Ela W. Knapik, M.D.


Faculty Appointments
Professor of Medicine Professor of Cell & Developmental Biology
M.D., Medicine, Jagiellonian University, Krakow, Poland
Office Address
1165B Light Hall
2215 Garland Avenue
Nashville, TN 37232
Research Description
We have focused our research on three main areas:
(i) The mechanisms and pathways directing extracellular matrix traffic and deposition
(ii) The pathophysiology of diseases, including developmental and neuropsychiatric disorders
(iii) Modeling of human variants for drug development and testing

The Knapik laboratory uses in vivo approaches in zebrafish (Danio rerio) because this model system is superbly suited for genetic and developmental analyses by being accessible for manipulation and direct live observation. We use genetic mutants induced by CRISPR genome editing or chemically induced random variants to assess developmental phenotypes, gene function and pathway interactions. In parallel, we use mammalian cell culture and biochemical approaches.

(i) Disruptions in the synthesis, processing or secretion of extracellular matrix (ECM) macromolecules are associated with human diseases, including osteogenesis imperfecta (OI), multiple epiphyseal dysplasia, cranio-lenticulo-sutural dysplasia, and congenital disorders of glycosylation (CDG). Our laboratory has successfully modeled these human diseases in zebrafish and contributed to understanding basic developmental mechanisms and cellular pathways that direct ECM traffic and deposition. Using phenotype-driven forward genetic screens and positional cloning, we have identified point mutations responsible for skeletal malformations in zebrafish, and currently, we are working to show how defects in the secretory pathway affect skeletal biology, chondrocyte cell shape and ECM deposition.

(ii) Additionally, we are modeling Mendelian disorders such as chylomicron retention disease and zinc transporter deficits, as well as comorbidities associated with complex neuropsychiatric diseases (ASD, MDD, SCZ, BD, ADHD, OCD) such as skeletal dysmorphology, seizures and gastrointestinal disturbances. In collaboration with the Vanderbilt Genetics Institute (VGI) investigators, we examine effects of genetic variation, identified by statistical genetic methods in BioVU, on gene function and resulting phenotypic spectrum. Using CRISPR/Cas9 genome editing, we are generating zebrafish knockout and transgenic lines that are evaluated by in vivo and ex vivo methods for discovery of primary genetic mechanisms underlying the pathophysiology of these diseases.

(iii) Zebrafish is ideally suited for modeling of human single nucleotide polymorphisms (SNPs) in genes identified through BioVU variant investigations. We can test whether a specific SNP increases or decreases gene activity, thus altering protein function, such as receptor activity. These models are particularly helpful in testing responses to known pharmacological agents and in drug screens for new pharmaceuticals. We are using CRISPR/Cas9–based knockout and knockin strategies in stable zebrafish lines that are then evaluated for phenotype and gene function. This early functional genomics assessment model offers rapid and powerful tool in drug discovery pipeline.
Research Keywords
Protein Secretion, Extracellular Matrix, Modeling Human Developmental and Neuropsychiatric Disorders, DNA Biobank (BioVU), Regulation of Cell Shape Changes in Morphogenesis
Bayraktar EC, La K, Karpman K, Unlu G, Ozerdem C, Ritter DJ, Alwaseem H, Molina H, Hoffmann HH, Millner A, Atilla-Gokcumen GE, Gamazon ER, Rushing AR, Knapik EW, Basu S, Birsoy K. Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism. Nat Metab [print-electronic]. 2020 Jun; 2(6): 487-98. PMID: 32694732, PMCID: PMC7384252, PII: 10.1038/s42255-020-0206-9, DOI: 10.1038/s42255-020-0206-9, ISSN: 2522-5812.

Unlu G, Qi X, Gamazon ER, Melville DB, Patel N, Rushing AR, Hashem M, Al-Faifi A, Chen R, Li B, Cox NJ, Alkuraya FS, Knapik EW. Phenome-based approach identifies RIC1-linked Mendelian syndrome through zebrafish models, biobank associations and clinical studies. Nat Med [print-electronic]. 2020 Jan; 26(1): 98-109. PMID: 31932796, PMCID: PMC7147997, PII: 10.1038/s41591-019-0705-y, DOI: 10.1038/s41591-019-0705-y, ISSN: 1546-170X.

Unlu G, Gamazon ER, Qi X, Levic DS, Bastarache L, Denny JC, Roden DM, Mayzus I, Breyer M, Zhong X, Konkashbaev AI, Rzhetsky A, Knapik EW, Cox NJ. GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish. Am. J. Hum. Genet [print-electronic]. 2019 Mar 3/7/2019; 104(3): 503-19. PMID: 30827500, PMCID: PMC6407495, PII: S0002-9297(19)30017-5, DOI: 10.1016/j.ajhg.2019.01.017, ISSN: 1537-6605.

Cox NJ, Unlu G, Bisnett BJ, Meister TR, Condon BM, Luo PM, Smith TJ, Hanna M, Chhetri A, Soderblom EJ, Audhya A, Knapik EW, Boyce M. Dynamic Glycosylation Governs the Vertebrate COPII Protein Trafficking Pathway. Biochemistry [print-electronic]. 2018 Jan 1/9/2018; 57(1): 91-107. PMID: 29161034, PMCID: PMC5767944, DOI: 10.1021/acs.biochem.7b00870, ISSN: 1520-4995.

Hockman D, Burns AJ, Schlosser G, Gates KP, Jevans B, Mongera A, Fisher S, Unlu G, Knapik EW, Kaufman CK, Mosimann C, Zon LI, Lancman JJ, Dong PDS, Lickert H, Tucker AS, Baker CVH. Evolution of the hypoxia-sensitive cells involved in amniote respiratory reflexes. Elife. 2017 Apr 4/7/2017; 6: PMID: 28387645, PMCID: PMC5438250, DOI: 10.7554/eLife.21231, ISSN: 2050-084X.

Luderman LN, Unlu G, Knapik EW. Zebrafish Developmental Models of Skeletal Diseases. Curr. Top. Dev. Biol [print-electronic]. 2017; 124: 81-124. PMID: 28335865, PII: S0070-2153(16)30190-9, DOI: 10.1016/bs.ctdb.2016.11.004, ISSN: 1557-8933.

Zou P, Wu SY, Koteiche HA, Mishra S, Levic DS, Knapik E, Chen W, Mchaourab HS. A conserved role of aA-crystallin in the development of the zebrafish embryonic lens. Exp. Eye Res [print-electronic]. 2015 Sep; 138: 104-13. PMID: 26149094, PMCID: PMC4638411, PII: S0014-4835(15)00220-1, DOI: 10.1016/j.exer.2015.07.001, ISSN: 1096-0007.

Levic DS, Minkel JR, Wang WD, Rybski WM, Melville DB, Knapik EW. Animal model of Sar1b deficiency presents lipid absorption deficits similar to Anderson disease. J. Mol. Med [print-electronic]. 2015 Feb; 93(2): 165-76. PMID: 25559265, PMCID: PMC4319984, DOI: 10.1007/s00109-014-1247-x, ISSN: 1432-1440.

Tanwar V, Bylund JB, Hu J, Yan J, Walthall JM, Mukherjee A, Heaton WH, Wang WD, Potet F, Rai M, Kupershmidt S, Knapik EW, Hatzopoulos AK. Gremlin 2 promotes differentiation of embryonic stem cells to atrial fate by activation of the JNK signaling pathway. Stem Cells. 2014 Jul; 32(7): 1774-88. PMID: 24648383, PMCID: PMC4123739, DOI: 10.1002/stem.1703, ISSN: 1549-4918.

Niu X, Hong J, Zheng X, Melville DB, Knapik EW, Meng A, Peng J. The nuclear pore complex function of Sec13 protein is required for cell survival during retinal development. J. Biol. Chem [print-electronic]. 2014 Apr 4/25/2014; 289(17): 11971-85. PMID: 24627485, PMCID: PMC4002104, PII: M114.547190, DOI: 10.1074/jbc.M114.547190, ISSN: 1083-351X.

Unlu G, Levic DS, Melville DB, Knapik EW. Trafficking mechanisms of extracellular matrix macromolecules: insights from vertebrate development and human diseases. Int. J. Biochem. Cell Biol [print-electronic]. 2014 Feb; 47: 57-67. PMID: 24333299, PMCID: PMC3915713, PII: S1357-2725(13)00343-9, DOI: 10.1016/j.biocel.2013.11.005, ISSN: 1878-5875.

Vacaru AM, Unlu G, Spitzner M, Mione M, Knapik EW, Sadler KC. In vivo cell biology in zebrafish - providing insights into vertebrate development and disease. J. Cell. Sci. 2014 Feb 2/1/2014; 127(Pt 3): 485-95. PMID: 24481493, PMCID: PMC4007761, PII: 127/3/485, DOI: 10.1242/jcs.140194, ISSN: 1477-9137.

Venkateswaran A, Sekhar KR, Levic DS, Melville DB, Clark TA, Rybski WM, Walsh AJ, Skala MC, Crooks PA, Knapik EW, Freeman ML. The NADH oxidase ENOX1, a critical mediator of endothelial cell radiosensitization, is crucial for vascular development. Cancer Res [print-electronic]. 2014 Jan 1/1/2014; 74(1): 38-43. PMID: 24247717, PMCID: PMC3947320, PII: 0008-5472.CAN-13-1981, DOI: 10.1158/0008-5472.CAN-13-1981, ISSN: 1538-7445.

Lee RT, Knapik EW, Thiery JP, Carney TJ. An exclusively mesodermal origin of fin mesenchyme demonstrates that zebrafish trunk neural crest does not generate ectomesenchyme. Development [print-electronic]. 2013 Jul; 140(14): 2923-32. PMID: 23739134, PMCID: PMC3699280, PII: dev.093534, DOI: 10.1242/dev.093534, ISSN: 1477-9129.

Müller II, Melville DB, Tanwar V, Rybski WM, Mukherjee A, Shoemaker MB, Wang WD, Schoenhard JA, Roden DM, Darbar D, Knapik EW, Hatzopoulos AK. Functional modeling in zebrafish demonstrates that the atrial-fibrillation-associated gene GREM2 regulates cardiac laterality, cardiomyocyte differentiation and atrial rhythm. Dis Model Mech [print-electronic]. 2013 Mar; 6(2): 332-41. PMID: 23223679, PMCID: PMC3597016, PII: dmm.010488, DOI: 10.1242/dmm.010488, ISSN: 1754-8411.

Wang WD, Melville DB, Montero-Balaguer M, Hatzopoulos AK, Knapik EW. Tfap2a and Foxd3 regulate early steps in the development of the neural crest progenitor population. Dev. Biol [print-electronic]. 2011 Dec 12/1/2011; 360(1): 173-85. PMID: 21963426, PMCID: PMC3236700, PII: S0012-1606(11)01263-2, DOI: 10.1016/j.ydbio.2011.09.019, ISSN: 1095-564X.

Melville DB, Montero-Balaguer M, Levic DS, Bradley K, Smith JR, Hatzopoulos AK, Knapik EW. The feelgood mutation in zebrafish dysregulates COPII-dependent secretion of select extracellular matrix proteins in skeletal morphogenesis. Dis Model Mech [print-electronic]. 2011 Nov; 4(6): 763-76. PMID: 21729877, PMCID: PMC3209646, PII: dmm.007625, DOI: 10.1242/dmm.007625, ISSN: 1754-8411.

Eames BF, Yan YL, Swartz ME, Levic DS, Knapik EW, Postlethwait JH, Kimmel CB. Mutations in fam20b and xylt1 reveal that cartilage matrix controls timing of endochondral ossification by inhibiting chondrocyte maturation. PLoS Genet [print-electronic]. 2011 Aug; 7(8): e1002246. PMID: 21901110, PMCID: PMC3161922, PII: PGENETICS-D-11-00175, DOI: 10.1371/journal.pgen.1002246, ISSN: 1553-7404.

Liu D, Wang WD, Melville DB, Cha YI, Yin Z, Issaeva N, Knapik EW, Yarbrough WG. Tumor suppressor Lzap regulates cell cycle progression, doming, and zebrafish epiboly. Dev. Dyn [print-electronic]. 2011 Jun; 240(6): 1613-25. PMID: 21523853, PMCID: PMC3287344, DOI: 10.1002/dvdy.22644, ISSN: 1097-0177.

Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR. An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci. G3 (Bethesda). 2011 Jun 6/1/2011; 1(1): 3-9. PMID: 21949597, PMCID: PMC3178105, DOI: 10.1534/g3.111.000190, ISSN: 2160-1836.

Melville DB, Knapik EW. Traffic jams in fish bones: ER-to-Golgi protein transport during zebrafish development. Cell Adh Migr [print-electronic]. 2011 Mar; 5(2): 114-8. PMID: 21178403, PMCID: PMC3084976, PII: 14377, ISSN: 1933-6926.

Sarmah S, Barrallo-Gimeno A, Melville DB, Topczewski J, Solnica-Krezel L, Knapik EW. Sec24D-dependent transport of extracellular matrix proteins is required for zebrafish skeletal morphogenesis. PLoS ONE. 2010; 5(4): e10367. PMID: 20442775, PMCID: PMC2860987, DOI: 10.1371/journal.pone.0010367, ISSN: 1932-6203.

Kucenas S, Wang WD, Knapik EW, Appel B. A selective glial barrier at motor axon exit points prevents oligodendrocyte migration from the spinal cord. J. Neurosci. 2009 Dec 12/2/2009; 29(48): 15187-94. PMID: 19955371, PMCID: PMC2837368, PII: 29/48/15187, DOI: 10.1523/JNEUROSCI.4193-09.2009, ISSN: 1529-2401.

Granero-Moltó F, Sarmah S, O'Rear L, Spagnoli A, Abrahamson D, Saus J, Hudson BG, Knapik EW. Goodpasture antigen-binding protein and its spliced variant, ceramide transfer protein, have different functions in the modulation of apoptosis during zebrafish development. J. Biol. Chem [print-electronic]. 2008 Jul 7/18/2008; 283(29): 20495-504. PMID: 18424781, PMCID: PMC2459293, PII: M801806200, DOI: 10.1074/jbc.M801806200, ISSN: 0021-9258.

Bradley KM, Elmore JB, Breyer JP, Yaspan BL, Jessen JR, Knapik EW, Smith JR. A major zebrafish polymorphism resource for genetic mapping. Genome Biol. 2007; 8(4): R55. PMID: 17428331, PMCID: PMC1896001, PII: gb-2007-8-4-r55, DOI: 10.1186/gb-2007-8-4-r55, ISSN: 1474-760X.

Montero-Balaguer M, Lang MR, Sachdev SW, Knappmeyer C, Stewart RA, De La Guardia A, Hatzopoulos AK, Knapik EW. The mother superior mutation ablates foxd3 activity in neural crest progenitor cells and depletes neural crest derivatives in zebrafish. Dev. Dyn. 2006 Dec; 235(12): 3199-212. PMID: 17013879, DOI: 10.1002/dvdy.20959, ISSN: 1058-8388.

Lang MR, Lapierre LA, Frotscher M, Goldenring JR, Knapik EW. Secretory COPII coat component Sec23a is essential for craniofacial chondrocyte maturation. Nat. Genet [print-electronic]. 2006 Oct; 38(10): 1198-203. PMID: 16980978, PII: ng1880, DOI: 10.1038/ng1880, ISSN: 1061-4036.

Müller II, Knapik EW, Hatzopoulos AK. Expression of the protein related to Dan and Cerberus gene--prdc--During eye, pharyngeal arch, somite, and swim bladder development in zebrafish. Dev. Dyn. 2006 Oct; 235(10): 2881-8. PMID: 16921498, DOI: 10.1002/dvdy.20925, ISSN: 1058-8388.

Barrallo-Gimeno A, Holzschuh J, Driever W, Knapik EW. Neural crest survival and differentiation in zebrafish depends on mont blanc/tfap2a gene function. Development [print-electronic]. 2004 Apr; 131(7): 1463-77. PMID: 14985255, PII: dev.01033, DOI: 10.1242/dev.01033, ISSN: 0950-1991.

Holzschuh J, Barrallo-Gimeno A, Ettl AK, Durr K, Knapik EW, Driever W. Noradrenergic neurons in the zebrafish hindbrain are induced by retinoic acid and require tfap2a for expression of the neurotransmitter phenotype. Development [print-electronic]. 2003 Dec; 130(23): 5741-54. PMID: 14534139, PII: dev.00816, DOI: 10.1242/dev.00816, ISSN: 0950-1991.

Dethleffsen K, Heinrich G, Lauth M, Knapik EW, Meyer M. Insert-containing neurotrophins in teleost fish and their relationship to nerve growth factor. Mol. Cell. Neurosci. 2003 Oct; 24(2): 380-94. PMID: 14572460, PII: S1044743103001957, ISSN: 1044-7431.

Sachdev SW, Dietz UH, Oshima Y, Lang MR, Knapik EW, Hiraki Y, Shukunami C. Sequence analysis of zebrafish chondromodulin-1 and expression profile in the notochord and chondrogenic regions during cartilage morphogenesis. Mech. Dev. 2001 Jul; 105(1-2): 157-62. PMID: 11429291, PII: S0925477301004178, ISSN: 0925-4773.

Knapik EW. ENU mutagenesis in zebrafish--from genes to complex diseases. Mamm. Genome. 2000 Jul; 11(7): 511-9. PMID: 10886014, PII: 10.1007/s003350010098, ISSN: 0938-8990.

Chevrette M, Joly L, Tellis P, Knapik EW, Miles J, Fishman M, Ekker M. Characterization of a zebrafish/mouse somatic cell hybrid panel. Genomics. 2000 Feb 2/15/2000; 64(1): 119-26. PMID: 10708527, PII: S0888-7543(99)96124-4, DOI: 10.1006/geno.1999.6124, ISSN: 0888-7543.

Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson D, de Sauvage F, Jacob H, Fishman MC. Zebrafish genetic map with 2000 microsatellite markers. Genomics. 1999 Jun 6/15/1999; 58(3): 219-32. PMID: 10373319, PII: S0888-7543(99)95824-X, DOI: 10.1006/geno.1999.5824, ISSN: 0888-7543.

Förnzler D, Her H, Knapik EW, Clark M, Lehrach H, Postlethwait JH, Zon LI, Beier DR. Gene mapping in zebrafish using single-strand conformation polymorphism analysis. Genomics. 1998 Jul 7/15/1998; 51(2): 216-22. PMID: 9722944, PII: S0888-7543(98)95386-1, DOI: 10.1006/geno.1998.5386, ISSN: 0888-7543.

Knapik EW, Goodman A, Ekker M, Chevrette M, Delgado J, Neuhauss S, Shimoda N, Driever W, Fishman MC, Jacob HJ. A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat. Genet. 1998 Apr; 18(4): 338-43. PMID: 9537415, DOI: 10.1038/ng0498-338, ISSN: 1061-4036.

Postlethwait JH, Yan YL, Gates MA, Horne S, Amores A, Brownlie A, Donovan A, Egan ES, Force A, Gong Z, Goutel C, Fritz A, Kelsh R, Knapik E, Liao E, Paw B, Ransom D, Singer A, Thomson M, Abduljabbar TS, Yelick P, Beier D, Joly JS, Larhammar D, Rosa F, Westerfield M, Zon LI, Johnson SL, Talbot WS. Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 1998 Apr; 18(4): 345-9. PMID: 9537416, DOI: 10.1038/ng0498-345, ISSN: 1061-4036.

Knapik EW, Goodman A, Atkinson OS, Roberts CT, Shiozawa M, Sim CU, Weksler-Zangen S, Trolliet MR, Futrell C, Innes BA, Koike G, McLaughlin MG, Pierre L, Simon JS, Vilallonga E, Roy M, Chiang PW, Fishman MC, Driever W, Jacob HJ. A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development. 1996 Dec; 123: 451-60. PMID: 9007262, ISSN: 0950-1991.

Neuman T, Keen A, Knapik E, Shain D, Ross M, Nornes HO, Zuber MX. ME1 and GE1: basic helix-loop-helix transcription factors expressed at high levels in the developing nervous system and in morphogenetically active regions. Eur. J. Neurosci. 1993 Apr 4/1/1993; 5(4): 311-8. PMID: 8261111, ISSN: 0953-816X.

Nornes HO, Dressler GR, Knapik EW, Deutsch U, Gruss P. Spatially and temporally restricted expression of Pax2 during murine neurogenesis. Development. 1990 Aug; 109(4): 797-809. PMID: 1977575, ISSN: 0950-1991.