{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T15:42:04Z","timestamp":1776786124114,"version":"3.51.2"},"posted":{"date-parts":[[2026,4,17]]},"group-title":"Systems Biology","reference-count":82,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["R35 GM119850"],"award-info":[{"award-number":["R35 GM119850"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100002429","name":"Amgen Inc","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100002429","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Chinese hamster ovary (CHO) cells are the dominant host for therapeutic protein production, yet intra- and inter-clonal heterogeneity in manufacturing phenotypes, and the underlying metabolic and secretory circuitry, remain poorly defined at single-cell resolution. Here, we apply secretion encoded single-cell sequencing (SEC-seq) to simultaneously measure transcriptomes and secreted IgG in single-cells from a parental production cell line and five CHO clones, each varying in cell-specific productivity. IgG mRNA and recombinant protein secretion are only moderately correlated across single cells, indicating that transcription alone does not explain intra-clonal secretion heterogeneity. By integrating SEC-seq with single-cell metabolic and secretory task scoring, we find that CHO cells accommodating recombinant protein expression burden have more active translation-associated pathways and suppressed energy-intensive endogenous secreted protein processing. Three high-secreting clones converge on this translation-focused state but differ in their subpopulation composition and energy\/redox programs coupled to IgG output: one highly productive clone shows a low-growth, glycolytic, NAD\/one-carbon\u2013associated and UPR-activated program; a second shows increased oxidative phosphorylation and fatty-acid \u03b2-oxidation, and a third shows higher lipid-uptake with modest central carbon metabolism. Genes such as\n                  <jats:italic>Aldoa, Ndufab1, Acsl5, Mthfd2<\/jats:italic>\n                  showed clone-specific correlations with IgG, linking glycolysis, mitochondrial respiration, fatty-acid metabolism, and redox to secretion. Together, these results demonstrate that SEC-seq can resolve IgG-coupled metabolic-secretory wiring within and between CHO clones, providing a framework to identify subpopulation and circuit features to engineer or select for improved recombinant protein production.\n                <\/jats:p>","DOI":"10.64898\/2026.04.14.718270","type":"posted-content","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T19:05:22Z","timestamp":1776452722000},"source":"Crossref","is-referenced-by-count":0,"title":["SEC-seq reveals translation-focused metabolic strategies for high IgG productivity in clonal CHO cells"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5969-7416","authenticated-orcid":false,"given":"Jasmine","family":"Tat","sequence":"first","affiliation":[{"name":"Drug Substance Technologies, Amgen, Inc., Thousand Oaks, CA, USA"},{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3177-2092","authenticated-orcid":false,"given":"Fides D.","family":"Lay","sequence":"additional","affiliation":[{"name":"Drug Substance Technologies, Amgen, Inc., Thousand Oaks, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4081-4696","authenticated-orcid":false,"given":"Jennitte","family":"Stevens","sequence":"additional","affiliation":[{"name":"Drug Substance Technologies, Amgen, Inc., Thousand Oaks, CA, USA"},{"name":"insitro Inc., South San Francisco, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7700-3654","authenticated-orcid":false,"given":"Nathan E.","family":"Lewis","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA"},{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA"},{"name":"Center for Molecular Medicine, Complex Carbohydrate Research Center, and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 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