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January in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression

List by Barbora Knotkova, Matthew Davies, Felipe Del Valle Batalla, Girish Kale, Vibha SINGH

Preprints:

Biochemistry/metabolism

Valosin-containing Protein is Cargo in Amyloid Precursor Protein Extracellular Vesicles

Yue Lu, Mohammad Abdullah, Liam R. Healy, Marc D. Tambini

https://www.biorxiv.org/content/10.1101/2025.01.20.633888v1

This preprint identifies VCP, an autophagy-related protein, as cargo in amyloid-containing extracellular vesicles. Both VCP and amyloid proteins are associated with neurodegeneration. The authors suggest that these extracellular vesicles may have a new role in clearance of protein aggregates.

Picked by: Matthew Davies

Structure and function of the EDEM:PDI ERAD checkpoint complex

Charlie J. Hitchman, Andrea Lia, Gabriela N. Chiritoiu, Cristian V A Munteanu, Juan Ortigosa, Simona Ghenea, Christos G. Savva, Maria De Benedictis, Gabor Tax, Yusupha Bayo, Irene Crescioli, Dominic L. Alonzi, Andrew Quigley, Carlos P. Modenutti, Stefana M Petrescu, Angelo Santino, Bibek Gooptu, Pietro Roversi

https://www.biorxiv.org/content/10.1101/2025.01.29.635535v1

This preprint provides the first structural information and deeper mechanistic insights into the recognition of misfolded glycoproteins in the ER by the EDEM:PDI checkpoint protein complex.

Picked by: Barbora Knotkova

 

Sexually dimorphic ATF4 expression in the fat confers female stress tolerance in Drosophila melanogaster

Lydia Grmai, Melissa Mychalczuk, Aditya Arkalgud, Deepika Vasudevan

https://www.biorxiv.org/content/10.1101/2024.12.27.630478v1

This preprint looks at the basis of sexual dimorphism in fat tissue metabolism, determining that dimorphic expression of transcription factor ATF4 is responsible and confers higher tolerance to nutrient stress in females. Sexual dimorphism is an often overlooked variable and this preprint demonstrates, especially in metabolic studies, that researchers should be aware of its potential influence.

Picked by: Matthew Davies

From Grmai et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

Cell migration

Fast adaptation of Myosin II activity to confinement sustains neutrophil migration in capillaries

Mathieu Deygas, Mathilde Bernard, Pierre Nivoit, Lucie Barbier, Li Wang, Mathieu Maurin, Emmanuel Tejerina, Theresa Jakuszeit, Alexandre Deslys, Moira Garcia-Gomez, Oumaima Baaziz, Serge Garbay, Emmanuel Terriac, Rafaele Attia, Guillaume Duménil, Matthieu Piel, Pablo Vargas

https://www.biorxiv.org/content/10.1101/2025.01.08.631737v1

This preprint describes neutrophils under confinement dynamically adapting their actomyosin cytoskeleton within seconds which drives their fast migration in capillaries. These cytoskeleton changes were reversible, rapid, and independent from the confinement imposed on these cells. These findings provide crucial insights into autonomous mechanisms that inhibit tissue damage upon inflammation.

Picked by: Vibha Singh

Optogenetic control of a GEF of RhoA uncovers a signaling switch from retraction to protrusion

Jean De Seze, Maud Bongaerts, Benoit Boulevard, Mathieu Coppey

https://www.biorxiv.org/content/10.1101/2023.09.07.556666v4

This preprint identifies a single protein (RhoGEF) that can control opposing cell behaviors—protrusion or retraction—based on its concentration in the cell. While low levels cause retraction and high levels trigger protrusion. This switch within RhoGEF is controlled by the dynamics of Cdc42 activation and RhoA sequestration.

Picked by: Vibha Singh

CD44 and Ezrin restrict EGF receptor mobility to generate a novel spatial arrangement of cytoskeletal signaling modules driving bleb-based migration

Ankita Jha, Ankit Chandra, Payam Farahani, Jared Toettcher, Jason M. Haugh, Clare M. Waterman

https://www.biorxiv.org/content/10.1101/2024.12.31.630838v1

This paper is interesting because it reveals that in confined, non-adhesive environments, metastatic melanoma cells use a unique rear-to-front EGFR/PI3K signaling gradient, established by CD44 and ERM proteins restricting EGFR mobility, to drive stable bleb-based migration.

Picked by: Felipe Del Valle Batalla

From Jha et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

Cell organelles and organisation

Centriole Loss in Embryonic Development Disrupts Axonal Pathfinding and Muscle Integrity

Beatriz González, Júlia Sellés-Altés, Jèrica Pla-Parron, Judith Castro-Ribera, Sofia J. Araújo

https://www.biorxiv.org/content/10.1101/2025.01.26.634909v1

Despite being the major microtubule (MTs) nucleator in dividing cells, centrosomes are less required in differentiated cells, with MTs often arising non-centrosomally. Here, the authors confirm that nucleation from centrosomes is needed for correct axonal pathfinding.

Picked by: Matthew Davies

Protein Kinase C positively regulates peroxisome biogenesis by promoting peroxisome-endoplasmic reticulum interaction

Anya Borisyuk, Charlotte Howman, Sundararaghavan Pattabiraman, Daniel Kaganovich, Triana Amen

https://www.biorxiv.org/content/10.1101/2025.01.21.634043v1

This preprint helps to resolve some of the obscurity that still surrounds peroxisomes and links their biogenesis to Protein kinase C signalling.

Picked by: Barbora Knotkova

From Borisyuk et al. This image is made available under a CC-BY 4.0 International license.

Redistribution of proteasomes through diffusion and cytoskeleton-dependent mechanisms upon stress induced by protein aggregates

Michael J Morten, Yu Zhang, Bing Li, Jonathan X Meng, Kun Jiang, Liina Sirvio, Ji Eun Lee, Anna Helena Lippert, Matilda Burridge, Katiuska Daniela Pulgar Prieto, Alexander Roy Carr, Aleks Ponjavic, Steven F Lee, Daniel Finley, David Klenerman, Yu Ye

https://www.biorxiv.org/content/10.1101/487702v2

This preprint uncovers differences in proteasomal distribution and movement under different cellular conditions including proteotoxic stress and depolarisation. It is suggested that these differences may influence rate of protein aggregate degradation.

Picked by: Matthew Davies

Giant KASH proteins and ribosomes synergistically establish cytoplasmic biophysical properties in vivo

Xiangyi Ding, Hongyan Hao, Daniel Elnatan, Patrick Neo Alinaya, Shilpi Kalra, Abby Kaur, Sweta Kumari, Liam J. Holt, G. W. Gant Luxton, Daniel A. Starr

https://www.biorxiv.org/content/10.1101/2025.01.10.632479v1

This preprint uses a novel approach to study cytoplasmic biophysical properties on C. elegans.  The study employs genetically encoded multimeric nanoparticles (GEMs) as rheological tools directly within the living organism. This enables the observation of cytoplasmic properties in their natural environment, avoiding potential alterations introduced by cell isolation and culture.

Picked by: Felipe Del Valle Batalla

From Ding et al. This image is made available under a CC-BY-NC 4.0 International license.

MISO Regulates Mitochondria Dynamics and mtDNA Homeostasis by Establishing Inner Membrane Subdomains

Yue Zhang, Yuchen Xia, Xinhui Wang, Shang Wu, Jianshuang Li, Xuan Guo, Qinghua Zhou, Li He

https://www.biorxiv.org/content/10.1101/2025.01.05.631328v1

This preprint describes a novel mitochondrial organising protein called MISO. Through oligomerisation, MISO forms subdomains of the inner mitochondrial membrane which recruit mtDNA, promote fission at the periphery of the mitochondrial network and are associated with mitophagy.

Picked by: Barbora Knotkova

Cell signalling and mechanosensing

Mitochondrial Ca2+ flickers on endoplasmic reticulum (ER)-mitochondrial contact sites to suppress store-operated Ca2+ entry

Yu-Chiao Lin, Feng-Chiao Tsai

https://www.biorxiv.org/content/10.1101/2025.01.17.633482v1

In this preprint the authors show that calcium flickering at ER-mitochondria contact sites does not lower ER calcium levels through transfer of calcium from the ER to mitochondria, but via decrease of calcium uptake by store-operated calcium entry.

Picked by: Barbora Knotkova

Matrix stiffness modulated release of spheroid-derived extracellular vesicles and discovery of Piezo1 cargo

Maulee Sheth, Manju Sharma, Supasek Kongsomros, Maria Lehn, Takanori Takebe, Vinita Takiar, Trisha Wise-Draper, Somchai Chutipongtanate, Leyla Esfandiari

https://www.biorxiv.org/content/10.1101/2025.01.13.632826v1

This preprint is relevant because it investigates how extracellular matrix (ECM) stiffness affects the release and composition of extracellular vesicles (EVs) from cancer cells . It also shows that EVs carry parental molecular cargo, including mechanosensitive Piezo1.

Picked by: Felipe Del Valle Batalla

Genetically encoded mechano-sensors with versatile readouts and compact size

Yuan Ren, Jie Yang, Takumi Saito, Oliver Glomb, Sayed Iman Mousavi, Brigitte Naughton, Christina de Fontnouvelle, Barbara Fujita, Christian Schlieker, Shaul Yogev, Yongli Zhang, Julien Berro

https://www.biorxiv.org/content/10.1101/2025.01.16.633409v1

A new kind of tension sensor using coiled-coil protein domains. The length of the domain determines the force sensitivity, making them tuneable depending on the experimental requirements and expectations.

Picked by: Girish Kale

From Ren et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

Tissue-dependent mechanosensing by cells derived from human tumors

Kshitiz Parihar, Jonathan Nukpezah, Daniel V Iwamoto, Katrina Cruz, Fitzroy J Byfield, LiKang Chin, Maria E Murray, Melissa G Mendez, Anne S van Oosten, Anne Herrmann, Elisabeth E Charrier, Peter A Galie, Megan Donlick, Tongkeun Lee, Paul A Janmey, Ravi Radhakrishnan

https://www.biorxiv.org/content/10.1101/2025.01.11.632563v1

Not all tumors are the same! This preprint tests how the response of cancerous cells to different extracellular environments (mechanical and chemical) depends on where these cells originate from, i.e., their native tissue type. This has strong implications for the metastatic potential of tumors in different tissues.

Picked by: Girish Kale

Linking Molecular Tension and Cellular Tractions: A Multiscale Approach to Focal Adhesion Mechanics

Samet Aytekin, Laurens Kimps, Quinten Coucke, Débora Linhares, Swaraj Deodhar, Ruth Cardinaels, Mar Cóndor, Jorge Barrasa-Fano, Hans Van Oosterwyck, Susana Rocha

https://www.biorxiv.org/content/10.1101/2025.01.09.632081v1

This preprint links tension measurements using (intra-cellular) FRET-based tension probes and (extra-cellular) traction exerted by the cells.

Picked by: Girish Kale

Fibroblast contractility drives network reorganization and epithelial proliferation in intestinal polyposis

Mei-Lan Li, Yuying Wang, Maria Figetakis, David Gonzalez, Jason Jin, Elizabeth S. McDonald, Nadia A. Ameen, Kaelyn Sumigray

https://www.biorxiv.org/content/10.1101/2025.01.08.632004v1

This study identifies fibroblasts, not epithelial cells, as the first regulator of epithelial dysregulation implicated in polyposis disease. A stepwise molecular mechanism delineates how fibroblast signaling and cell mechanics relate to epithelial homeostasis and offers novel understandings of the commencement of the disease and possible therapeutic targets.

Picked by: Vibha Singh

Genetics/gene expression

Evidence for increased stress resistance due to polyploidy from synthetic autotetraploid Caenorhabditis elegans

Laetitia Chauve, Emma Bazzani, Clément Verdier, Liam Butler, Martha E. Atimise, Aoibhín McGarry, Aoife McLysaght

https://www.biorxiv.org/content/10.1101/2023.06.28.546823v4

This preprint looks at the evolutionary advantage of randomly-occurring whole genome duplication (WGD). This is actually a common event resulting in another copy of the entire genome being present in the nucleus. Here, the authors show that induced WGD in C elegans gives increased stress resistance under cold conditions, causing decreased induction of the zip-10 cold-activated cell death programme.

Picked by: Matthew Davies

 

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Biochemistry

Enzymatic access to the rare ΔUA (1→4) Glc 3, 6, N-sulfated heparin disaccharide, implications for heparin quality control

T. K. Kandola, C. J. Mycroft-West, M. L. Andrade De Lima, et al.

Selected by 03 January 2025

Adriani Felix et al.

Biochemistry

Factor XI localization in human deep venous thrombus and function of activated factor XI on venous thrombus formation and hemostasis in rabbit

Nobuyuki Oguri, Toshihiro Gi, Eriko Nakamura, et al.

Selected by 03 January 2025

Adriani Felix et al.

Biochemistry

Also in the cell biology category:

Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons

Klaudia Strucinska, Parker Kneis, Travis Pennington, et al.

Selected by 11 February 2025

Felipe Del Valle Batalla

Cell Biology

Mechanical stresses govern myoblast fusion and myotube growth

Yoann Le Toquin, Sushil Dubey, Aleksandra Ardaševa, et al.

Selected by 29 January 2025

Vibha SINGH, Prasanna Padmanaban

Cell Biology

Polystyrene nanoplastics promote neurodegeneration by catalyzing TDP43 hyperphosphorylation

Winanto, Li-Yi Tan, Wai Hon Chooi, et al.

Selected by 08 January 2025

Manuel Lessi

Neuroscience

Also in the genetics category:

Intracellular diffusion in the cytoplasm increases with cell size in fission yeast

Catherine Tan, Michael C. Lanz, Matthew Swaffer, et al.

Selected by 18 October 2024

Leeba Ann Chacko, Sameer Thukral

Cell Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA

Brett T. Wisniewski, Laura L. Lackner

Selected by 30 August 2024

Leeba Ann Chacko

Cell Biology

Also in the molecular biology category:

Levetiracetam prevents Aβ42 production through SV2a-dependent modulation of App processing in Alzheimer’s disease models

Nalini R. Rao, Olivia DeGulis, Toshihiro Nomura, et al.

Selected by 11 January 2025

Jawdat Sandakly

Neuroscience

Chromosomal instability in human trophoblast stem cells and placentas

Danyang Wang, Andrew Cearlock, Katherine Lane, et al.

Selected by 31 December 2024

Carly Guiltinan

Cell Biology

Germplasm stability in zebrafish requires maternal Tdrd6a and Tdrd6c

Alessandro Consorte, Yasmin El Sherif, Fridolin Kielisch, et al.

Selected by 13 December 2024

Justin Gutkowski

Developmental Biology