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"Consensus guidelines for the use and interpretation of angiogenesis assays" with MO discussion

"Consensus guidelines for the use and interpretation of angiogenesis assays" contains a very good discussion of Morpholinos and specificity. Nowak-Sliwinska et al. extensively cite the Stainier et al. "Guidelines for Morpholino Use in Zebrafish". There is a theme in the Morpholino discussion in Nowak-Sliwinska et al.'s paper with which I disagree. They state "However, the best and generally accepted validation for any MO phenotype is confirmation of the same phenotype in a zebrafish genetic mutant." [1] Is this best, or does it exclude a valuable function of Morpholinos? Following Stainier et al., I advocate that performing a specificity control by using a targeting Morpholino in a null background for the same transcript is a better validation for the MO. In a mutant undergoing compensatory changes in gene expression, Morpholinos checked with that method which produce no additional observed effects (in a compensated background) might present with more extreme phenotypes when used in a wild-type background (in the absence of compensation) and reveal useful information about gene function which is obscured in the mutants. Later in their discussion Nowak-Sliwinska et al. do address the utility of morphants whose phenotypes diverge from their corresponding mutants:

"Fourth, recent work has shown that upregulation of related compensating gene family members can sometimes occur in genetic mutants (by mechanisms that are not yet clear), while this does not appear to take place in MOs-injected animals [277], arguably making MOs a better representation of targeted loss of gene function in these cases."

To accept that a Morpholino might be producing accurate transcript-specific information even when mutant and morphant phenotypes differ, a rigorous specificity control is needed. Stainier et al. write: "A decisive approach to determine the optimal sequence and dose of a MO that does not cause off-target effects is to inject the MO into embryos whose genome (and whose mother’s genome, for maternally expressed genes) has been edited so as to eliminate the MO-binding site or to eliminate the function of the target gene" [2]. Using this specificity control allows application of Morpholinos to probe gene functions which are concealed by compensation in some mutants. I argue it is a better validation than observing agreement of mutant and morphant phenotypes because it is applicable to a broader range of genes.

[1] Nowak-Sliwinska P, Alitalo K, Allen E, Anisimov A, Aplin AC, Auerbach R, Augustin HG, Bates DO, van Beijnum JR, Bender RHF, Bergers G, Bikfalvi A, Bischoff J, Böck BC, Brooks PC, Bussolino F, Cakir B, Carmeliet P, Castranova D, Cimpean AM, Cleaver O, Coukos G, Davis GE, De Palma M, Dimberg A, Dings RPM, Djonov V, Dudley AC, Dufton NP, Fendt SM, Ferrara N, Fruttiger M, Fukumura D, Ghesquière B, Gong Y, Griffin RJ, Harris AL, Hughes CCW, Hultgren NW, Iruela-Arispe ML, Irving M, Jain RK, Kalluri R, Kalucka J, Kerbel RS, Kitajewski J, Klaassen I, Kleinmann HK, Koolwijk P, Kuczynski E, Kwak BR, Marien K, Melero-Martin JM, Munn LL, Nicosia RF, Noel A, Nurro J, Olsson AK, Petrova TV, Pietras K, Pili R, Pollard JW, Post MJ, Quax PHA, Rabinovich GA, Raica M, Randi AM, Ribatti D, Ruegg C, Schlingemann RO, Schulte-Merker S, Smith LEH, Song JW, Stacker SA, Stalin J, Stratman AN, Van de Velde M, van Hinsbergh VWM, Vermeulen PB, Waltenberger J, Weinstein BM, Xin H, Yetkin-Arik B, Yla-Herttuala S, Yoder MC, Griffioen AW.
Consensus guidelines for the use and interpretation of angiogenesis assays.
Angiogenesis. 2018 May 15. doi: 10.1007/s10456-018-9613-x. [Epub ahead of print] Review.

[2] Stainier DYR, Raz E, Lawson ND, Ekker SC, Burdine RD, Eisen JS, Ingham PW, Schulte-Merker S, Yelon D, Weinstein BM, Mullins MC, Wilson SW, Ramakrishnan L, Amacher SL, Neuhauss SCF, Meng A, Mochizuki N, Panula P, Moens CB. Guidelines for morpholino use in zebrafish. PLoS Genet. 2017 Oct 19;13(10):e1007000. doi: 10.1371/journal.pgen.1007000. eCollection 2017 Oct.

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