
==== Front
Am J Respir Cell Mol Biol
Am J Respir Cell Mol Biol
ajrcmb
American Journal of Respiratory Cell and Molecular Biology
1044-1549
1535-4989
American Thoracic Society

38696272
2024-0166ED
10.1165/rcmb.2024-0166ED
Editorials
Long Story Short: Understanding Isoform-Specific Expression of FAM13A
McDonald Cera A.
Langlois Ryan A.
Department of Microbiology and Immunology
University of Minnesota
Minneapolis, Minnesota
2 5 2024
1 9 2024
2 5 2024
71 3 257258
Copyright © 2024 by the American Thoracic Society
2024
https://creativecommons.org/licenses/by-nc-nd/4.0/ This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0. For commercial usage and reprints, please e-mail Diane Gern.
==== Body
pmcMulticiliated cells maintain the flow of pulmonary mucus through the coordinated beating of cilia (1). When mucociliary clearance is impaired, pathogens and environmental contaminants may linger or accumulate in the lung, increasing the risk of infection (2) and the development of diseases such as chronic obstructive pulmonary disease (COPD) (3). In this issue of the Journal, Howes and colleagues (pp. 282–293) provide the first report investigating the expression and potential function of the COPD-associated risk gene FAM13A (Family with Sequence Similarity 13 Member A) long isoform in the multiciliary cells of humans and Xenopus laevis (4). Given the increasing disease burden of COPD globally (5), it is of particular importance to investigate the mechanisms by which COPD-associated genes contribute to pulmonary cell function and health.

Howes and colleagues first compare isoform-specific conservation of the FAM13A gene across model animal species. FAM13A is most broadly studied in the context of the lung, based on SNPs within the gene and their strong correlation with COPD and other respiratory diseases (6). There are also a number of studies using human adipose tissue (7–9). Howes and colleagues found that although mice exclusively express the truncated, short isoform of the gene, both human and Xenopus encode for a RhoGAP-containing long isoform. They also tested and confirmed the GAP (GTPase activating protein) activity of the human long isoform by overexpressing in 293T cells and measuring a subsequent reduction in active amounts of RhoA, a GTPase associated with actin cytoskeletal rearrangement and stress fiber formation (9).

Promoter activity analysis performed to compare isoform-specific expression in silico using the Functional Annotation of Mammalian Genome 5 (FANTOM5) project promoter expression atlas (10) indicates that the long FAM13A isoform is preferentially expressed within specific cell types in the airway. To experimentally test this, they used a primary human pulmonary cell culture model in which primary human bronchial epithelial cells (hBECs) are grown and differentiated at ALI (air–liquid interface), resulting in a diverse primary cell culture characterized by air–liquid contact and mucus production (11). After differentiation, they analyzed the mature epithelial cells with a novel flow cytometry panel to distinguish basal, secretory, and multiciliated cell types based on surface marker expression. Although both short and long isoforms of FAM13A were expressed broadly in the differentiating cells of the ALI culture, CD133+CD66a/c/e− multiciliated cells preferentially expressed the long isoform of the gene.

This work underscores the necessity of using isoform-specific models for functional gene studies. Mouse models are routinely used to investigate the contribution of Fam13a to pulmonary cell function and disease, although the current study shows that the short isoform lacking the RhoGAP domain is expressed exclusively. This work adds to a growing body of literature demonstrating that tissue- and cell-line–specific expression of gene isoforms have critical roles in organismal biology (12, 13), further supporting the investigation of isoform-specific expression as a means of more completely understanding transcription and regulation in a given cell type.

To investigate whether the long isoform of FAM13A contributes to the differentiation or function of multiciliated cells, Howes and colleagues knocked down the long isoform in both hBEC ALI culture and in Xenopus embryos. These models are routinely used to study ciliary function in the context of human airway diseases as they are decorated externally in multiciliated cells, which form an easily observable mucociliary epidermis (14). Although knockdown of the long isoform of FAM13A in hBECs and the conserved Fam13a gene in Xenopus embryos did not affect the ability of the cells to differentiate toward multiciliated cell fate, knockdown of the gene did impair cilia function in both models. In Xenopus embryos, fluorescent beads traveled more slowly across the surface of the external multiciliated cells on Fam13a knockdown embryos relative to controls, whereas the gentle drifting movement typically observed in the wild-type embryos attributed to the multiciliated cells was lost. Complementing this result, FAM13A knockdown in hBECs resulted in measurably decreased cilia activity, moving area, and coordinated movement.

Howes and colleagues suggest that the long isoform of FAM13A is required for ciliary coordination, as reduction of the gene’s expression in the knockdown studies resulted in impaired ciliary movement in both hBEC ALI culture and in Xenopus embryos. In this model (Figure 1), the RhoGAP domain identified in the long isoform of FAM13A may regulate actin organization at the base of the cilia. One limitation to this theory, acknowledged by the authors, is that ciliogenesis did not seem to be impaired in either knockdown model, even though actin is strongly associated with both ciliary assembly and disassembly (15). However, other reports have shown that FAM13A knockout has resulted in nonciliary actin cytoskeleton remodeling in non–small cell lung cancer cells (16) and in A549 lung cancer cells (17). These findings indicate that FAM13A influences actin cytoskeletal dynamics beyond the scope of ciliogenesis. An additional limitation of this work is that mice lacking the long isoform of Fam13a do not experience the decreased ciliary function that was observed in the knockdown human and Xenopus cells. Future studies should investigate the specific mechanism by which FAM13A interacts with the actin cytoskeleton in the context of mucociliary movement, as well as how mouse cells are able to compensate for the absence of the long isoform.

Figure 1. Under wild-type conditions (left), the beating of cilia generates a current in the pulmonary mucus, clearing environmental contaminants from the lungs. In the model proposed by Howes and colleagues (right), FAM13A knockdown disrupts the actin cytoskeleton supporting the base of the cilia, resulting in impaired beating and the slower clearance or accumulation of environmental contaminants in the mucus and potentially contributing to the onset of chronic obstructive pulmonary disease.

As the global burden of COPD grows, it becomes increasingly important to understand the mechanisms behind both the disease and its associated genetic risk factors. Although it is currently incompletely understood why SNPs in FAM13A are risk alleles for COPD, this work by Howes and colleagues demonstrates that FAM13A is required for ciliary coordination and builds on previously published work demonstrating a link between the gene and actin cytoskeletal regulation. Furthermore, this work identifies for the first time the cell type–specific isoform expression of FAM13A and should inspire future investigation into how isoform expression may affect not only the function of a cell type of interest but also the localization and behavior of a risk gene during pathologies. Finally, this study identifies important avenues of future investigation, such as the effect of known FAM13A SNPs on ciliary function, the mechanism by which FAM13A regulates actin in multiciliary cells, and the effect of actin misregulation in mucociliary clearance.

Originally Published in Press as DOI: 10.1165/rcmb.2024-0166ED on May 2, 2024

Author disclosures are available with the text of this article at www.atsjournals.org.
==== Refs
References

1. Bustamante-Marin XM Ostrowski LE Cilia and mucociliary clearance Cold Spring Harb Perspect Biol 2017 9 a028241 27864314
2. Tilley AE Walters MS Shaykhiev R Crystal RG Cilia dysfunction in lung disease Annu Rev Physiol 2015 77 379 406 25386990
3. Yaghi A Dolovich MB Airway epithelial cell cilia and obstructive lung disease Cells 2016 5 40 27845721
4. Howes A Rogerson C Belyaev N Karagyozova T Rapiteanuet R Fradique R et al. The FAM13A long isoform regulates cilia movement and coordination in airway mucociliary transport Am J Repir Cell Mol Biol 2024 71 282 293
5. Hurst JR Siddharthan T Global burden of COPD Haring R Kickbusch I Ganten D Moeti M Handbook of global health Cham, Switzerland Springer International Publishing 2020 1 20
6. Kim WJ Lee SD Candidate genes for COPD: current evidence and research Int J Chron Obstruct Pulmon Dis 2015 10 2249 2255 26527870
7. Fathzadeh M Li J Rao A Cook N Chennamsetty I Seldin M et al. FAM13A affects body fat distribution and adipocyte function Nat Commun 2020 11 1465 32193374
8. Tang J Zhou H Sahay K Xu W Yang J Zhang W et al. Obesity-associated family with sequence similarity 13, member A (FAM13A) is dispensable for adipose development and insulin sensitivity Int J Obes 2019 43 1269 1280
9. Wardhana DA Ikeda K Barinda AJ Nugroho DB Qurania KR Yagi K et al. Family with sequence similarity 13, member A modulates adipocyte insulin signaling and preserves systemic metabolic homeostasis Proc Natl Acad Sci USA 2018 115 1529 1534 29386390
10. Forrest ARR Kawaji H Rehli M Baillie JK de Hoon MJL Haberle V et al. FANTOM Consortium and the RIKEN PMI and CLST (DGT) A promoter-level mammalian expression atlas Nature 2014 507 462 470 24670764
11. Silva S Bicker J Falcão A Fortuna A Air-liquid interface (ALI) impact on different respiratory cell cultures Eur J Pharm Biopharm 2023 184 62 82 36696943
12. Wang C Shi Z Huang Q Liu R Su D Chang L et al. Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development PLoS Biol 2024 22 e3002505 38363809
13. Booeshaghi AS Yao Z van Velthoven C Smith K Tasic B Zeng H et al. Isoform cell-type specificity in the mouse primary motor cortex Nature 2021 598 195 199 34616073
14. Walentek P Quigley IK What we can learn from a tadpole about ciliopathies and airway diseases: using systems biology in Xenopus to study cilia and mucociliary epithelia Genesis 2017 55 10.1002/dvg.23001
15. Hoffman HK Prekeris R Roles of the actin cytoskeleton in ciliogenesis J Cell Sci 2022 135 jcs259030 35575063
16. Ziółkowska-Suchanek I Podralska M Żurawek M Łaczmańska J Iżykowska K Dzikiewicz-Krawczyk A et al. Hypoxia-induced FAM13A regulates the proliferation and metastasis of non-small cell lung cancer cells Int J Mol Sci 2021 22 4302 33919074
17. Corvol H Rousselet N Thompson KE Berdah L Cottin G Foussigniere T et al. FAM13A is a modifier gene of cystic fibrosis lung phenotype regulating rhoa activity, actin cytoskeleton dynamics and epithelial-mesenchymal transition J Cyst Fibros 2018 17 190 203 29239766
