Cell Biology

Transcriptomic profile of embryoid bodies under hypoxia at single cell level

1. Bárbara Acosta-Iborra
2. Yosra Berrouayel
3. Laura Puente-Santamaría
4. Luis del Peso
5. Benilde Jiménez

• Curated by GigaByte

  Editors Assessment:

  This is a Data Release paper describing a mouse embryoid body single-cell RNA-seq dataset generated to study how oxygen availability shapes early cell differentiation. Acosta-Iborra et al. differentiated R1 mouse embryonic stem cells into embryoid bodies for 8 or 10 days, exposing them to hypoxia or normoxia for the final 16 or 48 hours of differentiation, then profiled thousands of cells per condition using droplet-based scRNA-seq from 10X. This yielding eight raw/filtered HDF5 count matrices across the four conditions. This was validated with flow cytometry, immunofluorescence, and EdU assays, confirming that hypoxia increased endothelial marker expression and vascular network complexity while inducing cell cycle arrest. This pattern mirrored transcriptionally, with hypoxic samples showing markedly higher proportions of cells in G0/G1 phase and elevated hypoxia gene-signature scores. QC analysis (and peer review in GigaByte) confirmed high data quality across samples, and conservative low-resolution clustering revealed a largely homogeneous progenitor population with a smaller, more differentiated subset. While there are limitations (mature endothelial cells were too sparse to robustly test the original hypothesis) the authors present this as an open, well-validated resource for comparative studies of hypoxia responses, benchmarking single-cell computational tools, and investigating early lineage specification and oxygen signaling more broadly.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Identification of nuclear pore proteins at plasmodesmata: potential role in intercellular transport?

1. T Moritz Schladt
2. Manuel Miras
3. Jona Obinna Ejike
4. Mathieu Pottier
5. Lin Xi
6. Andrea Restrepo-Escobar
7. Masayoshi Nakamura
8. Niklas Pütz
9. Sebastian Hänsch
10. Chen Gao
11. Julia Engelhorn
12. Marcel Dickmanns
13. Gwendolyn V Davis
14. Ahan Dalal
15. Sven Gombos
16. Ronja Lange
17. Rüdiger Simon
18. Waltraud X Schulze
19. Wolf B Frommer

• Curated by eLife

  eLife Assessment

  Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport at plasmodesmata and into the nucleus, the authors present the bold and potentially transformational hypothesis that nuclear pore complex proteins (NUPs) might be involved in plasmodesmata function. Here, the authors localize a subset of NUPs to plasmodesmata using proteomics and fluorescent imaging. They acknowledge many limitations to their work, including potential artifacts and the lack of functional validation of multiple NUPs, which may complicate the interpretation of their mostly solid results. Further experiments will be necessary to fully test this fundamental hypothesis about the function of NUPs at plasmodesmata.

Reviewed by eLife

Peripheral lysosomes recruit PLEKHG3 to focal adhesions and restrain protrusion dynamics

1. Rainer Ettelt
2. Ana-Maria Sandru
3. Georg Vucak
4. Sebastian Didusch
5. Biljana Riemelmoser
6. Karin Ehrenreiter
7. Markus Hartl
8. Lukas A. Huber
9. Manuela Baccarini

Reviewed by Review Commons

Muscular dystrophy-associated lamin variants disrupt cellular organization through a nucleolar-ribosomal axis controlling cytoplasmic macromolecular crowding

1. Xiangyi Ding
2. Sweta Kumari
3. Ellen Gregory
4. Daniel A. Starr
5. G. W. Gant Luxton

Reviewed by Arcadia Science

Syntaxin11 Deficiency Inhibits CRAC Channel Priming to Suppress Cytotoxicity and Gene Expression in T Lymphocytes

1. Sritama Datta
2. Abhikarsh Gupta
3. Kunal Mukesh Jagetiya
4. Resmi Bera
5. Vikas Tiwari
6. Atharva Rahul Yande
7. Megumi Yamashita
8. Abdul Rishad
9. Vishal Malik
10. Sreejith Raran-Kurussi
11. Sandra Ammann
12. Mohammad Shahrooei
13. Kalyaneswar Mandal
14. Ramanathan Sowdhamini
15. Murali Prakriya
16. Adish Dani
17. Monika Vig

• Curated by eLife

  eLife Assessment

  This study reports a novel function for syntaxin 11, a specialized SNARE protein critical for the immune system whose mutations cause familial hemophagocytic lymphohistiocytosis type 4. The data convincingly show that depletion of STX11 impairs store-operated calcium entry in Jurkat T cells and that this defect is recapitulated in primary cells from a patient suffering from the disease; the authors further show that the syntaxin interacts with the pore subunit of the ORAI1 channel and propose that it primes the channel by promoting the assembly of multimers before activation by its endogenous ligand, the ER Ca2+ sensing protein STIM1. This is a conceptually important claim that challenges the prevailing view that all structural transitions in ORAI1 are STIM-driven. The data are high-quality and broadly consistent with the interpretation, but alternative mechanisms for the defects are not considered; additional work should rule out vesicular trafficking, discuss other mechanisms, and address methodological issues.

Reviewed by eLife