An evolutionarily acquired microRNA shapes development of mammalian cortical projections Jessica L. Diaza,1, Verl B. Siththanandana,1, Victoria Lua,1, Nicole Gonzalez-Navaa, Lincoln Pasquinab,c, Jessica L. MacDonaldb,c,2, Mollie B. Woodworthb,c,d, Abdulkadir Ozkanb,c, Ramesh Naire, Zihuai Hea, Vibhu Sahnib,c,3, Peter Sarnowf, Theo D. Palmera, Jeffrey D. Macklisb,c,4,5, and Suzanne Tharina,g,4,5 aDepartment of Neurosurgery, Stanford University, Stanford, CA 94305; bDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138; cCenter for Brain Science, Harvard University, Cambridge, MA 02138; dDepartment of Ophthalmology, Stanford University, Stanford, CA 94305; eDepartment of Genetics, Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305; fDepartment of Microbiology and Immunology, Stanford University, Stanford, CA 94305; and gDivision of Neurosurgery, Palo Alto Veterans Affairs Health Care System, Palo Alto, CA 94304 Edited by Carla J. Shatz, Stanford University, Stanford, CA, and approved September 29, 2020 (received for review April 8, 2020) The corticospinal tract is unique to mammals and the corpus layers (13). In the mouse, CSMN and a subset of CPN are gen- callosum is unique to placental mammals (eutherians). The emer- erated around embryonic day 13.5 (e13.5), and both reside in the gence of these structures is thought to underpin the evolutionary deep cortical layer V (Fig. 1A). A larger subset of CPN is gener- acquisition of complex motor and cognitive skills. Corticospinal ated around e15.5, and it populates the superficial cortical layer(s) motor neurons (CSMN) and callosal projection neurons (CPN) are II/III (Fig. 1A). A body of research from the last ∼15 y has un- the archetypal projection neurons of the corticospinal tract and covered a set of key molecules, largely transcriptional regulators, corpus callosum, respectively. Although a number of conserved that control cortical projection neuron development. These dis- transcriptional regulators of CSMN and CPN development have coveries have been central to defining the current paradigm of been identified in vertebrates, none are unique to mammals and combinatorial transcription factor controls (6–8). most are coexpressed across multiple projection neuron subtypes. A number of transcription factors required for cortical pro- Here, we discover 17 CSMN-enriched microRNAs (miRNAs), 15 of jection neuron development have been identified as differen- which map to a single genomic cluster that is exclusive to euthe- tially expressed by CSMN, CPN, and other cortical projection rians. One of these, miR-409-3p, promotes CSMN subtype identity neuron subtypes, and their roles delineated by functional anal- NEUROSCIENCE in part via repression of LMO4, a key transcriptional regulator of yses. For example, Fezf2 is a transcription factor required for CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is a demonstration of an evolu- tionarily acquired miRNA in eutherians that refines cortical projec- Significance tion neuron subtype development. Our findings implicate miRNAs in the eutherians’ increase in neuronal subtype and projection di- The mammalian central nervous system contains unique pro- versity, the anatomic underpinnings of their complex behavior. jections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and cerebral cortex | cortical development | microRNA | motor neuron | corpus callosum. The neurons giving rise to these projections— projection neuron corticospinal and callosal projection neurons—develop from the same progenitors, but acquire strikingly different fates. The he size and complexity of the mammalian brain dramatically broad evolutionary conservation of known genes controlling Tincreased with the evolution of placental mammals (euthe- cortical projection neuron fates raises the question of how the rians). Eutherian evolutionary innovations included the consol- more narrowly conserved corticospinal and callosal projections idation of the motor cortex, the completion of the corticospinal evolved. We identify a microRNA cluster selectively expressed by tract, and the appearance of the corpus callosum (1–4). This corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate evolution expanded both the overall number and the number of via regulation of the callosal gene LMO4, suggesting a mecha- distinct subtypes of cortical projection neurons—the large, ex- nism whereby microRNA regulation during development pro- citatory pyramidal neurons with axons that project long distances motes evolution of neuronal diversity. to deep, contralateral, or subcerebral structures. The archetypal cortical projection neurons of the eutherian Author contributions: J.L.D., V.B.S., V.L., P.S., T.D.P., J.D.M., and S.T. designed research; corticospinal tract and corpus callosum are, respectively, corti- J.L.D., V.B.S., V.L., N.G.-N., L.P., J.L.M., A.O., V.S., and S.T. performed research; R.N., Z.H., cospinal motor neurons (CSMN) and callosal projection neurons and S.T. contributed new reagents/analytic tools; J.L.D., V.B.S., N.G.-N., M.B.W., R.N., Z.H., (CPN). CSMN project from the motor cortex via the cortico- and S.T. analyzed data; and M.B.W., P.S., T.D.P., J.D.M., and S.T. wrote the paper. spinal tract to the spinal cord. They are centrally involved in the Competing interest statement: C.J.S. and authors J.L.D., V.B.S., V.L., N.G.-N., M.B.W., R.N., Z.H., P.S., T.D.P., and S.T. are affiliated with Stanford University. most skilled voluntary movement. By contrast, CPN project from the cerebral cortex via the corpus callosum to the contralateral This article is a PNAS Direct Submission. cortex. They are involved in associative and integrative function This open access article is distributed under Creative Commons Attribution-NonCommercial- NoDerivatives License 4.0 (CC BY-NC-ND). (5). Despite their dramatically different projections and func- 1J.L.D., V.B.S., and V.L. contributed equally to this work. tions, CSMN and CPN are closely related in their development; 2 CSMN and deep-layer CPN are born at the same time and share Present address: Department of Biology, Program in Neuroscience, Syracuse University, – Syracuse, NY 13244. common progenitors (5 8). 3Present address: Burke Neurological Institute, Weill-Cornell Medicine, White Plains, CSMN, CPN, and other cortical projection neurons develop NY 10605. through waves of neurogenesis, radial migration, and differen- 4J.D.M. and S.T. contributed equally to this work. tiation from radial glial progenitors of the ventricular zone and 5To whom correspondence may be addressed. Email: [email protected] or intermediate progenitor cells of the subventricular zone (9–12). [email protected]. The six-layered mammalian neocortex is generated in an inside- This article contains supporting information online at https://www.pnas.org/lookup/suppl/ out fashion, with the earliest-born neurons populating the deepest doi:10.1073/pnas.2006700117/-/DCSupplemental. layers, and the last-born neurons populating the most superficial www.pnas.org/cgi/doi/10.1073/pnas.2006700117 PNAS Latest Articles | 1of10 Downloaded by guest on September 26, 2021 Fig. 1. miRNAs are differentially expressed by CSMN vs. CPN during their development. (A) Schematic of CSMN (red) and CPN (blue) development in mice. IPC: Intermediate Progenitor Cell; RGC: Radial Glial Cell. (B) Volcano plot of differential miRNA expression by CSMN vs. CPN on P1, with fold change expressed as RQ plotted against statistical significance expressed as FDR-adjusted P value (q-value), reveals 19 miRNA candidates enriched at least 4-fold in CSMN relative to CPN with a q-value of less than 0.2 (colored dots). (C) Two confirmed miRNA clusters, comprising 17 differentially expressed candidate miRNAs, and representative results of independent validation via qPCR on P2. miR-409-3p from megacluster is 6-fold enriched (RQ = 6) in CSMN vs. CPN on P2; miR193b-3p is 5,630-fold enriched in CSMN vs. CPN on P2. Error bars represent SEM. specification of CSMN and other deep-layer subcerebral pro- Results jection neuron subtypes (14, 15). Fezf2 acts as a selector gene, miRNAs Are Differentially Expressed by CSMN and CPN during regulating the expression of neurotransmitter and axon guidance Development. Multiple genes critical to cortical projection neu- – receptor genes in CSMN (15 20). SATB2, on the other hand, is a ron development are differentially expressed by CSMN vs. CPN transcription factor required for CPN identity. SATB2 regulates across eutherians, extensively studied in mice (6, 15, 22, 30–35). – the expression of a distinct set of downstream genes (21 23). Our studies considered the possibility that this differential mRNA Curiously, SATB2 is also required for early CSMN development, expression is in part controlled by miRNAs, which are known to including extension of CSMN axons to the corticospinal tract (23). coordinately regulate gene expression (27, 36). In a first series of LIM domain Only 4 (LMO4) is a LIM-homeodomain transcrip- experiments to address this question, we investigated whether tion factor that is initially expressed by both CSMN and CPN, but miRNA expression is regulated in a neuron subtype-specific way in becomes progressively restricted to CPN by late development (24). mice. We began by examining miRNA expression by CSMN vs. CPN LMO4 is important for the establishment of CPN areal identity at a critical developmental time point: on postnatal day 1 (P1), when (25) and is also required for projection target diversity of CPN these neurons express multiple lineage-restricted genes, but when within motor cortex (26). LMO4, along with Fezf2, SATB2, and the majority of their axons have not yet reached their targets (37). other developmental transcription factors, is coexpressed across CSMN and CPN were retrogradely labeled via ultrasound- multiple projection neuron subtypes early in their development guided nanoinjection of fluorescent latex microspheres into and is broadly conserved across noneutherian vertebrates (6).