Shaping human brain development and vulnerability through alternative splicing
Authors: Francisco Aya, Juan Valcárcel
Journal: Cell Genomics (2024)

Alternative splicing contributes to shaping lineage-specific gene expression and phenotypes. In this issue of Cell Genomics, Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar report that the balance between splicing isoforms of the microtubule-associated protein Tau in the brain is differentially regulated among primates by the RNA-binding protein MBNL2, with consequences for protein aggregation and neurodegeneration in humans. Alternative splicing contributes to shaping lineage-specific gene expression and phenotypes. In this issue of Cell Genomics, Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar report that the balance between splicing isoforms of the microtubule-associated protein Tau in the brain is differentially regulated among primates by the RNA-binding protein MBNL2, with consequences for protein aggregation and neurodegeneration in humans. Alternative splicing (AS) of messenger RNA precursors (pre-mRNA) allows the production of multiple transcripts and proteins from the same genomic locus and thus expands the information content of eukaryotic genes. AS is prevalent in the transcriptomes of multicellular organisms, but the underlying regulatory mechanisms remain poorly understood and the extent to which most alternatively spliced mRNA isoforms display distinct biological functions remains a matter of debate. In this issue of Cell Genomics, Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar study the evolution of AS in the brain of primates, then focus on the relative use of AS isoforms of the microtubule-associated protein Tau (encoded by the gene MAPT). Their results argue for lineage-specific differences in the balance between alternatively spliced MAPT isoforms, established through key interactions of MAPT pre-mRNA with the RNA-binding protein MBNL2. In turn, differences in the balance between MAPT isoforms can have consequences for the distinct susceptibility to MAPT protein aggregation and neurodegeneration in humans compared with other species. Large-scale transcriptome studies have identified species- and lineage-specific patterns of AS, even arguing that the splicing profiles of physiologically equivalent organs are more strongly related to the identity of a species than to an organ type, with the highest complexity among vertebrates being found in primates and in brains compared to other tissues.2Barbosa-Morais N.L. Irimia M. Pan Q. Xiong H.Y. Gueroussov S. Lee L.J. Slobodeniuc V. Kutter C. Watt S. Colak R. et al.The evolutionary landscape of alternative splicing in vertebrate species.Science. 2012; 338: 1587-1593https://doi.org/10.1126/science.1230612Crossref PubMed Scopus (701) Google Scholar,3Corsi A. Bombieri C. Valenti M.T. Romanelli M.G. Tau Isoforms: Gaining Insight into MAPT Alternative Splicing.Int. J. Mol. Sci. 2022; 2315383https://doi.org/10.3390/ijms232315383Crossref Scopus (12) Google Scholar Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar analyzed deep transcriptomic data from brains of seven primate species and used a statistical model to identify alternatively spliced exons that display lineage-restricted patterns of exon inclusion and skipping compatible with evolutionary selection. Intriguingly, exons displaying human-specific patterns of inclusion are enriched in genes relevant for the assembly of cilia, some of which play important functions in the development of the brain cortex. These observations suggest the appealing concept that lineage-specific AS patterns have been selected to shape functional differences among the brains of different primate species. The authors report more than 700 exons likely harboring a splicing shift in hominoids (humans and chimpanzees), which represent a rich regulatory potential to be explored in further studies. This potential also begs the related questions of what these molecular mechanisms that establish lineage-specific splicing patterns are and whether they are common for different AS events displaying similar lineage specificity. Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar chose to focus on the MAPT gene because of its particularly interesting AS patterns and the previous knowledge about the functional relevance of some of its protein isoforms. At least 6 of the 14 exons of the MAPT gene are alternatively spliced, with the AS event corresponding to inclusion or skipping of exon 10 being intensively studied because of its connection with neurodegenerative diseases (reviewed in Corsi et al.3Corsi A. Bombieri C. Valenti M.T. Romanelli M.G. Tau Isoforms: Gaining Insight into MAPT Alternative Splicing.Int. J. Mol. Sci. 2022; 2315383https://doi.org/10.3390/ijms232315383Crossref Scopus (12) Google Scholar). In contrast to its nearly 100% inclusion in adult brain from mouse or 80% inclusion in New or Old World monkeys, exon 10 is included in approximately 50% of the transcripts of adult brains from hominoids.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar This balance is likely important for neuronal function because mutations in the MAPT gene that lead to alterations in this ratio have been associated with neurodegenerative disorders (Figure 1). For example, mutations in the 5′ splice site—a sequence at the 5′ end of introns recognized by the splicing complex U1 snRNP—flanking exon 10 enhance its inclusion and are believed to cause certain subtypes of frontotemporal lobar degeneration associated with tau (FTLD-tau).4Charizanis K. Lee K.Y. Batra R. Goodwin M. Zhang C. Yuan Y. Shiue L. Cline M. Scotti M.M. Xia G. et al.Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy.Neuron. 2012; 75: 437-450https://doi.org/10.1016/j.neuron.2012.05.029Abstract Full Text Full Text PDF PubMed Scopus (259) Google Scholar The proposed effects of these mutations are the disruption of a secondary RNA structure sequestering the 5′ splice site from recognition by U1 snRNP4Charizanis K. Lee K.Y. Batra R. Goodwin M. Zhang C. Yuan Y. Shiue L. Cline M. Scotti M.M. Xia G. et al.Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy.Neuron. 2012; 75: 437-450https://doi.org/10.1016/j.neuron.2012.05.029Abstract Full Text Full Text PDF PubMed Scopus (259) Google Scholar (Figure 1). The nucleotides involved in this secondary structure are, however, conserved across primates, and therefore, this mechanism cannot explain the differences in exon 10 inclusion in adult brain between these species (Figure 1). Indeed, the results of Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar point to a different mechanism defining the balance between exon 10 inclusion and skipping across species. MBNL2 belongs to a family of RNA-binding proteins with important post-transcriptional regulatory roles during embryo development.4Charizanis K. Lee K.Y. Batra R. Goodwin M. Zhang C. Yuan Y. Shiue L. Cline M. Scotti M.M. Xia G. et al.Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy.Neuron. 2012; 75: 437-450https://doi.org/10.1016/j.neuron.2012.05.029Abstract Full Text Full Text PDF PubMed Scopus (259) Google Scholar Thus, the timing of increased expression of MBNL2 coincides with increased inclusion of important developmentally regulated exons, including MAPT exon 10, and experimentally reduced levels of MBNL2 lead to slow down or inhibition of such splicing switches.4Charizanis K. Lee K.Y. Batra R. Goodwin M. Zhang C. Yuan Y. Shiue L. Cline M. Scotti M.M. Xia G. et al.Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy.Neuron. 2012; 75: 437-450https://doi.org/10.1016/j.neuron.2012.05.029Abstract Full Text Full Text PDF PubMed Scopus (259) Google Scholar Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar now argue that the number and affinity of MBNL2 binding sites in MAPT intron 10 determine the levels of exon 10 inclusion in adult brain (Figure 1). According to this model, developmental changes in the levels of MBNL2 protein may be similar across species, but different pre-mRNAs can modulate the response to these uniform changes by evolving different levels of interaction with the regulatory factor, thus accommodating lineage-specific needs for specific splicing isoforms. This is an attractive, simple model for the evolution of lineage-specific splicing, which likely involves contributions from other regulatory sequences and factors as well.3Corsi A. Bombieri C. Valenti M.T. Romanelli M.G. Tau Isoforms: Gaining Insight into MAPT Alternative Splicing.Int. J. Mol. Sci. 2022; 2315383https://doi.org/10.3390/ijms232315383Crossref Scopus (12) Google Scholar,5Lin L. Shen S. Jiang P. Sato S. Davidson B.L. Xing Y. Evolution of alternative splicing in primate brain transcriptomes.Hum. Mol. Genet. 2010; 19: 2958-2973https://doi.org/10.1093/hmg/ddq201Crossref PubMed Scopus (40) Google Scholar,6Mazin P.V. Jiang X. Fu N. Han D. Guo M. Gelfand M.S. Khaitovich P. Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques.RNA. 2018; 24: 585-596https://doi.org/10.1261/rna.064931.117Crossref PubMed Scopus (8) Google Scholar Why is the balance between different MAPT protein isoforms relevant? Depending on exclusion or inclusion of exon 10, mRNAs are translated into MAPT isoforms with 3 or 4 repeats of 18 amino acids that compose the microtubule-binding domain.7Hutton M. Lendon C.L. Rizzu P. Baker M. Froelich S. Houlden H. Pickering-Brown S. Chakraverty S. Isaacs A. Grover A. et al.Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17.Nature. 1998; 393: 702-705https://doi.org/10.1038/31508Crossref PubMed Scopus (3033) Google Scholar This region is important for promoting microtubule assembly and stability and for Tau liquid-liquid phase separation and self-aggregation.8Ambadipudi S. Biernat J. Riedel D. Mandelkow E. Zweckstetter M. Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau.Nat. Commun. 2017; 8: 275https://doi.org/10.1038/s41467-017-00480-0Crossref PubMed Scopus (474) Google Scholar,9Wegmann S. Eftekharzadeh B. Tepper K. Zoltowska K.M. Bennett R.E. Dujardin S. Laskowski P.R. MacKenzie D. Kamath T. Commins C. et al.Tau protein liquid-liquid phase separation can initiate tau aggregation.EMBO J. 2018; 37e98049https://doi.org/10.15252/embj.201798049Crossref PubMed Scopus (606) Google Scholar Dysregulation of the ratio between isoforms has been associated with the development of FTLD-tau and Alzheimer's disease (AD). The mechanistic insights by Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar may guide the design of future therapeutic interventions to prevent excessive inclusion of the exon (e.g., in the case of FTLD-tau with MAPT mutations that break the secondary RNA structure mentioned above). The use of intrathecal antisense oligonucleotides targeting intron 9 to decrease the expression of tau protein in AD has been evaluated in the clinic,10Mummery C.J. Börjesson-Hanson A. Blackburn D.J. Vijverberg E.G.B. De Deyn P.P. Ducharme S. Jonsson M. Schneider A. Rinne J.O. Ludolph A.C. et al.Tau-targeting antisense oligonucleotide MAPTRx in mild Alzheimer's disease: a phase 1b, randomized, placebo-controlled trial.Nat. Med. 2023; 29: 1437-1447https://doi.org/10.1038/s41591-023-02326-3Crossref PubMed Scopus (64) Google Scholar and a similar strategy could be used to target MBNL2-binding sites. As a proof of principle, Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar show that engineering an RNA-protein (CRISPR) complex to sterically occlude the access of MBNL2 to specific binding sites does, indeed, decrease MAPT exon 10 inclusion (Figure 1). Collectively, the results of Recinos, Bao, Wang, et al.1Recinos Y. Bao S. Wang X. Phillips B.L. Yeh Y.-T. Weyn-Vanhentenryck S.M. Swanson M.S. Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell Genom. 2024; 4100563https://doi.org/10.1016/j.xgen.2024.100563Abstract Full Text Full Text PDF Google Scholar illustrate the relevance of alternative splicing regulation for brain development, for shaping lineage-specific gene expression, and for the design of therapeutic approaches to neurodegeneration. Work in the authors' laboratory is supported by the European Research Council (ERC), the European Innovation Council (EIC), Ministerio de Ciencia e Innovación (Spain), and AGAUR (Catalonian Government). The authors declare no competing interests. Lineage-specific splicing regulation of MAPT gene in the primate brainRecinos et al.Cell GenomicsMay 20, 2024In BriefRecinos et al. identified over 1,000 alternative exons showing evolutionarily divergent splicing under stabilizing selection in primate brains. Among them, they found microtubule-associated protein tau (MAPT) exon 2 and exon 10 underwent anticorrelated, two-step splicing shifts, which may suggest adaptation of tau function. Full-Text PDF Open Access