A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells

Pablo Di Giusto; Dong Hyuk Choi; Athanasios Antonakoudis; Vikash Gokul Duraikannan; Pierrick Craveur; Nicholas Luke Cowie; Tejaswini Ganapathy; Kannan Ramesh; Santiago Benavidez-López; Camila A. Orellana; Natalia E. Jiménez; Leo Alexander Dworkin; James Morrissey; Igor Marin de Mas; Benjamin Strain; Norma A. Valdez-Cruz; Mauricio A. Trujillo-Roldán; Jannis Marzluf; Verónica S. Martínez; Leopold Zehetner; Claudia Altamirano; Ana Maria Vega-Letter; Bradley Priem; Haoyu Chris Cao; Martin Hold; Junyu Ma; Yi Fan Hong; Saratram Gopalakrishnan; Blaise Manga Enuh; Chaimaa Tarzi; Kuin Tian Pang; Claudio Angione; Jürgen Zanghellini; Cleo Kontoravdi; Hooman Hefzi; Michael J. Betenbaugh; Lars K. Nielsen; Meiyappan Lakshmanan; Dong Yup Lee; Anne Richelle; Nathan E. Lewis

doi:10.1016/j.cels.2026.101574

A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells

Pablo Di Giusto
, Dong Hyuk Choi
, Athanasios Antonakoudis
, Vikash Gokul Duraikannan
, Pierrick Craveur
, Nicholas Luke Cowie
, Tejaswini Ganapathy
, Kannan Ramesh
, Santiago Benavidez-López
, Camila A. Orellana
, Natalia E. Jiménez
, Leo Alexander Dworkin
, James Morrissey
, Igor Marin de Mas
, Benjamin Strain
, Norma A. Valdez-Cruz
, Mauricio A. Trujillo-Roldán
, Jannis Marzluf
, Verónica S. Martínez
, Leopold Zehetner

Claudia Altamirano, Ana Maria Vega-Letter, Bradley Priem, Haoyu Chris Cao, Martin Hold, Junyu Ma, Yi Fan Hong, Saratram Gopalakrishnan, Blaise Manga Enuh, Chaimaa Tarzi, Kuin Tian Pang, Claudio Angione, Jürgen Zanghellini, Cleo Kontoravdi, Hooman Hefzi, Michael J. Betenbaugh, Lars K. Nielsen, Meiyappan Lakshmanan^*, Dong Yup Lee^*, Anne Richelle^*, Nathan E. Lewis^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Genome-scale metabolic models (GEMs) are indispensable for studying cellular metabolism. We present iCHO3K, a community-consensus, manually curated reconstruction of the Chinese hamster metabolic network. Spanning 11,004 reactions linked to 3,597 genes, iCHO3K augments the network with 3,489 protein structures and physicochemical descriptors for >70% of 7,377 metabolites, enabling structure-aware analyses. We applied iCHO3K to contextualize transcriptomics and metabolomics from a fed-batch Chinese hamster ovary (CHO) cell line engineered to abolish lactate secretion. The model indicated reduced glycolytic flux with enhanced tricarboxylic acid (TCA) activity and elevated intracellular NADH and phosphoenolpyruvate (PEP), consistent with experimental measurements. Leveraging iCHO3K's structural annotations, we evaluated potential off-target binding of NADH and PEP across early glycolytic enzymes and identified a putative allosteric PEP interaction with phosphofructokinase, suggesting a structural mechanism underlying reduced glucose uptake and glycolytic flux. Overall, iCHO3K provides a framework for systematic multi-omics integration, improved flux prediction, and structure-guided mechanistic insight, advancing CHO cell engineering and biomanufacturing. A record of this paper's transparent peer review process is included in the supplemental information.

Original language	English
Article number	101574
Journal	Cell Systems
DOIs	https://doi.org/10.1016/j.cels.2026.101574
State	Accepted/In press - 2026
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2026 Elsevier Inc.

Keywords

CHO bioprocessing
Chinese hamster
Warburg effect
enzyme-constrained flux balance analysis
genome-scale metabolic model
iCHO3K
structural systems biology

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10.1016/j.cels.2026.101574

Cite this

Di Giusto, P., Choi, D. H., Antonakoudis, A., Duraikannan, V. G., Craveur, P., Cowie, N. L., Ganapathy, T., Ramesh, K., Benavidez-López, S., Orellana, C. A., Jiménez, N. E., Dworkin, L. A., Morrissey, J., Marin de Mas, I., Strain, B., Valdez-Cruz, N. A., Trujillo-Roldán, M. A., Marzluf, J., Martínez, V. S., ... Lewis, N. E. (Accepted/In press). A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells. Cell Systems, Article 101574. https://doi.org/10.1016/j.cels.2026.101574

@article{7c81b43828614648836ba9cfbbcefb0e,

title = "A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells",

abstract = "Genome-scale metabolic models (GEMs) are indispensable for studying cellular metabolism. We present iCHO3K, a community-consensus, manually curated reconstruction of the Chinese hamster metabolic network. Spanning 11,004 reactions linked to 3,597 genes, iCHO3K augments the network with 3,489 protein structures and physicochemical descriptors for >70\% of 7,377 metabolites, enabling structure-aware analyses. We applied iCHO3K to contextualize transcriptomics and metabolomics from a fed-batch Chinese hamster ovary (CHO) cell line engineered to abolish lactate secretion. The model indicated reduced glycolytic flux with enhanced tricarboxylic acid (TCA) activity and elevated intracellular NADH and phosphoenolpyruvate (PEP), consistent with experimental measurements. Leveraging iCHO3K's structural annotations, we evaluated potential off-target binding of NADH and PEP across early glycolytic enzymes and identified a putative allosteric PEP interaction with phosphofructokinase, suggesting a structural mechanism underlying reduced glucose uptake and glycolytic flux. Overall, iCHO3K provides a framework for systematic multi-omics integration, improved flux prediction, and structure-guided mechanistic insight, advancing CHO cell engineering and biomanufacturing. A record of this paper's transparent peer review process is included in the supplemental information.",

keywords = "CHO bioprocessing, Chinese hamster, Warburg effect, enzyme-constrained flux balance analysis, genome-scale metabolic model, iCHO3K, structural systems biology",

author = "\{Di Giusto\}, Pablo and Choi, \{Dong Hyuk\} and Athanasios Antonakoudis and Duraikannan, \{Vikash Gokul\} and Pierrick Craveur and Cowie, \{Nicholas Luke\} and Tejaswini Ganapathy and Kannan Ramesh and Santiago Benavidez-L{\'o}pez and Orellana, \{Camila A.\} and Jim{\'e}nez, \{Natalia E.\} and Dworkin, \{Leo Alexander\} and James Morrissey and \{Marin de Mas\}, Igor and Benjamin Strain and Valdez-Cruz, \{Norma A.\} and Trujillo-Rold{\'a}n, \{Mauricio A.\} and Jannis Marzluf and Mart{\'i}nez, \{Ver{\'o}nica S.\} and Leopold Zehetner and Claudia Altamirano and Vega-Letter, \{Ana Maria\} and Bradley Priem and Cao, \{Haoyu Chris\} and Martin Hold and Junyu Ma and Hong, \{Yi Fan\} and Saratram Gopalakrishnan and Enuh, \{Blaise Manga\} and Chaimaa Tarzi and Pang, \{Kuin Tian\} and Claudio Angione and J{\"u}rgen Zanghellini and Cleo Kontoravdi and Hooman Hefzi and Betenbaugh, \{Michael J.\} and Nielsen, \{Lars K.\} and Meiyappan Lakshmanan and Lee, \{Dong Yup\} and Anne Richelle and Lewis, \{Nathan E.\}",

note = "Publisher Copyright: {\textcopyright} 2026 Elsevier Inc.",

year = "2026",

doi = "10.1016/j.cels.2026.101574",

language = "English",

journal = "Cell Systems",

issn = "2405-4712",

publisher = "Cell Press",

}

Di Giusto, P, Choi, DH, Antonakoudis, A, Duraikannan, VG, Craveur, P, Cowie, NL, Ganapathy, T, Ramesh, K, Benavidez-López, S, Orellana, CA, Jiménez, NE, Dworkin, LA, Morrissey, J, Marin de Mas, I, Strain, B, Valdez-Cruz, NA, Trujillo-Roldán, MA, Marzluf, J, Martínez, VS, Zehetner, L, Altamirano, C, Vega-Letter, AM, Priem, B, Cao, HC, Hold, M, Ma, J, Hong, YF, Gopalakrishnan, S, Enuh, BM, Tarzi, C, Pang, KT, Angione, C, Zanghellini, J, Kontoravdi, C, Hefzi, H, Betenbaugh, MJ, Nielsen, LK, Lakshmanan, M, Lee, DY, Richelle, A & Lewis, NE 2026, 'A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells', Cell Systems. https://doi.org/10.1016/j.cels.2026.101574

TY - JOUR

T1 - A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells

AU - Di Giusto, Pablo

AU - Choi, Dong Hyuk

AU - Antonakoudis, Athanasios

AU - Duraikannan, Vikash Gokul

AU - Craveur, Pierrick

AU - Cowie, Nicholas Luke

AU - Ganapathy, Tejaswini

AU - Ramesh, Kannan

AU - Benavidez-López, Santiago

AU - Orellana, Camila A.

AU - Jiménez, Natalia E.

AU - Dworkin, Leo Alexander

AU - Morrissey, James

AU - Marin de Mas, Igor

AU - Strain, Benjamin

AU - Valdez-Cruz, Norma A.

AU - Trujillo-Roldán, Mauricio A.

AU - Marzluf, Jannis

AU - Martínez, Verónica S.

AU - Zehetner, Leopold

AU - Altamirano, Claudia

AU - Vega-Letter, Ana Maria

AU - Priem, Bradley

AU - Cao, Haoyu Chris

AU - Hold, Martin

AU - Ma, Junyu

AU - Hong, Yi Fan

AU - Gopalakrishnan, Saratram

AU - Enuh, Blaise Manga

AU - Tarzi, Chaimaa

AU - Pang, Kuin Tian

AU - Angione, Claudio

AU - Zanghellini, Jürgen

AU - Kontoravdi, Cleo

AU - Hefzi, Hooman

AU - Betenbaugh, Michael J.

AU - Nielsen, Lars K.

AU - Lakshmanan, Meiyappan

AU - Lee, Dong Yup

AU - Richelle, Anne

AU - Lewis, Nathan E.

PY - 2026

Y1 - 2026

N2 - Genome-scale metabolic models (GEMs) are indispensable for studying cellular metabolism. We present iCHO3K, a community-consensus, manually curated reconstruction of the Chinese hamster metabolic network. Spanning 11,004 reactions linked to 3,597 genes, iCHO3K augments the network with 3,489 protein structures and physicochemical descriptors for >70% of 7,377 metabolites, enabling structure-aware analyses. We applied iCHO3K to contextualize transcriptomics and metabolomics from a fed-batch Chinese hamster ovary (CHO) cell line engineered to abolish lactate secretion. The model indicated reduced glycolytic flux with enhanced tricarboxylic acid (TCA) activity and elevated intracellular NADH and phosphoenolpyruvate (PEP), consistent with experimental measurements. Leveraging iCHO3K's structural annotations, we evaluated potential off-target binding of NADH and PEP across early glycolytic enzymes and identified a putative allosteric PEP interaction with phosphofructokinase, suggesting a structural mechanism underlying reduced glucose uptake and glycolytic flux. Overall, iCHO3K provides a framework for systematic multi-omics integration, improved flux prediction, and structure-guided mechanistic insight, advancing CHO cell engineering and biomanufacturing. A record of this paper's transparent peer review process is included in the supplemental information.

AB - Genome-scale metabolic models (GEMs) are indispensable for studying cellular metabolism. We present iCHO3K, a community-consensus, manually curated reconstruction of the Chinese hamster metabolic network. Spanning 11,004 reactions linked to 3,597 genes, iCHO3K augments the network with 3,489 protein structures and physicochemical descriptors for >70% of 7,377 metabolites, enabling structure-aware analyses. We applied iCHO3K to contextualize transcriptomics and metabolomics from a fed-batch Chinese hamster ovary (CHO) cell line engineered to abolish lactate secretion. The model indicated reduced glycolytic flux with enhanced tricarboxylic acid (TCA) activity and elevated intracellular NADH and phosphoenolpyruvate (PEP), consistent with experimental measurements. Leveraging iCHO3K's structural annotations, we evaluated potential off-target binding of NADH and PEP across early glycolytic enzymes and identified a putative allosteric PEP interaction with phosphofructokinase, suggesting a structural mechanism underlying reduced glucose uptake and glycolytic flux. Overall, iCHO3K provides a framework for systematic multi-omics integration, improved flux prediction, and structure-guided mechanistic insight, advancing CHO cell engineering and biomanufacturing. A record of this paper's transparent peer review process is included in the supplemental information.

KW - CHO bioprocessing

KW - Chinese hamster

KW - Warburg effect

KW - enzyme-constrained flux balance analysis

KW - genome-scale metabolic model

KW - iCHO3K

KW - structural systems biology

UR - https://www.scopus.com/pages/publications/105036450708

U2 - 10.1016/j.cels.2026.101574

DO - 10.1016/j.cels.2026.101574

M3 - Article

AN - SCOPUS:105036450708

SN - 2405-4712

JO - Cell Systems

JF - Cell Systems

M1 - 101574

ER -

A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells

Abstract

Bibliographical note

Keywords

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