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Here, we apply a deep-learning-based graph-guided variational autoencoder (MeRN; Metabolic Representation Network) to infer single-cell metabolic activity and states from scRNA-seq data of mouse embryogenesis. By analyzing folate-deficient embryogenesis from E7.0\u2013E9.0, we identify a transient state within the nascent neural lineage that is acutely sensitive to folate availability, leading to an interconnected disruption between key bioenergetic pathways and\n                  <jats:italic>de novo<\/jats:italic>\n                  purine biosynthesis. Moreover, metabolically induced growth defects lead to permanent morphological disruptions along the dorsal-ventral axis, which we confirm by generating whole-embryo fate maps using a prime-editing-based lineage recorder (PEtracer). Collectively, our results establish a highly scalable framework for interpreting dynamic changes in embryonic metabolism and elucidating the mechanistic bases underlying environmentally linked congenital disorders.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Research highlights<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Developing embryos adopt metabolic states that are distinct from cell lineage<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Metabolic states are organized temporally and spatially along key body axes<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Neural tube development depends on a rapid transition between metabolic states<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Activation of transient neural metabolic states is highly sensitive to disrupted folate absorption<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>The floor plate is preferentially resistant to folate deprivation and distorts subsequent neural patterning<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.18.752622","type":"posted-content","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:20:24Z","timestamp":1790342424000},"source":"Crossref","is-referenced-by-count":0,"title":["Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0873-7245","authenticated-orcid":false,"given":"Nicolas","family":"Dias","sequence":"first","affiliation":[{"name":"Department of Genetics and the Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4868-7847","authenticated-orcid":false,"given":"Daniel P.","family":"Lewinsohn","sequence":"additional","affiliation":[{"name":"Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8328-4672","authenticated-orcid":false,"given":"William N.","family":"Colgan","sequence":"additional","affiliation":[{"name":"Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA"},{"name":"Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA"},{"name":"David H. 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