appendicular skeletogenesis.
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      • Li C.
      • Zheng Z.
      • Ha P.
      • Jiang W.
      • Berthiaume E.A.
      • Lee S.
      • Mills Z.
      • Pan H.
      • Chen E.C.
      • Jiang J.
      • Culiat C.T.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neural EGFL like 1 as a potential pro-chondrogenic, anti-inflammatory dual-functional disease-modifying osteoarthritis drug.
      a definite association is lacking in human studies. Nonetheless, some promising results have emerged from the connection between NELL1 and other metabolic diseases, such as lipid-metabolism disorders.

      Osteoporosis

      Osteoporosis is an aging-related bone-degenerative disease characterized by compromised bone strength and an increased risk for fracture.
      • Rivadeneira F.
      • Styrkársdottir U.
      • Estrada K.
      • Halldórsson B.V.
      • Hsu Y.-H.
      • Richards J.B.
      • Zillikens M.C.
      • Kavvoura F.K.
      • Amin N.
      • Aulchenko Y.S.
      • Cupples L.A.
      • Deloukas P.
      • Demissie S.
      • Grundberg E.
      • Hofman A.
      • Kong A.
      • Karasik D.
      • van Meurs J.B.
      • Oostra B.
      • Pastinen T.
      • Pols H.A.P.
      • Sigurdsson G.
      • Soranzo N.
      • Thorleifsson G.
      • Thorsteinsdottir U.
      • Williams F.M.K.
      • Wilson S.G.
      • Zhou Y.
      • Ralston S.H.
      • van Duijn C.M.
      • Spector T.
      • Kiel D.P.
      • Stefansson K.
      • Ioannidis J.P.A.
      • Uitterlinden A.G.
      Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
      ,
      • Kiel D.P.
      • Demissie S.
      • Dupuis J.
      • Lunetta K.L.
      • Murabito J.M.
      • Karasik D.
      Genome-wide association with bone mass and geometry in the Framingham heart study.
      Genetic determinants in the progression of osteoporosis have been identified.
      • Rivadeneira F.
      • Styrkársdottir U.
      • Estrada K.
      • Halldórsson B.V.
      • Hsu Y.-H.
      • Richards J.B.
      • Zillikens M.C.
      • Kavvoura F.K.
      • Amin N.
      • Aulchenko Y.S.
      • Cupples L.A.
      • Deloukas P.
      • Demissie S.
      • Grundberg E.
      • Hofman A.
      • Kong A.
      • Karasik D.
      • van Meurs J.B.
      • Oostra B.
      • Pastinen T.
      • Pols H.A.P.
      • Sigurdsson G.
      • Soranzo N.
      • Thorleifsson G.
      • Thorsteinsdottir U.
      • Williams F.M.K.
      • Wilson S.G.
      • Zhou Y.
      • Ralston S.H.
      • van Duijn C.M.
      • Spector T.
      • Kiel D.P.
      • Stefansson K.
      • Ioannidis J.P.A.
      • Uitterlinden A.G.
      Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
      Bone mineral density (BMD) is frequently used to predict osteoporotic fracture and remains the single best trait for the analysis of its prognosis.
      • Styrkarsdottir U.
      • Halldorsson B.V.
      • Gretarsdottir S.
      • Gudbjartsson D.F.
      • Walters G.B.
      • Ingvarsson T.
      • Jonsdottir T.
      • Saemundsdottir J.
      • Center J.R.
      • Nguyen T.V.
      • Bagger Y.
      • Gulcher J.R.
      • Eisman J.A.
      • Christiansen C.
      • Sigurdsson G.
      • Kong A.
      • Thorsteinsdottir U.
      • Stefansson K.
      Multiple genetic loci for bone mineral density and fractures.
      Previous GWASs have revealed >20 susceptible gene loci associated with a low BMD.
      • Rivadeneira F.
      • Styrkársdottir U.
      • Estrada K.
      • Halldórsson B.V.
      • Hsu Y.-H.
      • Richards J.B.
      • Zillikens M.C.
      • Kavvoura F.K.
      • Amin N.
      • Aulchenko Y.S.
      • Cupples L.A.
      • Deloukas P.
      • Demissie S.
      • Grundberg E.
      • Hofman A.
      • Kong A.
      • Karasik D.
      • van Meurs J.B.
      • Oostra B.
      • Pastinen T.
      • Pols H.A.P.
      • Sigurdsson G.
      • Soranzo N.
      • Thorleifsson G.
      • Thorsteinsdottir U.
      • Williams F.M.K.
      • Wilson S.G.
      • Zhou Y.
      • Ralston S.H.
      • van Duijn C.M.
      • Spector T.
      • Kiel D.P.
      • Stefansson K.
      • Ioannidis J.P.A.
      • Uitterlinden A.G.
      Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
      ,
      • Styrkarsdottir U.
      • Halldorsson B.V.
      • Gretarsdottir S.
      • Gudbjartsson D.F.
      • Walters G.B.
      • Ingvarsson T.
      • Jonsdottir T.
      • Saemundsdottir J.
      • Center J.R.
      • Nguyen T.V.
      • Bagger Y.
      • Gulcher J.R.
      • Eisman J.A.
      • Christiansen C.
      • Sigurdsson G.
      • Kong A.
      • Thorsteinsdottir U.
      • Stefansson K.
      Multiple genetic loci for bone mineral density and fractures.
      In the Framingham study, performed by Karasik et al,
      • Karasik D.
      • Hsu Y.H.
      • Zhou Y.
      • Cupples L.A.
      • Kiel D.P.
      • Demissie S.
      Genome-wide pleiotropy of osteoporosis-related phenotypes: the Framingham study.
      analysis of data from 2073 US patients showed that rs10766761, located in intron 12 of the NELL1 gene, was nominally associated with low BMD of both the femoral neck (P = 7.9 × 10−4) and the lumbar spine (P = 3.3 × 10−4). The study brought into perspective the different traits of osteoporosis and investigated the relationship between phenotype and the percentage of shared SNPs. NELL1 was among the 10 associated genes identified by more than one proxy for osteoporosis.
      Acute lymphoblastic leukemia leads to bone loss in some affected patients,
      • Cox C.L.
      • Zhu L.
      • Kaste S.C.
      • Srivastava K.
      • Barnes L.
      • Nathan P.C.
      • Wells R.J.
      • Ness K.K.
      Modifying bone mineral density, physical function, and quality of life in children with acute lymphoblastic leukemia.
      which can result either from the disease itself or from concomitant physical conditions.
      • Cox C.L.
      • Zhu L.
      • Kaste S.C.
      • Srivastava K.
      • Barnes L.
      • Nathan P.C.
      • Wells R.J.
      • Ness K.K.
      Modifying bone mineral density, physical function, and quality of life in children with acute lymphoblastic leukemia.
      The BMD of lumbar vertebrae L1/L2 investigated in a study of the genetic risk factors for BMD loss in patients with acute lymphoblastic leukemia
      • Inaba H.
      • Cao X.
      • Han A.Q.
      • Panetta J.C.
      • Ness K.K.
      • Metzger M.L.
      • Rubnitz J.E.
      • Ribeiro R.C.
      • Sandlund J.T.
      • Jeha S.
      • Cheng C.
      • Pui C.H.
      • Relling M.V.
      • Kaste S.C.
      Bone mineral density in children with acute lymphoblastic leukemia.
      suggested NELL-1 as being significant for a decrease in BMD.
      • Inaba H.
      • Cao X.
      • Han A.Q.
      • Panetta J.C.
      • Ness K.K.
      • Metzger M.L.
      • Rubnitz J.E.
      • Ribeiro R.C.
      • Sandlund J.T.
      • Jeha S.
      • Cheng C.
      • Pui C.H.
      • Relling M.V.
      • Kaste S.C.
      Bone mineral density in children with acute lymphoblastic leukemia.
      Similarly, an SNP in intron 12 of NELL1, rs11025915, was found to be positively associated with BMD loss in patients with acute lymphoblastic leukemia.
      Studies of the functions of NELL-1 in modulating osteogenesis have been underway for decades.
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      ,
      • Shen J.
      • James A.W.
      • Zhang X.
      • Pang S.
      • Zara J.N.
      • Asatrian G.
      • Chiang M.
      • Lee M.
      • Khadarian K.
      • Nguyen A.
      • Lee K.S.
      • Siu R.K.
      • Tetradis S.
      • Ting K.
      • Soo C.
      Novel Wnt regulator NEL-like molecule-1 antagonizes adipogenesis and augments osteogenesis induced by bone morphogenetic protein 2.
      • Lee S.
      • Zhang X.
      • Shen J.
      • James A.W.
      • Chung C.G.
      • Hardy R.
      • Li C.
      • Girgius C.
      • Zhang Y.
      • Stoker D.
      • Wang H.
      • Wu B.M.
      • Peault B.
      • Ting K.
      • Soo C.
      Brief report:human perivascular stem cells and Nel-like protein-1 synergistically enhance spinal fusion in osteoporotic rats.
      • James A.W.
      • Chiang M.
      • Asatrian G.
      • Shen J.
      • Goyal R.
      • Chung C.G.
      • Chang L.
      • Shrestha S.
      • Turner A.S.
      • Seim 3rd, H.B.
      • Zhang X.
      • Wu B.M.
      • Ting K.
      • Soo C.
      Vertebral implantation of NELL-1 enhances bone formation in an osteoporotic sheep model.
      Systemic delivery of NELL-1 to mice with ovariectomy-induced osteoporosis is associated with increased BMD, possibly by enhancement of the osteoblast differentiation and inhibition of the osteoclast-directed bone resorption.
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      Similarly, in a sheep model of osteoporosis, local delivery of NELL-1 was associated with a significant increase in bone formation, as evidenced by increased BMD, bone volume, and mean cortical length.
      • James A.W.
      • Shen J.
      • Zhang X.
      • Asatrian G.
      • Goyal R.
      • Kwak J.H.
      • Jiang L.
      • Bengs B.
      • Culiat C.T.
      • Turner A.S.
      • Seim H.B.
      • Wu B.M.
      • Lyons K.
      • Adams J.S.
      • Ting K.
      • Soo C.
      NELL-1 in the treatment of osteoporotic bone loss.
      ,
      • James A.W.
      • Chiang M.
      • Asatrian G.
      • Shen J.
      • Goyal R.
      • Chung C.G.
      • Chang L.
      • Shrestha S.
      • Turner A.S.
      • Seim 3rd, H.B.
      • Zhang X.
      • Wu B.M.
      • Ting K.
      • Soo C.
      Vertebral implantation of NELL-1 enhances bone formation in an osteoporotic sheep model.
      Furthermore, NELL-1 is associated with counteraction of the adverse effect of adipose-filled, poor-quality bone in bone morphogenetic protein (BMP)-2–induced skeletal repair, possibly by directing BMP-2–treated cells away from adipogenesis and toward osteogenesis.
      • Shen J.
      • James A.W.
      • Zhang X.
      • Pang S.
      • Zara J.N.
      • Asatrian G.
      • Chiang M.
      • Lee M.
      • Khadarian K.
      • Nguyen A.
      • Lee K.S.
      • Siu R.K.
      • Tetradis S.
      • Ting K.
      • Soo C.
      Novel Wnt regulator NEL-like molecule-1 antagonizes adipogenesis and augments osteogenesis induced by bone morphogenetic protein 2.

      Triglyceride-Related Metabolic Diseases

      Triglycerides (TGs) are circulating lipoproteins, the serum concentration of which reflects lipid status in clinical practice.
      • Sandesara P.B.
      • Virani S.S.
      • Fazio S.
      • Shapiro M.D.
      The forgotten lipids: triglycerides, remnant cholesterol, and atherosclerotic cardiovascular disease risk.
      Apart from serving as structural components, TGs are the energy reservoir that provide fuel for the body.
      • Sandesara P.B.
      • Virani S.S.
      • Fazio S.
      • Shapiro M.D.
      The forgotten lipids: triglycerides, remnant cholesterol, and atherosclerotic cardiovascular disease risk.
      In a genetic study, individuals with a weaker TG response to a treatment drug had a genetic profile different from those with a normal response.
      • Kraja A.T.
      • Borecki I.B.
      • Tsai M.Y.
      • Ordovas J.M.
      • Hopkins P.N.
      • Lai C.Q.
      • Frazier-Wood A.C.
      • Straka R.J.
      • Hixson J.E.
      • Province M.A.
      • Arnett D.K.
      Genetic analysis of 16 NMR-lipoprotein fractions in humans, the GOLDN study.
      Del-Aguila et al
      • Del-Aguila J.L.
      • Beitelshees A.L.
      • Cooper-Dehoff R.M.
      • Chapman A.B.
      • Gums J.G.
      • Bailey K.
      • Gong Y.
      • Turner S.T.
      • Johnson J.A.
      • Boerwinkle E.
      Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
      conducted a GWAS of the TG response to hydrochlorothiazide, a drug widely prescribed for use in the treatment of patients with hypertension, which can cause hypertriglyceridemia. That study was performed in two independent populations composed of 425 European Americans and 342 African Americans.
      • Del-Aguila J.L.
      • Beitelshees A.L.
      • Cooper-Dehoff R.M.
      • Chapman A.B.
      • Gums J.G.
      • Bailey K.
      • Gong Y.
      • Turner S.T.
      • Johnson J.A.
      • Boerwinkle E.
      Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
      Two SNPs, rs12279250 and rs4319515, both in intron 16 of NELL1, showed genome-wide significance, while 77 SNPs in 27 genomic regions exhibited suggestive significance in the African-American population. The investigators conjectured that hydrochlorothiazide might regulate adipocyte differentiation through NELL-1, as NELL-1 was found to repress adipogenic differentiation.
      • Del-Aguila J.L.
      • Beitelshees A.L.
      • Cooper-Dehoff R.M.
      • Chapman A.B.
      • Gums J.G.
      • Bailey K.
      • Gong Y.
      • Turner S.T.
      • Johnson J.A.
      • Boerwinkle E.
      Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
      In another study, Rudkowska et al
      • Rudkowska I.
      • Guénard F.
      • Julien P.
      • Couture P.
      • Lemieux S.
      • Barbier O.
      • Calder P.C.
      • Minihane A.M.
      • Vohl M.C.
      Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation.
      probed the effects of supplementation with long-chain Ω-3 polyunsaturated fatty acids on the risk-related loci of inadequate plasma TG response. The study included 141 Canadians classified as responders or nonresponders. NELL1, among 13 loci, had suggestive significant association; rs752088, located in intron 2 of the NELL1 gene, was more frequent in nonresponders than in responders.
      • Rudkowska I.
      • Guénard F.
      • Julien P.
      • Couture P.
      • Lemieux S.
      • Barbier O.
      • Calder P.C.
      • Minihane A.M.
      • Vohl M.C.
      Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation.
      Similarly, Aslibekyan et al
      • Aslibekyan S.
      • An P.
      • Frazier-Wood A.C.
      • Kabagambe E.K.
      • Irvin M.R.
      • Straka R.J.
      • Tiwari H.K.
      • Tsai M.Y.
      • Hopkins P.N.
      • Borecki I.B.
      • Ordovas J.M.
      • Arnett D.K.
      Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
      performed a study of the changes in circulating adiponectin levels in response to fenofibrate therapy in 793 individuals from the United States. Several SNPs located on NELL1 were of suggestive significant association with baseline adiponectin level.
      In an in vitro study, NELL1 was associated with reduced adipogenic differentiation in a human preadipocyte cell line, as evidenced by decreases in lipid droplet formation and expression of all of the adipogenic genes examined.
      • James A.W.
      • Pan A.
      • Chiang M.
      • Zara J.N.
      • Zhang X.
      • Ting K.
      • Soo C.
      A new function of Nell-1 protein in repressing adipogenic differentiation.
      In a study in a rodent model of femoral segmental defect, NELL-1 was reported to guide target cells away from adipogenesis.
      • Shen J.
      • James A.W.
      • Zhang X.
      • Pang S.
      • Zara J.N.
      • Asatrian G.
      • Chiang M.
      • Lee M.
      • Khadarian K.
      • Nguyen A.
      • Lee K.S.
      • Siu R.K.
      • Tetradis S.
      • Ting K.
      • Soo C.
      Novel Wnt regulator NEL-like molecule-1 antagonizes adipogenesis and augments osteogenesis induced by bone morphogenetic protein 2.
      Considering the well-established genome-wide association of NELL1 with lipid metabolism, and the valid function testing of NELL-1 in animal studies, the development NELL-1–related drugs to combat excessive fat production in diseases in humans is foreseeable.

      Neuropsychiatric and Neurodegenerative Disorders

      NELL-1 exhibits the highest expression in human and mouse brain tissues
      • Kuroda S.
      • Tanizawa K.
      Involvement of epidermal growth factor-like domain of NELL proteins in the novel protein-protein interaction with protein kinase C.
      and plays an important role in skull morphogenesis.
      • Zhang X.
      • Kuroda S.
      • Carpenter D.
      • Nishimura I.
      • Soo C.
      • Moats R.
      • Iida K.
      • Wisner E.
      • Hu F.
      • Miao S.
      • Beanes S.
      • Dang C.
      • Vastardis H.
      • Longaker M.
      • Tanizawa K.
      • Kanayama N.
      • Saito N.
      • Ting K.
      Craniosynostosis in transgenic mice overexpressing Nell-1.
      For these reasons, there is speculation that NELL-1 might play a role in neuropsychiatric and neurodegenerative disorders. Significantly, the discovery of Cntnap-4 as the NELL-1–specific receptor
      • Li C.
      • Zheng Z.
      • Ha P.
      • Chen X.
      • Jiang W.
      • Sun S.
      • Chen F.
      • Asatrian G.
      • Berthiaume E.A.
      • Kim J.K.
      • Chen E.C.
      • Pang S.
      • Zhang X.
      • Ting K.
      • Soo C.
      Neurexin superfamily cell membrane receptor contactin-associated protein like-4 (Cntnap4) is involved in neural EGFL-like 1 (Nell-1)-responsive osteogenesis.
      has prompted exploration of the potential regulatory role of NELL-1 in the nervous system in animal models. GWASs have revealed NELL1 to be one of the genes frequently associated with neural disorders.
      • Lord C.
      • Elsabbagh M.
      • Baird G.
      • Veenstra-Vanderweele J.
      Seminar Autism spectrum disorder.
      • Lord C.
      • Elsabbagh M.
      • Baird G.
      • Veenstra-Vanderweele J.
      Seminar Autism spectrum disorder.
      • Thompson A.J.
      • Baranzini S.E.
      • Geurts J.
      • Hemmer B.
      • Ciccarelli O.
      Seminar multiple sclerosis.

      Autism Spectrum Disorder

      Autism spectrum disorder (ASD) is a constellation of diseases characterized by repetitive, unusual sensorimotor behaviors and deficits in social communication.
      • Lord C.
      • Elsabbagh M.
      • Baird G.
      • Veenstra-Vanderweele J.
      Seminar Autism spectrum disorder.
      It has been reported that 74% to 93% of ASD risk is heritable.
      • Lord C.
      • Elsabbagh M.
      • Baird G.
      • Veenstra-Vanderweele J.
      Seminar Autism spectrum disorder.
      Evidence from a study in twins indicates that 16p11.2 deletions and CHD8 are among the top genetic variants associated with ASD.
      • Bailey A.
      • Le Couteur A.
      • Gottesman I.
      • Bolton P.
      • Simonoff E.
      • Yuzda E.
      • Rutter M.
      Autism as a strongly genetic disorder: evidence from a British twin study.
      Connolly et al
      • Connolly J.J.
      • Glessner J.T.
      • Hakonarson H.
      A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.
      performed a GWAS to detect susceptible genes associated with ASD. They selected endophenotypes from the commonly used behavioral assessments and included 2165 patients of European, Asian, or African descent. Among several of the candidate genes, NELL1 was found to be associated with endophenotypes of fainting, fits, or blackouts, and rs1429793, located in intron 5 of NELL1, showed genome-wide significance.
      The investigators proposed that the association of NELL-1 with ASD might be a result of the comorbidity of ASD and other conditions, such as epilepsy.
      • Connolly J.J.
      • Glessner J.T.
      • Hakonarson H.
      A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.
      The NELL-1 binding partner, PKCβ,
      • Li C.
      • Zhang X.
      • Zheng Z.
      • Nguyen A.
      • Ting K.
      • Soo C.
      Nell-1 is a key functional modulator in osteochondrogenesis and beyond.
      has been proposed as a target for anticonvulsant drugs.
      • Connolly J.J.
      • Glessner J.T.
      • Hakonarson H.
      A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.
      Notably, the NELL-1 receptor Cntnap-4 has been implicated in ASD.
      • Karayannis T.
      • Au E.
      • Patel J.C.
      • Kruglikov I.
      • Markx S.
      • Delorme R.
      • Héron D.
      • Salomon D.
      • Glessner J.
      • Restituito S.
      • Gordon A.
      • Rodriguez-Murillo L.
      • Roy N.C.
      • Gogos J.A.
      • Rudy B.
      • Rice M.E.
      • Karayiorgou M.
      • Hakonarson H.
      • Keren B.
      • Huguet G.
      • Bourgeron T.
      • Hoeffer C.
      • Tsien R.W.
      • Peles E.
      • Fishell G.
      Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission.
      Cntnap-4 normally acts to attenuate dopamine release through a presynaptic mechanism. Cntnap4-knockout mice exhibit perseverative behaviors, such as over-grooming, which remains a common behavior abnormality in ASD mice.
      • Karayannis T.
      • Au E.
      • Patel J.C.
      • Kruglikov I.
      • Markx S.
      • Delorme R.
      • Héron D.
      • Salomon D.
      • Glessner J.
      • Restituito S.
      • Gordon A.
      • Rodriguez-Murillo L.
      • Roy N.C.
      • Gogos J.A.
      • Rudy B.
      • Rice M.E.
      • Karayiorgou M.
      • Hakonarson H.
      • Keren B.
      • Huguet G.
      • Bourgeron T.
      • Hoeffer C.
      • Tsien R.W.
      • Peles E.
      • Fishell G.
      Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission.
      In addition, during human-gene analysis, patients diagnosed with ASD harbored exon deletion in the CNTNAP4 gene.
      • Karayannis T.
      • Au E.
      • Patel J.C.
      • Kruglikov I.
      • Markx S.
      • Delorme R.
      • Héron D.
      • Salomon D.
      • Glessner J.
      • Restituito S.
      • Gordon A.
      • Rodriguez-Murillo L.
      • Roy N.C.
      • Gogos J.A.
      • Rudy B.
      • Rice M.E.
      • Karayiorgou M.
      • Hakonarson H.
      • Keren B.
      • Huguet G.
      • Bourgeron T.
      • Hoeffer C.
      • Tsien R.W.
      • Peles E.
      • Fishell G.
      Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission.
      Investigative work to understand the role of NELL-1 in ASD is ongoing.

      Bipolar Disorder

      Bipolar disorder, or manic depression, is characterized by episodic and recurrent mood transition from extreme elation to severe depression.
      • Craddock N.
      • Sklar P.
      Bipolar disorder 1 - genetics of bipolar disorder.
      Inheritable factors play an important role in the pathogenesis of the disease, and family history is a clinical predictor.
      • McGuffin P.
      • Rijsdijk F.
      • Andrew M.
      • Sham P.
      • Katz R.
      • Cardno A.
      The heritability of bipolar affective disorder and the genetic relationship to unipolar depression.
      The diagnosis of bipolar disorder is primarily based on clinical features.
      • Craddock N.
      • Sklar P.
      Bipolar disorder 1 - genetics of bipolar disorder.
      The inclusion of a quantitative trait, emotional reactivity (the threshold and magnitude to which one responds in emotion-eliciting situations), has largely contributed to the identification of susceptible genes in bipolar disorder.
      Mathieu et al
      • Mathieu F.
      • Etain B.
      • Dizier M.H.
      • Lajnef M.
      • Lathrop M.
      • Cabon C.
      • Leboyer M.
      • Henry C.
      • Bellivier F.
      Genetics of emotional reactivity in bipolar disorders.
      performed a study of the genetic background of 281 patients from France who met the criteria for bipolar disorder. They selected emotional reactivity to quantify the severity of bipolar disorder. On GWAS, rs10766743, located in NELL1 intron 5, remained the single SNP with suggestive significance after adjustment for multiple comparisons using the Bonferroni correction.
      Similar to that in other diseases of the nervous system, the functional role of NELL-1 in bipolar disorder has not yet been tested. More functional experiments are required to verify the role of NELL-1 in bipolar disorder.

      Major Depressive Disorder

      Major depressive disorder is a group of psychosocial-dysfunction diseases manifested by a combination of emotional, neurovegetative, and neurocognitive symptoms.
      • Wray N.R.
      • Ripke S.
      • Mattheisen M.
      • Trzaskowski M.
      • Byrne E.M.
      • Abdellaoui A.
      • et al.
      Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
      In genetic studies, major depressive disorder has been reported as moderately inheritable through multiple genes.
      • Howard D.M.
      • Adams M.J.
      • Shirali M.
      • Clarke T.K.
      • Marioni R.E.
      • Davies G.
      • Coleman J.R.I.
      • Alloza C.
      • Shen X.
      • Barbu M.C.
      • Wigmore E.M.
      • Gibson J.
      • Hagenaars S.P.
      • Lewis C.M.
      • Ward J.
      • Smith D.J.
      • Sullivan P.F.
      • Haley C.S.
      • Breen G.
      • Deary I.J.
      • McIntosh A.M.
      Genome-wide association study of depression phenotypes in UK Biobank identifies variants in excitatory synaptic pathways.
      Lin et al
      • Lin E.
      • Kuo P.H.
      • Liu Y.L.
      • Yu Y.W.Y.
      • Yang A.C.
      • Tsai S.J.
      A deep learning approach for predicting antidepressant response in major depression using clinical and genetic biomarkers.
      implemented a study in 455 Taiwanese patients diagnosed with major depressive disorder to hone in a predictive model for an antidepressant response. The investigators first performed a GWAS to select the candidate gene loci. They then built a predictive model with a combination of patients' clinical and genetic biomarkers. In the association study, NELL1 was among the top 10 genes predictive of treatment response. The SNP located in intron 2 of NELL1, rs2139423, was detected to be of suggestive significance.
      As current studies have not implicated the functional role of NELL-1 in mediating psychiatric disorders, the antidepressant role of NELL-1 requires further elucidation.

      Multiple Sclerosis

      Multiple sclerosis is a degenerative disease of the central nervous system caused by neuroinflammation. The clinical manifestation of multiple sclerosis is dependent on the location of the affected central nervous system region and the extent of the inflammatory process.
      • Thompson A.J.
      • Baranzini S.E.
      • Geurts J.
      • Hemmer B.
      • Ciccarelli O.
      Seminar multiple sclerosis.
      ,
      • Grossman I.
      • Knappertz V.
      • Laifenfeld D.
      • Ross C.
      • Zeskind B.
      • Kolitz S.
      • Ladkani D.
      • Hayardeny L.
      • Loupe P.
      • Laufer R.
      • Hayden M.
      Pharmacogenomics strategies to optimize treatments for multiple sclerosis: insights from clinical research.
      Genetic factors play a prominent role in the development of the disease.
      • Thompson A.J.
      • Baranzini S.E.
      • Geurts J.
      • Hemmer B.
      • Ciccarelli O.
      Seminar multiple sclerosis.
      An association between a multiple sclerosis subtype and human leukocyte antigen DR isotype 15 and 16 has long been known and consistently replicated.
      • Thompson A.J.
      • Baranzini S.E.
      • Geurts J.
      • Hemmer B.
      • Ciccarelli O.
      Seminar multiple sclerosis.
      In a study of 608 Caucasians screened for the candidate genes that contribute to the outcomes of patients with multiple-sclerosis relapse, NELL1 was found to be of suggestive significance. The SNP rs7130553, located in intron 15, was suspected.
      • Tiwari H.
      • Patki A.
      • Cofield S.S.
      • Gustafson T.
      • Duggan D.
      • Jacobson S.
      • Wolinsky J.S.
      • Lublin F.D.
      • Cutter G.R.
      The CombiRx Investigator Group
      GWAS on relapse outcomes in CombiRx trial Poster presented at: 31st Congress of European Committee for Treatment and Research in Multiple Sclerosis (ECTRIMS), Barcelona, Spain, October 7-10.
      The fact that NELL-1 is highly expressed in brain tissue may have accounted for this observation. Studies of the function of NELL-1 in multiple sclerosis have not yet been performed.

      Inflammatory Diseases

      The first association of NELL1 with diseases in GWASs appeared in a 2007 study of the susceptibility of the gene in inflammatory bowel disease (IBD).
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      Indeed, NELL1 has been linked to other inflammatory diseases, including periodontitis and otitis media.

      Inflammatory Bowel Disease

      IBD is a group of chronic inflammatory disorders of the gastrointestinal tract, featured by two subtypes, Crohn disease, and ulcerative colitis.
      • Furey T.S.
      • Sethupathy P.
      • Sheikh S.Z.
      Redefining the IBDs using genome-scale molecular phenotyping.
      The onset and progression of IBD are attributed to the dysregulated immune response of the resident microbial communities in a genetically susceptible host. Genetic studies have revealed >240 loci that confer a risk for IBD, but the contribution of these genetic variants to the disease remains largely unknown.
      • Furey T.S.
      • Sethupathy P.
      • Sheikh S.Z.
      Redefining the IBDs using genome-scale molecular phenotyping.
      Among these genes, NELL1 has been shown by GWASs to be susceptible.
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      ,
      • Amre D.K.
      • MacK D.R.
      • Israel D.
      • Krupoves A.
      • Costea I.
      • Lambrette P.
      • Grimard G.
      • Dong J.
      • Levy E.
      NELL1, NCF4, and FAM92B genes are not major susceptibility genes for Crohn's disease in Canadian children and young adults.
      Franke et al
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      performed a multistage genome-wide scan in different panels. They first conducted the screening in a German panel of 393 cases of Crohn disease and 399 controls and identified the 200 most significant SNPs. In the subsequent replication study in an independent German panel, rs1793004, located in intron 1 of NELL1, showed a consistent association of suggestive significance with Crohn disease. The German panel comprised 942 patients, 1082 controls, and 375 trios, and rs1793004 was also associated with the ulcerative colitis case-control panel, highlighting NELL1 as a ubiquitous IBD-susceptibility gene. In the replication study, two additional SNPs, rs8176785 and rs8176786, located on exons 3 and 10 respectively, showed an association of suggestive significance with Crohn disease. The SNPs in the two exons both were missense mutations. Since the initial identification of NELL1 as a susceptible gene in IBD, several replication studies from other research centers have ensued. Studies in a Dutch-Belgian cohort and in a Canadian population failed to show statistical association with NELL1.
      • Amre D.K.
      • MacK D.R.
      • Israel D.
      • Krupoves A.
      • Costea I.
      • Lambrette P.
      • Grimard G.
      • Dong J.
      • Levy E.
      NELL1, NCF4, and FAM92B genes are not major susceptibility genes for Crohn's disease in Canadian children and young adults.
      ,
      • Weersma R.K.
      • Stokkers P.C.F.
      • Cleynen I.
      • Wolfkamp S.C.S.
      • Henckaerts L.
      • Schreiber S.
      • Dijkstra G.
      • Franke A.
      • Nolte I.M.
      • Rutgeerts P.
      • Wijmenga C.
      • Vermeire S.
      Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort.
      The fact that the German study included stringent criteria for Crohn disease, in which only patients with the severe phenotype
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      were included in the analysis, might account for the discrepancy among the studies.
      Apart from association studies, histologic and molecular studies in IBD patients have indicated interesting results. Substantial NELL1 transcript levels were detected in the colon and small intestine. However, no significant differences between normal and affected tissue were revealed by quantitative PCR. Localization of NELL-1 in colonic mucosa by immunohistochemistry analysis showed a confined expression in inflammatory cells in the lamina propria.
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      Although the association between IBD and NELL1 was susceptible to population stratification, interestingly, osteopenia and osteoporosis were among the top comorbidities in IBD patients.
      • Roux C.
      • Abitbol V.
      • Chaussade S.
      • Kolta S.
      • Guillemant S.
      • Dougados M.
      • Amor B.
      • Couturier D.
      Bone loss in patients with inflammatory bowel disease: a prospective study.
      ,
      • Abitbol V.
      • Roux C.
      • Chaussade S.
      • Guillemant S.
      • Kolta S.
      • Dougados M.
      • Couturier D.
      • Amor B.
      Metabolic bone assessment in patients with inflammatory bowel disease.
      Sophisticated diagnostic modalities also demonstrated that young IBD patients experienced more bone fragility.
      • Pepe J.
      • Zawadynski S.
      • Herrmann F.R.
      • Juillerat P.
      • Michetti P.
      • Ferrari-Lacraz S.
      • Belli D.
      • Ratib O.
      • Rizzoli R.
      • Chevalley T.
      • Ferrari S.L.
      Structural basis of bone fragility in young subjects with inflammatory bowel disease: a high-resolution pQCT study of the SWISS IBD cohort (SIBDC).
      It was suggested that BMD and bone microstructure could serve as early diagnostic criteria to better identify IBD patients.
      • Pepe J.
      • Zawadynski S.
      • Herrmann F.R.
      • Juillerat P.
      • Michetti P.
      • Ferrari-Lacraz S.
      • Belli D.
      • Ratib O.
      • Rizzoli R.
      • Chevalley T.
      • Ferrari S.L.
      Structural basis of bone fragility in young subjects with inflammatory bowel disease: a high-resolution pQCT study of the SWISS IBD cohort (SIBDC).
      Thus, it is reasonable to infer that NELL-1 may be associated with comorbidities of IBD rather than susceptibility to IBD per se.
      • Franke A.
      • Hampe J.
      • Rosenstiel P.
      • Becker C.
      • Wagner F.
      • Häsler R.
      • Little R.D.
      • Huse K.
      • Ruether A.
      • Balschun T.
      • Wittig M.
      • ElSharawy A.
      • Mayr G.
      • Albrecht M.
      • Prescott N.J.
      • Onnie C.M.
      • Fournier H.
      • Keith T.
      • Radelof U.
      • Platzer M.
      • Mathew C.G.
      • Stoll M.
      • Krawczak M.
      • Nürnberg P.
      • Schreiber S.
      Systematic association mapping identifies NELL1 as a novel IBD disease gene.
      Moreover, so far, two SNPs, rs8176785 and rs8176786, are the only NELL1 SNPs in the coding exons identified and associated in GWAS reports across many disorders in humans. In this case, the actual roles of the identified SNPs in the development of IBD could be pursued by the construction of the corresponding point-mutation vectors or by the use of the CRISPR/CAS9 gene-editing technique in both in vitro and in vivo models.
      • Liu H.
      • Leslie E.J.
      • Jia Z.
      • Smith T.
      • Eshete M.
      • Butali A.
      • Dunnwald M.
      • Murray J.
      • Cornell R.A.
      Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate.
      The verification and validation of the functions of NELL1 SNPs may be assayed as suggested elsewhere
      • Romero-Barrios N.
      • Legascue M.F.
      • Benhamed M.
      • Ariel F.
      • Crespi M.
      Splicing regulation by long noncoding RNAs.
      • Emadi E.
      • Akhoundi F.
      • Kalantar S.M.
      • Emadi-Baygi M.
      Predicting the most deleterious missense nsSNPs of the protein isoforms of the human HLA-G gene and in silico evaluation of their structural and functional consequences.
      • Yu C.H.
      • Dang Y.
      • Zhou Z.
      • Wu C.
      • Zhao F.
      • Sachs M.S.
      • Liu Y.
      Codon usage influences the local rate of translation elongation to regulate co-translational protein folding.
      • Li M.J.
      • Yan B.
      • Sham P.C.
      • Wang J.
      Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression.
      • Chu D.
      • Wei L.
      Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation.
      (Figure 2).
      Figure thumbnail gr2
      Figure 2Functional validation of candidate SNPs. For candidate SNPs of statistical significance revealed by GWASs, further bioinformatics analysis is applied to categorize them as coding or noncoding. Usually, a combination of multiple servers (more than three) with complementary algorithms was used to minimize errors.
      • Emadi E.
      • Akhoundi F.
      • Kalantar S.M.
      • Emadi-Baygi M.
      Predicting the most deleterious missense nsSNPs of the protein isoforms of the human HLA-G gene and in silico evaluation of their structural and functional consequences.
      In the GWASs in the literature, up to 88% of the SNPs screened are noncoding.
      • Li M.J.
      • Yan B.
      • Sham P.C.
      • Wang J.
      Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression.
      Coding SNPs were subclassified as nonsynonymous mutations, in which the amino acid and consequently the encoded protein is changed, and synonymous mutations.
      • Chu D.
      • Wei L.
      Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation.
      While nonsynonymous SNPs could have a direct impact on the protein structure, synonymous SNPs could lead to alternative splicing, or limit the speed of the translation.
      • Yu C.H.
      • Dang Y.
      • Zhou Z.
      • Wu C.
      • Zhao F.
      • Sachs M.S.
      • Liu Y.
      Codon usage influences the local rate of translation elongation to regulate co-translational protein folding.
      Noncoding SNPs can also be called regulatory SNPs, which can be located in the promoter, enhancer, 5′-untranslated region (UTR), 3′-UTR, or intronic region. First, GWAS, linkage analysis, and quantitative trait locus mapping are frequently used to detect causal regulatory SNPs.
      • Li M.J.
      • Yan B.
      • Sham P.C.
      • Wang J.
      Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression.
      Then, functional testing can be applied to determine the role of targeted SNPs to be transcription-factor binding, chromatin state maintenance, epigenetic modification,
      • Li M.J.
      • Yan B.
      • Sham P.C.
      • Wang J.
      Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression.
      or alternative splicing.
      • Romero-Barrios N.
      • Legascue M.F.
      • Benhamed M.
      • Ariel F.
      • Crespi M.
      Splicing regulation by long noncoding RNAs.
      The general framework of functional validation of noncoding SNPs is suggested elsewhere.
      • Li M.J.
      • Yan B.
      • Sham P.C.
      • Wang J.
      Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression.

      Chronic Periodontitis

      Chronic periodontitis is a progressive inflammatory disease characterized by gradual detachment of the periodontal tissue from the tooth and a loss of alveolar bone.
      • Hernández M.
      • Dutzan N.
      • García-Sesnich J.
      • Abusleme L.
      • Dezerega A.
      • Silva N.
      • González F.E.
      • Vernal R.
      • Sorsa T.
      • Gamonal J.
      Host-pathogen interactions in progressive chronic periodontitis.
      ,
      • Pérez-Chaparro P.J.
      • Gonçalves C.
      • Figueiredo L.C.
      • Faveri M.
      • Lobão E.
      • Tamashiro N.
      • Duarte P.
      • Feres M.
      Newly identified pathogens associated with periodontitis: a systematic review.
      The cause of chronic periodontitis involves a dynamic interaction between the periodontal microbiota and the host-defense system, which is under strong genetic control.
      • Hernández M.
      • Dutzan N.
      • García-Sesnich J.
      • Abusleme L.
      • Dezerega A.
      • Silva N.
      • González F.E.
      • Vernal R.
      • Sorsa T.
      • Gamonal J.
      Host-pathogen interactions in progressive chronic periodontitis.
      Studies in twins have verified the heritability of chronic periodontitis, and a handful of GWASs have begun to unravel the genetic susceptibility of the disease.
      • Pérez-Chaparro P.J.
      • Gonçalves C.
      • Figueiredo L.C.
      • Faveri M.
      • Lobão E.
      • Tamashiro N.
      • Duarte P.
      • Feres M.
      Newly identified pathogens associated with periodontitis: a systematic review.
      • Hong K.W.
      • Shin M.S.
      • Ahn Y.B.
      • Lee H.J.
      • Kim H.D.
      Genome-wide association study on chronic periodontitis in Korean population: results from the Yangpyeong health cohort.
      • Shimizu S.
      • Momozawa Y.
      • Takahashi A.
      • Nagasawa T.
      • Ashikawa K.
      • Terada Y.
      • Izumi Y.
      • Kobayashi H.
      • Tsuji M.
      • Kubo M.
      • Furuichi Y.
      A genome-wide association study of periodontitis in a Japanese population.
      To date, no gene has been found to be of genome-wide significance, although several bear suggestive significance.
      • Hong K.W.
      • Shin M.S.
      • Ahn Y.B.
      • Lee H.J.
      • Kim H.D.
      Genome-wide association study on chronic periodontitis in Korean population: results from the Yangpyeong health cohort.
      ,
      • Shimizu S.
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      • Izumi Y.
      • Kobayashi H.
      • Tsuji M.
      • Kubo M.
      • Furuichi Y.
      A genome-wide association study of periodontitis in a Japanese population.
      Five GWASs of chronic periodontitis were conducted in Caucasian and Asian populations.
      • Shaffer J.R.
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      • Feingold E.
      • Weeks D.E.
      • Lee M.K.
      • Cuenco K.T.
      • Weyant R.J.
      • Crout R.J.
      • McNeil D.W.
      • Marazita M.L.
      Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
      • Hong K.W.
      • Shin M.S.
      • Ahn Y.B.
      • Lee H.J.
      • Kim H.D.
      Genome-wide association study on chronic periodontitis in Korean population: results from the Yangpyeong health cohort.
      • Shimizu S.
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      • Nagasawa T.
      • Ashikawa K.
      • Terada Y.
      • Izumi Y.
      • Kobayashi H.
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      • Kubo M.
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      A genome-wide association study of periodontitis in a Japanese population.
      • Divaris K.
      • Monda K.L.
      • North K.E.
      • Olshan A.F.
      • Reynolds L.M.
      • Hsueh W.C.
      • Lange E.M.
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      Exploring the genetic basis of chronic periodontitis: a genome-wide association study.
      • Teumer A.
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      Genome-wide association study of chronic periodontitis in a general German population.
      However, none of them found a gene locus of genome-wide significant association.
      • Sanders A.E.
      • Sofer T.
      • Wong Q.
      • Kerr K.F.
      • Agler C.
      • Shaffer J.R.
      • Beck J.D.
      • Offenbacher S.
      • Salazar C.R.
      • North K.E.
      • Marazita M.L.
      • Laurie C.C.
      • Singer R.H.
      • Cai J.
      • Finlayson T.L.
      • Divaris K.
      Chronic periodontitis genome-wide association study in the Hispanic community health study/study of Latinos.
      ,
      • Pérez-Chaparro P.J.
      • Gonçalves C.
      • Figueiredo L.C.
      • Faveri M.
      • Lobão E.
      • Tamashiro N.
      • Duarte P.
      • Feres M.
      Newly identified pathogens associated with periodontitis: a systematic review.
      Then Sanders et al
      • Sanders A.E.
      • Sofer T.
      • Wong Q.
      • Kerr K.F.
      • Agler C.
      • Shaffer J.R.
      • Beck J.D.
      • Offenbacher S.
      • Salazar C.R.
      • North K.E.
      • Marazita M.L.
      • Laurie C.C.
      • Singer R.H.
      • Cai J.
      • Finlayson T.L.
      • Divaris K.
      Chronic periodontitis genome-wide association study in the Hispanic community health study/study of Latinos.
      performed a GWAS in 10,395 Hispanic/Latino participants, followed by a replication study in 4402 European Americans and 908 African Americans. They selected interproximal clinical attachment levels as the measurement of chronic periodontitis and reported one gene locus of genome-wide significance and four others of suggestive significance. The NELL1 gene, with its nearby SNP rs75715012, showed suggestive significance.
      Apart from association studies, in vitro and in vivo animal studies have also revealed the functional role of NELL-1 in tooth and periodontal tissues.
      • Thompson A.J.
      • Baranzini S.E.
      • Geurts J.
      • Hemmer B.
      • Ciccarelli O.
      Seminar multiple sclerosis.
      NELL-1 may promote osteogenic differentiation in human periodontal ligament stem cells.
      • Chen C.Y.
      • Liu Y.J.
      • Shi S.G.
      • Chen F.M.
      • Cai C.
      • Li B.
      • Wang J.
      • Shi L.
      • Li Y.
      • Liu Z.Y.
      • Niu Z.Y.
      Osteogenic differentiation of human periodontal ligament stem cells expressing lentiviral NEL-like protein 1.
      Moreover, NELL-1 demonstrated osteoinductive capacity to promote bone formation in alveolar bone areas within rhesus-monkey and rat models.
      • Wang B.
      • Wu Y.
      • Yu H.
      • Jiang L.
      • Fang B.
      • Guo Q.
      The effects of NELL on corticotomy-assisted tooth movement and osteogenesis in a rat model.
      ,
      • Zhang J.
      • Chen Y.
      • Xu J.
      • Wang J.
      • Li C.
      • Wang L.
      Tissue engineering using 3D printed nano-bioactive glass loaded with NELL1 gene for repairing alveolar bone defects.

      Acute Otitis Media

      Otitis media remains a highly prevalent childhood disease worldwide, of which acute otitis media (AOM) accounts for the largest percentage.
      • Van Ingen G.
      • Li J.
      • Goedegebure A.
      • Pandey R.
      • Rose Li Y.
      • March M.E.
      • Jaddoe V.W.V.
      • Bakay M.
      • Mentch F.D.
      • Thomas K.
      • Wei Z.
      • Chang X.
      • Hain H.S.
      • Uitterlinden A.G.
      • Moll H.A.
      • Van Duijn C.M.
      • Rivadeneira F.
      • Raat H.
      • De Jong R.J.B.
      • Sleiman P.M.
      • Van Der Schroeff M.P.
      • Hakonarson H.
      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      ,
      • Rye M.S.
      • Warrington N.M.
      • Scaman E.S.H.
      • Vijayasekaran S.
      • Coates H.L.
      • Anderson D.
      • Pennell C.E.
      • Blackwell J.M.
      • Jamieson S.E.
      Genome-wide association study to identify the genetic determinants of otitis media susceptibility in childhood.
      AOM is characterized by the presence of fluid in the middle-ear cavity, frequently accompanied by earache, fever, and upper respiratory tract infection.
      • Coker T.R.
      • Chan L.S.
      • Newberry S.J.
      • Limbos M.A.
      • Suttorp M.J.
      • Shekelle P.G.
      • Takata G.S.
      Diagnosis, microbial epidemiology, and antibiotic treatment of acute otitis media in children: a systematic review.
      The cause of AOM involves multiple aspects of the pathogen, host, and genetic factors.
      • Coker T.R.
      • Chan L.S.
      • Newberry S.J.
      • Limbos M.A.
      • Suttorp M.J.
      • Shekelle P.G.
      • Takata G.S.
      Diagnosis, microbial epidemiology, and antibiotic treatment of acute otitis media in children: a systematic review.
      ,
      • Daly K.A.
      • Hoffman H.J.
      • Kvaerner K.J.
      • Kvestad E.
      • Casselbrant M.L.
      • Homoe P.
      • Rovers M.M.
      Epidemiology, natural history, and risk factors: panel report from the Ninth International Research Conference on Otitis Media.
      The heritability of AOM is well established, and FNDC1 has been identified as a disease-contributing gene.
      • Van Ingen G.
      • Li J.
      • Goedegebure A.
      • Pandey R.
      • Rose Li Y.
      • March M.E.
      • Jaddoe V.W.V.
      • Bakay M.
      • Mentch F.D.
      • Thomas K.
      • Wei Z.
      • Chang X.
      • Hain H.S.
      • Uitterlinden A.G.
      • Moll H.A.
      • Van Duijn C.M.
      • Rivadeneira F.
      • Raat H.
      • De Jong R.J.B.
      • Sleiman P.M.
      • Van Der Schroeff M.P.
      • Hakonarson H.
      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      Furthermore, GWASs have unraveled several other susceptible gene loci in AOM.
      • Van Ingen G.
      • Li J.
      • Goedegebure A.
      • Pandey R.
      • Rose Li Y.
      • March M.E.
      • Jaddoe V.W.V.
      • Bakay M.
      • Mentch F.D.
      • Thomas K.
      • Wei Z.
      • Chang X.
      • Hain H.S.
      • Uitterlinden A.G.
      • Moll H.A.
      • Van Duijn C.M.
      • Rivadeneira F.
      • Raat H.
      • De Jong R.J.B.
      • Sleiman P.M.
      • Van Der Schroeff M.P.
      • Hakonarson H.
      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      ,
      • Rye M.S.
      • Warrington N.M.
      • Scaman E.S.H.
      • Vijayasekaran S.
      • Coates H.L.
      • Anderson D.
      • Pennell C.E.
      • Blackwell J.M.
      • Jamieson S.E.
      Genome-wide association study to identify the genetic determinants of otitis media susceptibility in childhood.
      ,
      • Allen E.K.
      • Manichaikul A.
      • Chen W.M.
      • Rich S.S.
      • Daly K.A.
      • Sale M.M.
      Evaluation of replication of variants associated with genetic risk of otitis media.
      Van Ingen et al
      • Van Ingen G.
      • Li J.
      • Goedegebure A.
      • Pandey R.
      • Rose Li Y.
      • March M.E.
      • Jaddoe V.W.V.
      • Bakay M.
      • Mentch F.D.
      • Thomas K.
      • Wei Z.
      • Chang X.
      • Hain H.S.
      • Uitterlinden A.G.
      • Moll H.A.
      • Van Duijn C.M.
      • Rivadeneira F.
      • Raat H.
      • De Jong R.J.B.
      • Sleiman P.M.
      • Van Der Schroeff M.P.
      • Hakonarson H.
      Genome-wide association study for acute otitis media in children identifies FNDC1 as disease contributing gene.
      performed a GWAS in AOM in an American population with 825 cases and 7936 controls. They discovered 1 gene of genome-wide significance and 8 genes of suggestive significance. In addition, they found that 45 of 82 genes demonstrated nominally significant association. The NELL1 gene, with its SNP rs11026076 in intron 15, fell into the latter category.
      Evidence of the association between NELL-1 and AOM is still at its preliminary stage. Further studies are needed to verify this association and to illustrate the possible functional role of NELL-1 in AOM.

      Non–Small Cell Lung Cancer

      Non–small cell lung cancer (NSCLC) is the most common type of lung cancer and accounts for nearly 80% of cases.
      • Hirsch F.R.
      • Scagliotti G.V.
      • Mulshine J.L.
      • Kwon R.
      • Curran W.J.
      • Wu Y.L.
      • Paz-Ares L.
      Lung cancer: current therapies and new targeted treatments.
      Although smoking is an important risk factor for NSCLC, a notable amount of NSCLC patients have never smoked.
      • Wu X.
      • Wang L.
      • Ye Y.
      • Aakre J.A.
      • Pu X.
      • Chang G.C.
      • Yang P.C.
      • Roth J.A.
      • Marks R.S.
      • Lippman S.M.
      • Chang J.Y.
      • Lu C.
      • Deschamps C.
      • Su W.C.
      • Wang W.C.
      • Huang M.S.
      • Chang D.W.
      • Li Y.
      • Pankratz V.S.
      • Minna J.D.
      • Hong W.K.
      • Hildebrandt M.A.T.
      • Hsiung C.A.
      • Yang P.
      Genome-wide association study of genetic predictors of overall survival for non-small cell lung cancer in never smokers.
      These observations led to the discovery that nonsmokers with NSCLC bear a distinct genetic profile in comparison to smokers with NSCLC.
      • Zhang L.
      • Villafranca A.
      • Karl L.
      • Kamal S.
      • Torres B.
      • Connor M.O.
      • Evers A.S.
      • Gradwohl S.
      • Lin N.
      • Palanca B.J.
      Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung.
      The ALK gene ranked top among the NSCLC oncogenes.
      • Hirsch F.R.
      • Scagliotti G.V.
      • Mulshine J.L.
      • Kwon R.
      • Curran W.J.
      • Wu Y.L.
      • Paz-Ares L.
      Lung cancer: current therapies and new targeted treatments.
      In order to investigate the genetic variants of NSCLC in nonsmokers, Wu et al
      • Wu X.
      • Wang L.
      • Ye Y.
      • Aakre J.A.
      • Pu X.
      • Chang G.C.
      • Yang P.C.
      • Roth J.A.
      • Marks R.S.
      • Lippman S.M.
      • Chang J.Y.
      • Lu C.
      • Deschamps C.
      • Su W.C.
      • Wang W.C.
      • Huang M.S.
      • Chang D.W.
      • Li Y.
      • Pankratz V.S.
      • Minna J.D.
      • Hong W.K.
      • Hildebrandt M.A.T.
      • Hsiung C.A.
      • Yang P.
      Genome-wide association study of genetic predictors of overall survival for non-small cell lung cancer in never smokers.
      conducted a GWAS. The study included as a screening panel 620 American patients and normal controls from two medical centers. The top 25 gene candidates generated from this study were replicated in 1256 Taiwanese patients. Only two genes were still significant after the replication analysis. The SNP in intron 4 of NELL1, rs10766739, ranked among the top candidate loci in the screening panel (P = 3.66 × 10−7) and was of borderline significance (P = 0.051) in the replication panel. Therefore, NELL1 emerged as a candidate tumor-suppressor gene. This is supported by its potentially protective role in other types of tumors, such as esophageal adenocarcinoma and colon cancer,
      • Jin Z.
      • Mori Y.
      • Yang J.
      • Sato F.
      • Ito T.
      • Cheng Y.
      • Paun B.
      • Hamilton J.P.
      • Kan T.
      • Olaru A.
      • David S.
      • Agarwal R.
      • Abraham J.M.
      • Beer D.
      • Montgomery E.
      • Meltzer S.J.
      Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma.
      ,
      • Mori Y.
      • Cai K.
      • Cheng Y.
      • Wang S.
      • Paun B.
      • Hamilton J.P.
      • Jin Z.
      • Sato F.
      • Berki A.T.
      • Kan T.
      • Ito T.
      • Mantzur C.
      • Abraham J.M.
      • Meltzer S.J.
      A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer.
      although more validation studies are needed.
      In parallel to GWAS, studies of the function of NELL-1 in tumorigenesis have yielded corroborating results. NELL1 promoter region is hypermethylated, a hallmark of gene inactivation, in colon cancer tissue compared to normal colon tissue.
      • Mori Y.
      • Cai K.
      • Cheng Y.
      • Wang S.
      • Paun B.
      • Hamilton J.P.
      • Jin Z.
      • Sato F.
      • Berki A.T.
      • Kan T.
      • Ito T.
      • Mantzur C.
      • Abraham J.M.
      • Meltzer S.J.
      A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer.
      Similarly, in esophageal adenocarcinoma, NELL1 exhibits a loss of heterozygosity and promoter hypermethylation, two mechanisms of gene inactivation.
      • Jin Z.
      • Mori Y.
      • Yang J.
      • Sato F.
      • Ito T.
      • Cheng Y.
      • Paun B.
      • Hamilton J.P.
      • Kan T.
      • Olaru A.
      • David S.
      • Agarwal R.
      • Abraham J.M.
      • Beer D.
      • Montgomery E.
      • Meltzer S.J.
      Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma.
      The application of demethylation agents could decrease promoter methylation and up-regulate NELL-1 expression in both colon cancer and esophageal adenocarcinoma cell lines.
      • Jin Z.
      • Mori Y.
      • Yang J.
      • Sato F.
      • Ito T.
      • Cheng Y.
      • Paun B.
      • Hamilton J.P.
      • Kan T.
      • Olaru A.
      • David S.
      • Agarwal R.
      • Abraham J.M.
      • Beer D.
      • Montgomery E.
      • Meltzer S.J.
      Hypermethylation of the nel-like 1 gene is a common and early event and is associated with poor prognosis in early-stage esophageal adenocarcinoma.
      ,
      • Mori Y.
      • Cai K.
      • Cheng Y.
      • Wang S.
      • Paun B.
      • Hamilton J.P.
      • Jin Z.
      • Sato F.
      • Berki A.T.
      • Kan T.
      • Ito T.
      • Mantzur C.
      • Abraham J.M.
      • Meltzer S.J.
      A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer.
      Furthermore, in a recent study in lung cancer stem-like cells,
      • Zhai Y.
      • Wei R.
      • Sha S.
      • Lin C.
      • Wang H.
      • Jiang X.
      • Liu G.
      Effect of NELL1 on lung cancer stem-like cell differentiation.
      overexpression of NELL-1 in a 95-D human cell line, a highly invasive and metastatic lung carcinoma cell line, was associated with cell differentiation and thus a reduction in metastasis. Together, these results support the promising tumor-suppressing role of NELL-1.

      Other Human Disorders

      In GWASs, NELL-1 has also been implicated in other human disorders that are not categorized readily, such as cardiovascular diseases and ovarian aging.

      Figarska S. Genetics of healthy ageing (dissertation). [Groningen, the Netherlands]: University of Groningen.

      ,

      Voorhuis M. Genetics of ovarian ageing: genetic association studies on natural. menopause and primary ovarian insufficiency (master's thesis). [Utrecht, the Netherlands]: Utrecht University.

      The SNP rs11026076, located in intron 15 of NELL1 gene, is positively associated with cardiovascular mortality with suggestive significance.

      Figarska S. Genetics of healthy ageing (dissertation). [Groningen, the Netherlands]: University of Groningen.

      In a human functional study by Chen et al,
      • Chen H.
      • Zhang Z.
      • Zhang L.
      • Wang J.
      • Zhang M.
      • Zhu B.
      miR-27a protects human mitral valve interstitial cell from TNF-α-induced inflammatory injury via up-regulation of NELL-1.
      NELL-1 protected the mitral valve from inflammatory injury. Another GWAS explored thiazide diuretics–induced QT-interval prolongation. A total of 78,199 Europeans, African Americans, and Hispanics were enrolled in that study, in which rs12225793 in intron 12 of NELL1 was of suggestive association with QT prolongation.
      • Seyerle A.A.
      • Sitlani C.M.
      • Noordam R.
      • Gogarten S.M.
      • Li J.
      • Li X.
      • et al.
      Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology.
      Two SNPs, rs7939346 and rs10833509, both in intron 14 of NELL1, were suggestively significantly associated with ovarian aging.

      Voorhuis M. Genetics of ovarian ageing: genetic association studies on natural. menopause and primary ovarian insufficiency (master's thesis). [Utrecht, the Netherlands]: Utrecht University.

      However, currently, no studies of the function of NELL-1 in ovarian aging are available.

      Conclusions and Future Perspectives

      In the relevant GWASs of NELL1, a spectrum of diseases, including bone-related metabolic diseases, lipid-metabolic diseases, inflammatory conditions, neuropsychiatric diseases, neurodegenerative disorders, and cancers have been implicated (Figure 3). Taking into account the high replicability of GWASs and verifications of the relevant function studies, NELL1 gene polymorphisms are likely to have significant associations with a wide variety of disorders in humans.
      Figure thumbnail gr3
      Figure 3Human disorders with NELL1 manifestation in GWASs.
      On the other hand, it is also apparent that these GWASs have some limitations. First, the heritability explained by GWASs is relatively low, and the biological significance and GWAS-based association of a certain gene could be disproportionate. So, the contribution of NELL-1 to the onset and progression of these diseases or to the responsiveness to specific treatments is uncertain. Second, the GWAS-based data on NELL1 presented in this review are all directly drawn from primary individual studies, which do not include preliminary results from indirect meta-analyses.
      • Galesloot T.E.
      • Verweij N.
      • Traglia M.
      • Barbieri C.
      • Van F.
      • Geurts-Moespot A.J.
      • Girelli D.
      • Kiemeney L.A.L.M.
      • Sweep F.C.G.J.
      • Swertz M.A.
      • Van Der Meer P.
      • Camaschella C.
      • Toniolo D.
      • Vermeulen S.H.
      • Van Der Harst P.
      • Swinkels D.W.
      Meta-GWAS and meta-analysis of exome array studies do not reveal genetic determinants of serum hepcidin.
      • Guénard F.
      • Bouchard-Mercier A.
      • Rudkowska I.
      • Lemieux S.
      • Patrick C.
      • Vohl M.-C.
      Genome-wide association study of dietary pattern scores.
      • Baumert J.
      • Huang J.
      • Mcknight B.
      • Sabater-lleal M.
      • Steri M.
      • Chu A.Y.
      • et al.
      No evidence for genome-wide interactions on plasma fibrinogen by smoking, alcohol consumption and body mass index: results from meta-analyses of 80607 subjects.
      Third, GWAS-based signals could be spurious because of cryptic population stratification. Thus, a sober perception of the exact role of NELL-1 in all of the aforementioned diseases should be further interrogated in post-GWAS function studies.
      While GWASs offer new perspectives on the genetic architecture of diseases, the results should be interpreted conservatively. The practical realization of whole-genome sequencing will tremendously improve studies on SNPs in the noncoding regions of NELL1. With a better understanding of multiple potential roles of the NELL1 gene in disorders in humans, this review highlights the future perspectives for research on NELL-1, shifting from investigations on associations to those on function and causation.

      Acknowledgments

      We thank Drs. Bihe Zhang and Dan Pan for their feedback on the figures. We also thank Joshua Yang and Yasamin Mohazeb for English-language editing.

      Author Contributions

      X.C. contributed to the investigation and drafted the manuscript; J.S. drafted the manuscript; Z.J. provided genetic interpretation and drafted the manuscript; P.H., C.S., and K.T. supervised the work; A.W.J. and B.S. supervised the work and critically revised the manuscript; X.Z. conceptualized and supervised the work and critically revised the manuscript; X.C., C.S., T.K., B.S., and X.Z. acquired funding. All of the authors approved the manuscript and are accountable for all aspects of the work.

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