Transcriptional landscape of the prenatal human brain

In the paper

“Each layer included genes with high laminar specificity (Fig. 2d), although the SZi profiles tended to overlap with the neighboring SZo and VZ.”

In the paper

“Remarkably, few genes met both criteria at 15–16 pcw: 39 genes were enriched in SZi (including several in module G3), while only eight were specifically enriched in SZo.”

In the paper

“Approximately 95% of RefSeq genes are expressed in developing neocortex, compared with 84% identified using these arrays in adult23.”

What the sources say

• Not checked yetcites [23] Hawrylycz, M. J. et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391–399 (2012) source

In the paper

“The next oldest neurons in CPi are additionally enriched for genes involved in forming connections, whereas the youngest neurons in CPo are primarily enriched for terms related to metabolism rather than mature neuronal function.”

In the paper

“Different layers show robust and unique molecular signatures, and samples group by layer using hierarchical clustering (using differential genes from ANOVA, p<10−29) at both timepoints (Fig. 2b).”

In the paper

“Module C38 contains genes enriched in germinal layers, and also decreased expression with age (Fig. 3b, upper left).”

In the paper

“The cortical progenitor markers TBR2 and PAX6 are enriched in germinal layers as in mouse, although PAX6 in mouse is restricted to VZ whereas it is also highly expressed in human SZ31.”

What the sources say

• Not checked yetcites [31] Englund, C. et al. Pax6, Tbr2, and Tbr1 are expressed sequentially by radial glia, intermediate progenitor cells, and postmitotic neurons in developing neocortex. J. Neurosci. 25, 247–251 (2005) source

In the paper

“For example, NPY is enriched in SP at 21pcw (but not 15–16pcw) as shown both by microarray and ISH (Fig. 4a).”

In the paper

“Finally, we identified a module (C31) with particular enrichment in SG and VZ (Fig. 3b, upper right), containing many interneuron-associated genes (Fig. 3c).”

In the paper

“We found eight co-expression modules with selective enrichment in either the SZ or the VZ (Fig. 3d,e), highly conserved between brains (p<10−50), and highly distinct.”

In the paper

“Samples also cluster with multidimensional scaling (MDS), where dimension one separates samples by layer, with germinal zones (VZ, SZi, SZo) distinct from layers containing primarily postmitotic cells, and dimension two roughly reflects rostrocaudal position (Fig. 2c).”

In the paper

“Here, most gene clusters (“modules”) corresponded to layers and/or changes with age, (Fig. 3a-b; Extended Data Fig. 4) while areal patterning appeared to be a more subtle transcriptional feature.”

In the paper

“These results are consistent with a previous study of laminar enrichment in 13–16pcw human prenatal cortex, which also found few genes specifically enriched in SZo (55) or SZi (61)2.”

What the sources say

• Not checked yetcites [2] Fietz, S. A. et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc. Natl Acad. Sci. USA 109, 11836–11841 (2012) source

In the paper

“However, while mouse Zic1 is expressed by virtually all Cajal-Retzius neurons34, our results indicate that this is not true in human as ZIC1 and CALB2 expression do not overlap in MZ (Figs. 1b and 2e).”

What the sources say

• Not checked yetcites [34] Inoue, T., Ogawa, M., Mikoshiba, K. & Aruga, J. Zic deficiency in the cortical marginal zone and meninges results in cortical lamination defects resembling those in type II lissencephaly. J. Neurosci. 28, 4712–4725 (2008) source

In the paper

“Conversely, module C22 is enriched in newly generated postmitotic neurons of the CP, and increases with age (Fig. 3b, lower left).”

In the paper

“Modules G2 and G3 are enriched in the SZi (Fig. 3d, white bars in bottom two rows), and G3 is enriched for genes marking Svet1+ IPs in E14 mouse SZ43, including ELAVL4, LRP8, NEUROD1, NRN1, SLC17A6, SSTR2, and TP53INP1.”

What the sources say

• Not checked yetcites [43] Kawaguchi, A. et al. Single-cell gene profiling defines differential progenitor subclasses in mammalian neurogenesis. Development 135, 3113–3124 (2008) source

In the paper

“For example, module C16 is enriched in SP (Fig. 3b, lower right), and shows hallmarks of mature neuronal function.”

In the paper

“Conversely, Trh and Nxph4 show enriched expression in mouse but not human SP (Fig. 4d; Extended Data Fig. 8b).”

In the paper

“Interestingly, FOXP2, implicated in the specialization of language areas54, is included in the module C16, and shows enrichment in parietal and temporal lobes including presumptive language areas (Extended Data Fig. 10).”

What the sources say

• Not checked yetcites [54] Enard, W. et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869–872 (2002) source

In the paper

“In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes.”

In the paper

“Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe.”

In the paper

“SP generation is protracted in primates8, and its thickness particularly expanded in human8.”

What the sources say

• Not checked yetcites [8] Smart, I., Dehay, C., Giroud, P., Berland, M. & Kennedy, H. Unique morphological features of the proliferative zones and postmitotic compartments of the neural epithelium giving rise to striate and extrastriate cortex in the monkey. Cereb.Cortex 12, 37–53 (2002) source

In the paper

“Both VZ-enriched modules (G7, G8) contained cell cycle genes and many astrocyte markers, suggesting that these modules may represent different RG populations.”

In the paper

“DLX1 and DLX2, homeobox transcription factors essential for interneuron migration and survival10, were central (“hub”) genes therein.”

What the sources say

• Not checked yetcites [10] Anderson, S. A., Eisenstat, D. D., Shi, L. & Rubenstein, J. L. Interneuron migration from basal forebrain to neocortex: dependence on Dlx genes. Science 278, 474–476 (1997) source

In the paper

“However, several recent studies have shown strong evidence that, as with rodents, primate interneurons are generated extracortically in the GEs11,14.”

What the sources say

• Not checked yetcites [11] Ma, T. et al. Subcortical origins of human and monkey neocortical interneurons. Nature Neurosci. 16, 1588–1597 (2013) source
• Not checked yetcites [14] Hansen, D. V. et al. Non-epithelial stem cells and cortical interneuron production in the human ganglionic eminences. Nature Neurosci. 16, 1576–1587 (2013) source

In the paper

“SZo-enriched categories primarily related to cell division and contained many astrocytic markers likely expressed in outer radial glia (ORG)7.”

What the sources say

• Not checked yetcites [7] Hansen, D. V., Lui, J., Parker, P. & Kriegstein, A. Neurogenic radial glia in the outer subventricular zone of human neocortex. Nature 464, 554–561 (2010) source

In the paper

“In mouse and other species18 this layer is molecularly distinct, and our laminar profiling also identified many SP-enriched genes in human (Fig. 2).”

What the sources say

• Not checked yetcites [18] Wang, W. Z. et al. Comparative aspects of subplate zone studied with gene expression in sauropsids and mammals. Cereb. Cortex 21, 2187–2203 (2011) source

In the paper

“Germinal layers contain various cortical progenitors including RG in the VZ, intermediate progenitors (IP) in the SZi, and ORG in the SZo (reviewed in41), and these RG may be quite diverse42.”

What the sources say

• Not checked yetcites [41] Gaspard, N. & Vanderhaeghen, P. Laminar fate specification in the cerebral cortex. F1000 Biol. Rep. 3, 6 (2011) source
• Not checked yetcites [42] Betizeau, M. et al. Precursor diversity and complexity of lineage relationships in the outer subventricular zone of the primate. Neuron 80, 442–457 (2013) source

In the paper

“Modules G4-G6 are enriched in the SZo (Fig. 3d, gray bars); however, these modules are enriched for neuron-associated categories likely expressed in postmitotic cells during their radial migration.”

In the paper

“Finally, expression of ZIC1, associated with Dandy-Walker congenital brain malformation33, was restricted to the pia mater overlying the cortex, therefore indicating that SG samples captured pial cells in addition to granule cells.”

What the sources say

• Not checked yetcites [33] Grinberg, I. et al. Heterozygous deletion of the linked genes ZIC1 and ZIC4 is involved in Dandy-Walker malformation. Nature Genet. 36, 1053–1055 (2004) source

In the paper

“This module has a large signature of glia and cell division, suggesting that these genes reflect decreasing progenitor cell division.”

In the paper

“The SP is a largely transient zone beneath the CP that plays an important role in establishment of thalamocortical connectivity (see35 for review).”

What the sources say

• Not checked yetcites [35] Kostović, I. & Judas, M. The development of the subplate and thalamocortical connections in the human foetal brain. Acta Paediatr. 99, 1119–1127 (2010) source

In the paper

“This human frontal asymmetry is most apparent in the outer postmitotic layers MZ and CPo (Fig. 5i), and in SZo, which generates most superficial CP neurons in primate7,8, suggesting that these genes may play a part in the expansion and reorganization of human PFC8.”

What the sources say

• Not checked yetcites [7] Hansen, D. V., Lui, J., Parker, P. & Kriegstein, A. Neurogenic radial glia in the outer subventricular zone of human neocortex. Nature 464, 554–561 (2010) source
• Not checked yetcites [8] Smart, I., Dehay, C., Giroud, P., Berland, M. & Kennedy, H. Unique morphological features of the proliferative zones and postmitotic compartments of the neural epithelium giving rise to striate and extrastriate cortex in the monkey. Cereb.Cortex 12, 37–53 (2002) source

In the paper

“Expression varies between cell populations, and more detailed analysis of layers of fetal mouse neocortex found >2500 genes differentially expressed between ventricular zone (VZ), SZ, intermediate zone (IZ), and cortical plate (CP)16.”

What the sources say

• Not checked yetcites [16] Ayoub, A. E. et al. Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc. Natl Acad. Sci. USA 108, 14950–14955 (2011) source

In the paper

“In mouse, nearly all originate from the striatal ganglionic eminences (GEs) of the ventral telencephalon10; however, the origin of human cortical interneurons remains controversial7,11–14.”

What the sources say

• Not checked yetcites [10] Anderson, S. A., Eisenstat, D. D., Shi, L. & Rubenstein, J. L. Interneuron migration from basal forebrain to neocortex: dependence on Dlx genes. Science 278, 474–476 (1997) source

In the paper

“CNSs are typically located by genes important for developmental regulation, and many show significant enhancer activity in brain5.”

What the sources say

• Not checked yetcites [5] Lambert, N. et al. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS ONE 6, e17753 (2011) source

In the paper

“Interestingly, Trh is also not expressed in the rat SP18, suggesting this pattern is specific to mouse.”

What the sources say

• Not checked yetcites [18] Wang, W. Z. et al. Comparative aspects of subplate zone studied with gene expression in sauropsids and mammals. Cereb. Cortex 21, 2187–2203 (2011) source

In the paper

“Species differences in distinct fetal transient zones, including the SZ2, SP17,18, CP6, and SG9, have also been described.”

What the sources say

• Not checked yetcites [2] Fietz, S. A. et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc. Natl Acad. Sci. USA 109, 11836–11841 (2012) source
• Not checked yetcites [17] Montiel, J. et al. Hypothesis on the dual origin of the mammalian subplate. Front. Neuroanat. 5, 25 (2011) source
• Not checked yetcites [18] Wang, W. Z. et al. Comparative aspects of subplate zone studied with gene expression in sauropsids and mammals. Cereb. Cortex 21, 2187–2203 (2011) source

In the paper

“Profiling of mid-gestational human brain3,5 identified many genes differentially expressed between major regions, including genes associated with human-accelerated conserved noncoding sequences (haCNSs)15.”

What the sources say

• Not checked yetcites [3] Johnson, M. B. et al. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62, 494–509 (2009) source
• Not checked yetcites [5] Lambert, N. et al. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS ONE 6, e17753 (2011) source
• Not checked yetcites [15] Prabhakar, S., Noonan, J., Pääbo, S. & Rubin, E. Accelerated evolution of conserved noncoding sequences in humans. Science 314, 786 (2006) source

In the paper

“The transient subplate zone (SP) is greatly expanded in human8, as is the subpial granular zone (SG), a transient compartment at the pial surface composed primarily of tangentially migrating neurons9.”

What the sources say

• Not checked yetcites [9] Brun, A. The subpial granular layer of the foetal cerebral cortex in man. Its ontogeny and significance in congenital cortical malformations. Acta Pathologica et Microbiologica Scandinavica 179 (suppl.). 3–98 (1965)

In the paper

“Genes near CNSs with significantly accelerated rates of substitution in the human lineage (haCNSs)15 are particularly likely to show differential expression between regions of developing human neocortex3,5, suggesting transcriptional regulation by haCNSs may be important in human-specific neurodevelopment.”

What the sources say

• Not checked yetcites [15] Prabhakar, S., Noonan, J., Pääbo, S. & Rubin, E. Accelerated evolution of conserved noncoding sequences in humans. Science 314, 786 (2006) source
• Not checked yetcites [3] Johnson, M. B. et al. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62, 494–509 (2009) source
• Not checked yetcites [5] Lambert, N. et al. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS ONE 6, e17753 (2011) source

In the paper

“A secondary progenitor zone, the subventricular zone (SZ) is present in all mammals, but is split into an outer and inner region in primates7.”

What the sources say

• Not checked yetcites [7] Hansen, D. V., Lui, J., Parker, P. & Kriegstein, A. Neurogenic radial glia in the outer subventricular zone of human neocortex. Nature 464, 554–561 (2010) source

In the paper

“Conversely, CBLN2 shows rostral enrichment in human CPo (Fig. 5f) and in mouse (Fig. 5g), with an abrupt expression cutoff, implicating CBLN2 in early rostral patterning.”

In the paper

“This result, which cannot be explained by over-representation of neural adhesion genes in IZ, suggests that IZ is of particular importance in areal cortical identity during human development53.”

What the sources say

• Not checked yetcites [53] Allendoerfer, K. L. & Shatz, C. J. The subplate, a transient neocortical structure: its role in the development of connections between thalamus and cortex. Annu. Rev. Neurosci. 17, 185–218 (1994) source

In the paper

“Gradient genes in VZ likely reflect intrinsic areal specification as VZ does not receive thalamic innervation.”

In the paper

“Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones.”

In the paper

“For example, FGFR3, which is known to cause defects in human temporal cortex when mutated50, shows significant caudal enrichment in all germinal layers in both species (Fig. 5d–e).”

What the sources say

• Not checked yetcites [50] Hevner, R. F. The cerebral cortex malformation in thanatophoric dysplasia: neuropathology and pathogenesis. Acta Neuropathol. 110, 208–221 (2005) source

In the paper

“Several genes showed enrichment in developing human but not mouse SP, including the hypocretin (orexin) receptor HCRTR2 (Fig. 4c; Extended Data Fig. 8a), which is thought to regulate sleep-wakefulness and is highly expressed in mouse hypothalamus45.”

What the sources say

• Not checked yetcites [45] Gerashchenko, D. et al. Hypocretin-2-saporin lesions of the lateral hypothalamus produce narcoleptic-like sleep behavior in the rat. J. Neurosci. 21, 7273–7283 (2001) source

In the paper

“Interestingly, we find more rostrally- than caudally-enriched genes in nearly every cortical layer (Fig. 5h), whereas two studies of gradient expression in prenatal mouse brain identified more49 or comparable51 caudally-enriched genes, indicating potential species differences related to areal patterning.”

What the sources say

• Not checked yetcites [49] Sansom, S. N. & Livesey, F. Gradients in the brain: the control of the development of form and function in the cerebral cortex. Cold Spring Harb. Perspect. Biol. 1, a002519 (2009) source
• Not checked yetcites [51] Pinto, L. et al. AP2γ regulates basal progenitor fate in a region- and layer-specific manner in the developing cortex. Nature Neurosci. 12, 1229–1237 (2009) source

In the paper

“Cortical patterning is likely a result of intrinsic signaling, controlled in part by graded expression of transcription factors during early cortical development, followed by extrinsic signaling from thalamic afferents after the start of corticogenesis46–49.”

What the sources say

• Not checked yetcites [46] Mallamaci, A. & Stoykova, A. Gene networks controlling early cerebral cortex arealization. Eur. J. Neurosci. 23, 847–856 (2006) source
• Not checked yetcites [47] O’Leary, D. D. Do cortical areas emerge from a protocortex? Trends Neurosci. 12, 400–406 (1989) source
• Not checked yetcites [48] Rakic, P. Specification of cerebral cortical areas. Science 241, 170–176 (1988) source
• Not checked yetcites [49] Sansom, S. N. & Livesey, F. Gradients in the brain: the control of the development of form and function in the cerebral cortex. Cold Spring Harb. Perspect. Biol. 1, a002519 (2009) source

In the paper

“Interestingly, FOXP2, implicated in the specialization of language areas54, is included in the module C16, and shows enrichment in parietal and temporal lobes including presumptive language areas (Extended Data Fig. 10).”

What the sources say

• Not checked yetcites [54] Enard, W. et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869–872 (2002) source

In the paper

“For example, the human neocortex has undergone massive evolutionary expansion, particularly in superficial layers, likely due to differences in rates of progenitor pool expansion during neurogenesis compared to other species6.”

What the sources say

• Not checked yetcites [6] Kriegstein, A., Noctor, S. & Martínez-Cerdeño, V. Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion. Nature Rev. Neurosci. 7, 883–890 (2006) source

In the paper

“Alternatively, this asymmetry could reflect temporal differences, as peak generation of excitatory neurons in visual cortex is delayed relative to frontal cortex52.”

What the sources say

• Not checked yetcites [52] Rakic, P. Neurogenesis in adult primates. Prog. Brain Res. 138, 3–14 (2002) source

In the paper

“The atlas of the mid-gestational human brain described here, part of the BrainSpan Atlas of the Developing Human Brain, builds on digital molecular brain atlasing efforts in mouse20,22,24 and adult human23 by providing transcriptome resources on prenatal specimens typically inaccessible for research.”

What the sources say

• Not checked yetcites [20] Paxinos, G. & Franklin, K. Paxinos and Franklin’s the Mouse Brain in Stereotaxic Coordinates 4th edn (Academic Press, 2012)
• Not checked yetcites [22] Dong, H. W. Allen Reference Atlas: a Digital Color Brain Atlas of the C57BL/6J Male Mouse (Wiley, 2008)
• Not checked yetcites [24] Lein, E. S. et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007) source
• Not checked yetcites [23] Hawrylycz, M. J. et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391–399 (2012) source

In the paper

“To control for batch effects, common RNA pool control samples were amplified and hybridized in each batch.”

In the paper

“Unless otherwise noted, all p-values are Bonferroni corrected for multiple comparisons.”

In the paper

“Biological outliers were identified by comparing samples from related structures using hierarchical clustering and inter-array correlation measures.”

In the paper

“This network will only identify intergenic relationships common to both brains, and should therefore produce robust co-expression relationships that exclude specimen-specific features or changes with age.”

In the paper

“A total of 1,225 samples passed sample quality control (QC), including 1,202 experimental samples and 23 control samples.”

In the paper

“Similarly, two genes associated with abnormal cortical development in holoprosencephaly, TGIF1 and SIX327, are also enriched in cortical germinal zones.”

What the sources say

• Not checked yetcites [27] Dubourg, C. et al. Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: mutation review and genotype–phenotype correlations. Hum. Mutat. 24, 43–51 (2004) source

In the paper

“All microarray data was subjected to QC and ERCC spike-in assessments, and any failing samples were omitted from the analysis.”

In the paper

“The average RNA Integrity Number (RIN) of all 1,202 passed experimental samples was 6.3.”