eLife

Latest preprint reviews

1. Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies

   This article has 9 authors:

   1. Spencer C Ding
   2. Jingru Yu
   3. Tiepeng Liao
   4. Lauren S Ahmann
   5. Yvette Y Yao
   6. Chandler Ho
   7. Linlin Wang
   8. Benjamin A Pinsky
   9. Wei Gu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work provides a new method to extract cfDNA from residual plasma from heparin separators for molecular testing. The evidence supporting the authors' claims is convincing, although some further metrics should also be evaluated. This finding will be interesting to people working in epigenomics and infectious disease diagnostics.

   Reviewed by eLife

2. Mediator Subunit MED16 Collaborates with UBP1-TFCP2 to Control Transcriptional Activation or Repression via Promoter Positional Specificity

   This article has 8 authors:

   1. Yuanming Zheng
   2. Xiaying Zhao
   3. Ming Yang
   4. Xinyi Yang
   5. Huanzhang Zhu
   6. Xiaofei Yu
   7. Qiang Zhou
   8. Gang Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The characterization of a dissociable Mediator subunit implicated in cellular pathways, particularly lung alveolar function and HIV latency, would be conceptually interesting. The authors have preliminary evidence for a stable Med16 subcomplex that may regulate specific genes. This work is useful in that it points to interactions between Med16 and UBP1, but the evidence is preliminary and incomplete.

   Reviewed by eLife

3. The genetic control of rapid genome content divergence in Arabidopsis thaliana

   This article has 2 authors:

   1. Christopher J Fiscus
   2. Daniel Koenig

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study systematically investigates repeat expansion in the plant Arabidopsis thaliana using a new k-mer-based method, expanding on smaller studies to more comprehensively identify cis- and trans-acting loci associated with repeat dynamics. The approach is methodologically sound and broadly applicable to large-scale short-read datasets for assessing copy number variation and genomic repeat content. While convincing in its scope and novelty, the findings would be further strengthened with exploratory analyses of datasets from other species with more or fewer repeats in their genomes.

   Reviewed by eLife

4. Decoding molecular mechanisms for loss-of-function variants in the human proteome

   This article has 3 authors:

   1. Matteo Cagiada
   2. Nicolas Jonsson
   3. Kresten Lindorff-Larsen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work introduces FunC-ESMs, a proteome-scale framework to classify loss-of-function missense variants into distinct mechanistic groups by combining two complementary state-of-the-art machine learning models. The strength of evidence is convincing, supported by solid benchmarking, integration with experimental datasets, and careful methodological design. The significance of the findings is valuable, providing a resource of clear interest to researchers and diagnostic laboratories working on variant interpretation.

   Reviewed by eLife

5. CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

   This article has 8 authors:

   1. Lanlan Ji
   2. An Wang
   3. Shreyash Sonthalia
   4. Seungmae Seo
   5. Daniel Q Naiman
   6. Laurent Younes
   7. Carlo Colantuoni
   8. Donald Geman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

   Reviewed by eLife

6. Mid-zone hepatocytes trade proliferation for survival via Atf4-Chop axis in early acute liver injury

   This article has 7 authors:

   1. Yaying Zhu
   2. Chengxiang Deng
   3. Bo Chen
   4. Jia He
   5. Yanan Liu
   6. Cheng Peng
   7. Zhao Shan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study addresses an important question in liver biology: how zonal hepatocytes balance survival and proliferation following injury; using spatial transcriptomics, mechanistic perturbations, and functional assays, the authors propose that a mid-zone Atf4-Chop axis to Btg2 program temporarily suppresses proliferation to promote survival during APAP-induced hepatotoxicity. The idea that distinct intrahepatic zones mount tailored stress responses is conceptually significant and has implications for regeneration and toxicology. The dataset is rich and the methodology modern, but several conclusions rely on assumptions about zonation under injury, limited injury models, and incomplete functional validation of the Atf4-Chop-Btg2 axis. With targeted revisions and additional experiments, the work has the potential to provide strong mechanistic insights into liver zonation and injury responses.

   Reviewed by eLife

7. Blocking Osteoprotegerin Reprograms Cancer Associated Fibroblast to Promotes Immune Infiltration into the Tumor Microenvironment

   This article has 12 authors:

   1. Yao Wang
   2. Hara Apostolopoulou
   3. Im Hong Sun
   4. Arjan Bains
   5. David Gibbs
   6. Sui Huang
   7. Tamara Alliston
   8. Ajay Maker
   9. Thea Tlsty
   10. Vasilis Ntranos
   11. James M Gardner
   12. Anil Bhushan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important finding by identifying OPG as a novel stromal checkpoint influencing T-cell anti-tumor responses, thereby shedding new light on the complex interplay between the tumor microenvironment and immune regulation. The data are robust and the experimental approaches are sound, providing solid support for the study's conclusions; however, there are a number of additional questions raised by the data. Of particular note are the questions raised on the mechanistic effects of TRAIL versus RANKL. In addition, it would broaden the interest in this study to include more translational human data to complement the work presented.

   Reviewed by eLife

8. Lipopolysaccharide stimulates dynamic changes in B cell metabolism to promote proliferation

   This article has 8 authors:

   1. Dana MS Cheung
   2. Momchil Razsolkov
   3. Fabrizia Bonacina
   4. Stephen Andrews
   5. Megan Sumoreeah
   6. Linda V Sinclair
   7. Andrew JM Howden
   8. J Simon C Arthur

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work reveals metabolic pathways and molecular events mechanistically linked to B cell activation. Using an unbiased, comprehensive proteome profiling method and various functional validation approaches, this study generated convincing evidence suggesting a role for amino acid uptake, cholesterol accumulation, and protein prenylation in the proliferation, survival, and biogenesis of B cells stimulated with LPS and other activating stimuli. The significance of the findings is considered to be fundamental, in that they will advance our understanding of cell metabolism during B cell activation.

   Reviewed by eLife

9. Evolution of a fuzzy ribonucleoprotein complex in viral assembly

   This article has 15 authors:

   1. Huaying Zhao
   2. Tiansheng Li
   3. Sergio A Hassan
   4. Ai Nguyen
   5. Siddhartha AK Datta
   6. Guofeng Zhang
   7. Camden Trent
   8. Agata M Czaja
   9. Di Wu
   10. Maria A Aronova
   11. Kin Kui Lai
   12. Grzegorz Piszczek
   13. Richard D Leapman
   14. Jonathan W Yewdell
   15. Peter Schuck

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is a valuable study that combines a wide range of approaches to provide a biophysical and evolutionary mechanism that could explain why some particular mutations in the SARS-CoV-2 protein N arose during the COVID-19 pandemic. The evidence is solid and relies on multiple experimental approaches. However, some of the results were dependent on extremely high protein concentrations, which may affect certain conclusions.

   Reviewed by eLife

10. A recursive pathway for isoleucine biosynthesis arises from enzyme promiscuity

    This article has 4 authors:

    1. Vittorio Rainaldi
    2. Stefano Donati
    3. Sarah D’Adamo
    4. Nico J Claassens

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      The study reports a potential pathway for isoleucine biosynthesis mediated by the underground activity of AHASII, which converts glyoxylate and pyruvate to 2-ketobutyrate. While the findings are valuable in revealing a possible alternative route for isoleucine production, the evidence presented remains incomplete. More comprehensive biochemical experiments are required to substantiate the physiological feasibility of this pathway.

    Reviewed by eLife