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Publications (10 of 12) Show all publications
Leyhr, J., Waldmann, L., Filipek-Górniok, B., Zhang, H., Allalou, A. & Haitina, T. (2022). A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint. eLIFE, 11, Article ID e75749.
Open this publication in new window or tab >>A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
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2022 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 11, article id e75749Article in journal (Refereed) Published
Abstract [en]

The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of nkx3.2 and leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.

Place, publisher, year, edition, pages
eLife Sciences Publications LtdeLife Sciences Publications, 2022
National Category
Developmental Biology
Identifiers
urn:nbn:se:uu:diva-493106 (URN)10.7554/elife.75749 (DOI)000961591300001 ()36377467 (PubMedID)
Funder
Swedish Research Council, 621-2012-4673Science for Life Laboratory, SciLifeLab, Development Project 2017Science for Life Laboratory, SciLifeLab, Technology Development grant 2018
Available from: 2023-01-12 Created: 2023-01-12 Last updated: 2024-01-15Bibliographically approved
Habicher, J., Varshney, G. K., Waldmann, L., Snitting, D., Allalou, A., Zhang, H., . . . Ledin, J. (2022). Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development. PLOS Genetics, 18(2), Article ID e1010067.
Open this publication in new window or tab >>Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development
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2022 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 18, no 2, article id e1010067Article in journal (Refereed) Published
Abstract [en]

Chondroitin/dermatan sulfate (CS/DS) proteoglycans are indispensable for animal development and homeostasis but the large number of enzymes involved in their biosynthesis have made CS/DS function a challenging problem to study genetically. In our study, we generated loss-of-function alleles in zebrafish genes encoding CS/DS biosynthetic enzymes and characterized the effect on development in single and double mutants. Homozygous mutants in chsy1, csgalnact1a, csgalnat2, chpfa, ust and chst7, respectively, develop to adults. However, csgalnact1a-/- fish develop distinct craniofacial defects while the chsy1-/- skeletal phenotype is milder and the remaining mutants display no gross morphological abnormalities. These results suggest a high redundancy for the CS/DS biosynthetic enzymes and to further reduce CS/DS biosynthesis we combined mutant alleles. The craniofacial phenotype is further enhanced in csgalnact1a-/-;chsy1-/- adults and csgalnact1a-/-;csgalnact2-/- larvae. While csgalnact1a-/-;csgalnact2-/- was the most affected allele combination in our study, CS/DS is still not completely abolished. Transcriptome analysis of chsy1-/-, csgalnact1a-/- and csgalnact1a-/-;csgalnact2-/- larvae revealed that the expression had changed in a similar way in the three mutant lines but no differential expression was found in any of fifty GAG biosynthesis enzymes identified. Thus, zebrafish larvae do not increase transcription of GAG biosynthesis genes as a consequence of decreased CS/DS biosynthesis. The new zebrafish lines develop phenotypes similar to clinical characteristics of several human congenital disorders making the mutants potentially useful to study disease mechanisms and treatment.

Place, publisher, year, edition, pages
Public Library of Science (PLoS), 2022
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-473635 (URN)10.1371/journal.pgen.1010067 (DOI)001004241700001 ()35192612 (PubMedID)
Funder
Science for Life Laboratory, SciLifeLab
Note

Correction in: The PLOS Genetics, vol. 18, issue 5, Article no e1010242.

DOI: 10.1371/journal.pgen.1010242

Available from: 2022-04-29 Created: 2022-04-29 Last updated: 2023-10-10Bibliographically approved
Waldmann, L., Leyhr, J., Zhang, H., Allalou, A., Öhman, C. & Haitina, T. (2022). The Role of Gdf5 in the Development of the Zebrafish Fin Endoskeleton. Developmental Dynamics, 251(9), 1535-1549
Open this publication in new window or tab >>The Role of Gdf5 in the Development of the Zebrafish Fin Endoskeleton
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2022 (English)In: Developmental Dynamics, ISSN 1058-8388, E-ISSN 1097-0177, Vol. 251, no 9, p. 1535-1549Article in journal (Refereed) Published
Abstract [en]

The development of the vertebrate skeleton requires a complex interaction of multiple factors to facilitate correct shaping and positioning of bones and joints. Growth and differentiation factor 5 (Gdf5), a member of the transforming growth factor-beta family (TGF-beta) is involved in patterning appendicular skeletal elements including joints. Expression of gdf5 in zebrafish has been detected within the first pharyngeal arch jaw joint, fin mesenchyme condensations and segmentation zones in median fins, however little is known about the functional role of Gdf5 outside of Amniota. 

We generated CRISPR/Cas9 knockout of gdf5 in zebrafish and analysed the resulting phenotype at different developmental stages. Homozygous gdf5 mutant zebrafish display truncated median fin endoskeletal elements and loss of posterior radials in the pectoral fins. 

These findings are consistent with phenotypes observed in human and mouse appendicular skeleton in response to Gdf5 knockout, suggesting a broadly conserved role for Gdf5 in Osteichthyes.

Place, publisher, year, edition, pages
John Wiley & SonsWiley, 2022
Keywords
gdf5, fin, joints, zebrafish, appendicular skeleton, CRISPR/Cas9 mutant
National Category
Developmental Biology
Identifiers
urn:nbn:se:uu:diva-430383 (URN)10.1002/dvdy.399 (DOI)000678743100001 ()
Funder
Swedish Research Council, 621-2012-4673Science for Life Laboratory, SciLifeLab
Available from: 2021-01-08 Created: 2021-01-08 Last updated: 2024-05-07Bibliographically approved
Zhang, H., Weström, S., Kappelin, P., Virtanen, M., Vahlquist, A. & Törmä, H. (2021). Exploration of novel candidate genes involved in epidermal keratinocyte differentiation and skin barrier repair in man. Differentiation, 119, 19-27
Open this publication in new window or tab >>Exploration of novel candidate genes involved in epidermal keratinocyte differentiation and skin barrier repair in man
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2021 (English)In: Differentiation, ISSN 0301-4681, E-ISSN 1432-0436, Vol. 119, p. 19-27Article in journal (Refereed) Published
Abstract [en]

A proper skin barrier function requires constant formation of stratum corneum, i.e. the outermost layer of epidermis composed of terminally differentiated keratinocytes. The complex process of converting proliferative basal keratinocytes into corneocytes relies on programmed changes in the activity of many well-established genes. Much remains however to be investigated about this process, e.g. in conjunction with epidermal barrier defects due to genetic errors as in ichthyosis. To this end, we re-analyzed two sets of microarray-data comparing altered gene expression in differentiated vs. proliferating keratinocytes and in the skin of patients with autosomal recessive congenital ichthyosis (ARCI) vs. healthy controls, respectively. We thus identified 24 genes to be upregulated in both sets of array and not previously associated with keratinocyte differentiation. For 10 of these genes (AKR1B10, BLNK, ENDOU, GCNT4, GLTP, RHCG, SLC15A1, TMEM45B, TMEM86A and VSNL1), qPCR analysis confirmed the array results and subsequent immunostainings of normal epidermis showed superficial expression of several of the proteins. Furthermore, induction of keratinocyte differentiation using phorbol esters (PMA) resulted in increased expression of eight of the genes, whereas siRNA silencing of PPAR delta, a transcription factor supporting differentiation, had the opposite effect. In summary, our results identify ten new candidate genes seemingly involved in human epidermal keratinocyte differentiation and possibly important for epidermal repair in a genetic skin disease characterized by barrier failure.

Place, publisher, year, edition, pages
ElsevierELSEVIER SCI LTD, 2021
Keywords
Biomarker, Epidermis, Ichthyosis, Genodermatoses, Oligoarray, Skin barrier repair
National Category
Dermatology and Venereal Diseases Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-446844 (URN)10.1016/j.diff.2021.04.001 (DOI)000657533300003 ()34029921 (PubMedID)
Available from: 2021-08-06 Created: 2021-08-06 Last updated: 2024-01-15Bibliographically approved
Waldmann, L., Leyhr, J., Zhang, H., Öhman, C., Allalou, A. & Haitina, T. (2021). The broad role of Nkx3.2 in the development of the zebrafish axial skeleton. PLOS ONE, 16(8), Article ID e0255953.
Open this publication in new window or tab >>The broad role of Nkx3.2 in the development of the zebrafish axial skeleton
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2021 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 16, no 8, article id e0255953Article in journal (Refereed) Published
Abstract [en]

The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. Previous Nkx3.2 knockdown and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while the function of this gene in broader skeletal development is not fully described. We generated a mutant allele of nkx3.2 in zebrafish with CRISPR/Cas9 and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing loss of the jaw joint, fusions in bones of the occiput, morphological changes in the Weberian apparatus, and the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae. Axial phenotypes are reminiscent of Nkx3.2 knockout in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role of nkx3.2 in zebrafish skeletal development and its context-specific functions in different skeletal elements.

Place, publisher, year, edition, pages
Public Library of Science (PLoS)Public Library of Science (PLoS), 2021
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-455491 (URN)10.1371/journal.pone.0255953 (DOI)000686373300086 ()34411150 (PubMedID)
Funder
Swedish Research Council, 621-2012-4673
Available from: 2021-10-18 Created: 2021-10-18 Last updated: 2024-01-15Bibliographically approved
del Pozo, A., Manuel, R., Iglesias Gonzalez, A. B., Koning, H. K., Habicher, J., Zhang, H., . . . Boije, H. (2020). Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration. eNeuro, 7(3), Article ID 0047-20.2020.
Open this publication in new window or tab >>Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration
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2020 (English)In: eNeuro, E-ISSN 2373-2822, Vol. 7, no 3, article id 0047-20.2020Article in journal (Refereed) Published
Abstract [en]

Vertebrate locomotion is orchestrated by spinal interneurons making up a central pattern generator. Proper coordination of activity, both within and between segments, is required to generate the desired locomotor output. This coordination is altered during acceleration to ensure the correct recruitment of muscles for the chosen speed. The transcription factor Dmrt3 has been proposed to shape the patterned output at different gaits in horses and mice. Here, we characterized dmrt3a mutant zebrafish, which showed a strong, transient, locomotor phenotype in developing larvae. During beat-and-glide swimming, mutant larvae showed fewer and shorter movements with decreased velocity and acceleration. Developmental compensation likely occurs as the analyzed behaviors did not differ from wild-type at older larval stages. However, analysis of maximum swim speed in juveniles suggests that some defects persist within the mature locomotor network of dmrt3a mutants. Our results reveal the pivotal role Dmrt3 neurons play in shaping the patterned output during acceleration in vertebrates.

Keywords
central pattern generator, Danio rerio, gait, locomotion, spinal cord, wt1
National Category
Developmental Biology
Identifiers
urn:nbn:se:uu:diva-424650 (URN)10.1523/ENEURO.0047-20.2020 (DOI)000571515500007 ()32357958 (PubMedID)
Funder
Swedish Research Council
Available from: 2020-11-09 Created: 2020-11-09 Last updated: 2023-10-09Bibliographically approved
Zhang, H., Waldmann, L., Manuel, R., Boije, H., Haitina, T. & Allalou, A. (2020). zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging. Biomedical Optics Express, 11(8), 4290-4305
Open this publication in new window or tab >>zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging
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2020 (English)In: Biomedical Optics Express, E-ISSN 2156-7085, Vol. 11, no 8, p. 4290-4305Article in journal (Refereed) Published
Abstract [en]

Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism.

Place, publisher, year, edition, pages
The Optical Society, 2020
National Category
Medical Image Processing
Identifiers
urn:nbn:se:uu:diva-419799 (URN)10.1364/BOE.393519 (DOI)000577451600016 ()32923043 (PubMedID)
Funder
Science for Life Laboratory, SciLifeLab
Available from: 2020-09-16 Created: 2020-09-16 Last updated: 2023-02-17Bibliographically approved
Waldmann, L., Leyhr, J., Filipek-Gorniok, B., Zhang, H., Allalou, A. & Haitina, T.An evolutionarily conserved cis-regulatory element of nkx3.2 drives jaw joint-specific expression in zebrafish.
Open this publication in new window or tab >>An evolutionarily conserved cis-regulatory element of nkx3.2 drives jaw joint-specific expression in zebrafish
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(English)Manuscript (preprint) (Other academic)
National Category
Developmental Biology
Identifiers
urn:nbn:se:uu:diva-430423 (URN)
Funder
Swedish Research Council, 621-2012-4673
Available from: 2021-01-10 Created: 2021-01-10 Last updated: 2023-01-09Bibliographically approved
Mazzaferro, E., Zhang, H., Mujica, E., Azizah, I., Loos, R. J. F., Larsson, A., . . . den Hoed, M.Characterizing candidate genes in GWAS-identified loci that may uncouple excess adiposity from its comorbidities.
Open this publication in new window or tab >>Characterizing candidate genes in GWAS-identified loci that may uncouple excess adiposity from its comorbidities
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(English)Manuscript (preprint) (Other academic)
National Category
Medical Genetics
Research subject
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-488860 (URN)
Available from: 2022-11-22 Created: 2022-11-22 Last updated: 2022-12-02Bibliographically approved
Mazzaferro, E., Mujica, E., Zhang, H., Emmanouilidou, A., Jenseit, A., Loos, R. J. F., . . . den Hoed, M.Characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.
Open this publication in new window or tab >>Characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning
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(English)Manuscript (preprint) (Other academic)
National Category
Medical Genetics
Research subject
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-488857 (URN)
Available from: 2022-11-22 Created: 2022-11-22 Last updated: 2022-11-29Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1746-5157

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