@article {70339, title = {Reconstituting mouse embryogenesis Ex utero from Gastrulation to fetal development reveals maternally independent metabolic programs}, journal = {bioRxiv}, year = {2026}, month = {2026 Mar 17}, abstract = {

Mammalian development takes place inside the maternal uterus, creating technological constraints that make difficult the study of embryogenesis in live developing embryos. A central challenge for understanding the role of metabolism in mammalian development is discriminating placental and uterine-regulated signals from embryo-intrinsic processes independent of maternal influence, a process that until now has remained inseparable during gastrulation and organogenesis1{\textendash}3. Ex utero culture systems allowing continuous growth of embryos during pre-gastrulation to organogenesis4,5 offer a promising solution to this challenge. Here, we present optimized ex utero culture platforms that support faithful development of mouse embryos from gastrulation (embryonic day 6.5/7.5) through the fetal period (embryonic day \~12.5) and harnessed these platforms for dissecting metabolic transitions in vivo during embryogenesis independently of uterus and placenta. We characterized the metabolome of in utero and ex utero whole embryos, fetal organs and culture medium between embryonic days E6.5 and E12.5 by liquid chromatography mass-spectrometry (LC-MS) metabolomics, isotope tracing, and single cell transcriptomics. These datasets present a comprehensive overview of the dynamic embryonic metabolism during gastrulation and organogenesis in utero and ex utero. This analysis revealed that the midgestational metabolic switch occurring at E10.5-E11.5 is faithfully recapitulated ex utero, indicating that this transition is intrinsically programmed in embryonic tissues and does not require direct maternal or placental cues. Notably, oxygen availability modulated the extent of this transition, but elevated oxygen was insufficient to induce it prematurely, demonstrating that the switch is developmentally timed and only partially environmental-responsive. We further harnessed the ex utero platform for identifying and perturbing a mitochondrial redox shift at E7.5-E8.5 that is critical for developmental progress after gastrulation. These findings uncover the remarkable metabolic plasticity of the mammalian embryo, demonstrating its capacity to sustain growth independently of maternal inputs from the establishment of the body plan through the onset of the fetal period. Moreover, they highlight the use of long-term ex utero culture as a unique framework for dissecting the mechanisms that shape embryogenesis under physiological and experimentally perturbed conditions, while functionally uncoupling embryonic programs from maternal and placental influences.

}, doi = {10.64898/2026.03.17.710314}, url = {https://www.biorxiv.org/content/early/2026/03/18/2026.03.17.710314}, author = {Lokshtanov, Dmitry and Gao, Shihong Max and Xu, Weizhi and Kosman, Avraham and Roncato, Francesco and De La Cruz, Nancy and Khan, Nawal A. and Woods, Andrea and Campbell, Ian and Woehler, Andrew and Christoforou, Christina and Ding, Lang and Hu, Amy and Copeland, Monique and Wang, Lihua and Yang, Xiushuai and Raley, Castle and Delventhal, Kym M. and Herrera, Antonio and Valente, Alessandro and Wright, Sylvia and Gomez-Cesar, Elidet and Shlomo, Raanan and Golenchenko, Sergey and Oldak, Bernardo and Yilmaz, Alperen and Gurhan-Sebinc, Gulben and Comar, Mehmet-Yunus and Viukov, Sergey and Novershtern, Noa and Zhang, Hua and Duong, Thao and Li, Lingjun and Khatib, Nizar and Kakun, Reli Rachel and Espinosa-Medina, Isabel and Florian-Rodriguez, Maria E. and LaManno, Gioele and Tillberg, Paul W. and Wang, Meng C. and Maza, Itay and Srivatsan, Sanjay and Solmonson, Ashley and Hanna, Jacob H. and Aguilera-Castrejon, Alejandro} } @article {69710, title = {Discovery of neuronal cell types by pairing whole cell reconstructions with RNA expression profiles}, journal = {bioRxiv}, year = {2024}, month = {12/2024}, abstract = {

Effective classification of neuronal cell types requires both molecular and morphological descriptors to be collected in situ at single cell resolution. However, current spatial transcriptomics techniques are not compatible with imaging workflows that successfully reconstruct the morphology of complete axonal projections. Here, we introduce a new methodology that combines tissue clearing, submicron whole-brain two photon imaging, and Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to assign molecular identities to fully reconstructed neurons in the mouse brain, which we call morphoFISH. We used morphoFISH to molecularly identify a previously unknown population of cingulate neurons projecting ipsilaterally to the dorsal striatum and contralaterally to higher-order thalamus. By pairing whole-brain morphometry, improved techniques for nucleic acid preservation and spatial gene expression, morphoFISH offers a quantitative solution for discovery of multimodal cell types and complements existing techniques for characterization of increasingly fine-grained cellular heterogeneity in brain circuits.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2024.12.30.630829}, url = {https://www.biorxiv.org/content/early/2024/12/31/2024.12.30.630829}, author = {The MouseLight Project Team and Ferreira, Tiago A. and Eddison, Mark and Copeland, Monique and Lay, Mary and Tenshaw, Emily and Weldon, Monet and Schauder, David and Olbris, Donald J. and Rokicki, Konrad and Spruston, Nelson and Tillberg, Paul W. and Korff, Wyatt and Dudman, Joshua T.} } @article {65584, title = {A Sparse, Spatially Biased Subtype of Mature Granule Cell Dominates Recruitment in Hippocampal-Associated Behaviors.}, journal = {Cell Reports}, volume = {31}, year = {2020}, month = {2020 Apr 28}, pages = {107551}, abstract = {

Animals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we find that a range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identify a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we map these traits onto a sparse and discrete granule cell subtype that is recruited at a 10-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, in behaviors known to involve hippocampal-dependent memory formation, a rare and spatially localized subtype dominates overall granule cell recruitment.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.107551}, author = {Erwin, Sarah R and Sun, Weinan and Copeland, Monique and Lindo, Sarah and Spruston, Nelson and Cembrowski, Mark S} } @article {49492, title = {The subiculum is a patchwork of discrete subregions.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Oct 30}, abstract = {

In the hippocampus, the classical pyramidal cell type of the subiculum acts as a primary output, conveying hippocampal signals to a diverse suite of downstream regions. Accumulating evidence suggests that the subiculum pyramidal cell population may actually be comprised of discrete subclasses. Here, we investigated the extent and organizational principles governing pyramidal cell heterogeneity throughout the mouse subiculum. Using single-cell RNA-seq, we find that the subiculum pyramidal cell population can be deconstructed into eight separable subclasses. These subclasses were mapped onto abutting spatial domains, ultimately producing a complex laminar and columnar organization with heterogeneity across classical dorsal-ventral, proximal-distal, and superficial-deep axes. We further show that these transcriptomically defined subclasses correspond to differential protein products and can be associated with specific projection targets. This work deconstructs the complex landscape of subiculum pyramidal cells into spatially segregated subclasses that may be observed, controlled, and interpreted in future experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.37701}, author = {Cembrowski, Mark S and Wang, Lihua and Lemire, Andrew L and Copeland, Monique and DiLisio, Salvatore F and Clements, Jody and Spruston, Nelson} }