Evidence map›Paper›PMID 41380680›Full record

ArticleCell systems2025

A reconstruction of the mammalian secretory pathway identifies mechanisms regulating antibody production.

Helen Masson, Jasmine Tat, Pablo Di Giusto, Athanasios Antonakoudis, Isaac Shamie, Hratch Baghdassarian, Mojtaba Samoudi, Caressa M Robinson, Chih-Chung Kuo, Natalia Koga and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Fantastic genes and where to find them expressed in CHO.Computational and structural biotechnology journal · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Helen MassonDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Jasmine TatDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Pablo Di GiustoDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Athanasios AntonakoudisSartorius Corporate Research, Royston SG8 5WY, UK.
Isaac ShamieBioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA.
Hratch BaghdassarianBioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA.
Mojtaba SamoudiDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Caressa M RobinsonDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Chih-Chung KuoDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Natalia KogaDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Sonia SinghDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Angel GezalyanDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Zerong LiDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Alexia MovsessianDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Anne RichelleSartorius Corporate Research, Brussels 1030, Belgium.
Nathan E LewisDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Molecular Medicine, Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. Electronic address: natelewis@uga.edu.

Funding

Unraveling the mammalian secretory pathway through systems biology and algorithm developmentR35GM119850 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LEWIS, NATHAN ENOCH · 2016 to 2025
$4.3M
ImmCellFIE: producing high-resolution snapshots of the functions of immune cellsUH2AI153029 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LEWIS, NATHAN ENOCH, ROBASKY, KIMBERLY JOAN · 2020 to 2021
$445k
NIAID NIH HHS UH2 AI153029NIGMS NIH HHS R35 GM119850
6 · The paper itself

Abstract

The secretory pathway processes >30% of mammalian proteins, orchestrating their synthesis, modification, trafficking, and quality control across multiple organelles via coordinated interactions, making its regulation difficult to decipher. To advance such research, we present secRecon, a reconstruction of the mammalian secretory pathway, comprising 1,127 manually curated genes organized within 77 secretory process terms, annotated with functional roles, subcellular localization, protein interactions, and complexes. Applying secRecon to omics data revealed distinct secretory topologies in antibody-producing plasma cells versus Chinese hamster ovary (CHO) cells, with CHO-specific deficiencies in proteostasis, translocation, and N-glycosylation genes, highlighting targets to enhance secretion. Analysis of single-cell SEC-seq data uncovered diversity in IgG-secreting plasma cells that is shaped by the unfolded protein response, endoplasmic reticulum (ER)-associated degradation, and vesicle trafficking and identified distinct secretory machinery genes as markers of plasma cell differentiation. These results show that secRecon enables the discovery of mechanisms controlling protein secretion and supports applications in both biomedical research and biotechnology. A record of this paper's transparent peer review process is included in the supplemental information.

Indexed as

Antibody FormationSecretory PathwayAnimalsCHO CellsCricetulusEndoplasmic ReticulumHumansMammalsPlasma CellsProtein TransportUnfolded Protein ResponseCHO cellsmulti-omicsplasma cellssecReconsecretory pathway reconstructionSEC-seq

Identifiers

PMID41380680
PMCPMC12704830

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.