eLife

Latest preprint reviews

1. JAK inhibition decreases the autoimmune burden in Down syndrome

   This article has 22 authors:

   1. Angela L Rachubinski
   2. Elizabeth Wallace
   3. Emily Gurnee
   4. Belinda A Enriquez-Estrada
   5. Kayleigh R Worek
   6. Keith P Smith
   7. Paula Araya
   8. Katherine A Waugh
   9. Ross E Granrath
   10. Eleanor Britton
   11. Hannah R Lyford
   12. Micah G Donovan
   13. Neetha Paul Eduthan
   14. Amanda A Hill
   15. Barry Martin
   16. Kelly D Sullivan
   17. Lina Patel
   18. Deborah J Fidler
   19. Matthew D Galbraith
   20. Cory A Dunnick
   21. David A Norris
   22. Joaquín M Espinosa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Rachubinski and colleagues provide an important manuscript that includes two major advances in understanding immune dysregulation in a large cohort of individuals with Down syndrome. The work comprises compelling, comprehensive, and state-of-the-art clinical, immunological, and autoantibody assessment of autoimmune/inflammatory manifestations. Additionally, the authors report promising results from a clinical trial with the JAK inhibitor tofacitinib for individuals with dermatological autoimmune disease.

   Reviewed by eLife

2. PPI-hotspotID for detecting protein–protein interaction hot spots from the free protein structure

   This article has 6 authors:

   1. Yao Chi Chen
   2. Karen Sargsyan
   3. Jon D Wright
   4. Yu-Hsien Chen
   5. Yi-Shuian Huang
   6. Carmay Lim

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript presents a machine-learning method to predict protein hotspot residues. The validation is incomplete, along with the misinterpretation of the results with other current methods like FTMap.

   Reviewed by eLife

3. A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epithelia

   This article has 10 authors:

   1. Xiaojiao Hua
   2. Chen Zhao
   3. Jianbo Tian
   4. Junbao Wang
   5. Xiaoping Miao
   6. Gen Zheng
   7. Min Wu
   8. Mei Ye
   9. Ying Liu
   10. Yan Zhou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Ctnnb1 encodes β-catenin, an essential component of the canonical Wnt signaling pathway. In this important study, the authors identify an upstream enhancer of Ctnnb1 responsible for the specific expression level of β-catenin in the gastrointestinal track. Deletion of this enhancer in mice and analyses of its association with human colorectal tumors provide compelling support that it controls the dosage of Wnt signaling critical to the homeostasis in intestinal epithelia and colorectal cancers.

   Reviewed by eLife

4. Neural geometry from mixed sensorimotor selectivity for predictive sensorimotor control

   This article has 4 authors:

   1. Yiheng Zhang
   2. Yun Chen
   3. Tianwei Wang
   4. He Cui

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study examines the neural activity in the motor cortex as a monkey reaches to intercept moving targets, focusing on how tuned single neurons contribute to an interesting overall population geometry. The presented results and analyses are solid, though the investigation of this novel task could be strengthened by clarifying the assumptions behind the single neuron analyses, and further analyses of the neural population activity and its relation to different features of behaviour.

   Reviewed by eLife

5. Pathway activation model for personalized prediction of drug synergy

   This article has 18 authors:

   1. Quang Thinh Trac
   2. Yue Huang
   3. Tom Erkers
   4. Päivi Östling
   5. Anna Bohlin
   6. Albin Osterroos
   7. Mattias Vesterlund
   8. Rozbeh Jafari
   9. Ioannis Siavelis
   10. Helena Backvall
   11. Santeri Kiviluoto
   12. Lukas Orre
   13. Mattias Rantalainen
   14. Janne Lehtiö
   15. Soren Lehmann
   16. Olli Kallioniemi
   17. Yudi Pawitan
   18. Trung Nghia Vu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents a deep learning framework for predicting synergistic drug combinations for cancer treatment in the AstraZeneca-Sanger (AZS) DREAM Challenge dataset. The level of evidence seems solid, although performance on some datasets seems unconvincing and further validation would be required to demonstrate the generalizability of the model and, in turn, its clinical relevance. The reported tool, DIPx, could be of use for personalized drug synergy prediction and exploring the activated pathways related to the effects of drug combinations.

   Reviewed by eLife

6. Sigh generation in preBötzinger complex

   This article has 5 authors:

   1. Yan Cui
   2. Evgeny Bondarenko
   3. Carolina Thörn Perez
   4. Delia N Chiu
   5. Jack L Feldman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study by Cui et al. investigates mechanisms generating sighs, which are crucial for respiratory function and linked to emotional states. Utilizing advanced methods in mice, they provide solid evidence that increased excitability in specific preBötzinger complex neuronal subpopulations expressing Neuromedin B receptors, gastrin-releasing peptide receptors, or somatostatin can induce sigh-like large amplitude inspirations. With additional technical clarifications and further elaboration of the limitations in terms of how the results are interpreted in the revised manuscript, the study will interest neuroscientists studying respiratory neurobiology and rhythmic motor systems.

   Reviewed by eLife

7. The glycoprotein quality control factor Malectin promotes coronavirus replication and viral protein biogenesis

   This article has 2 authors:

   1. Jonathan P Davies
   2. Lars Plate

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that utilizes proteomic and genetic approaches to identify the glycoprotein quality control factor malectin as a pro-viral host protein involved in the replication of coronavirus. The evidence supporting this conclusion is convincing, although continued elucidation of the mechanistic basis of malectin-mediated viral replication would further strengthen these findings. This work will be of interest to cell biologists studying the molecular mechanisms of glycoprotein quality control and virologists studying the host-pathogen interactions.

   Reviewed by eLife

8. Brown adipose tissue and skeletal muscle coordinately contribute to thermogenesis in mice

   This article has 12 authors:

   1. Yuna Izumi-Mishima
   2. Rie Tsutsumi
   3. Tetsuya Shiuchi
   4. Saori Fujimoto
   5. Momoka Taniguchi
   6. Mizuki Sugiuchi
   7. Manaka Tsutsumi
   8. Yuko Okamatsu-Ogura
   9. Takeshi Yoneshiro
   10. Masashi Kuroda
   11. Kazuhiro Nomura
   12. Hiroshi Sakaue

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a useful paper regarding the roles of brown adipose tissue and skeletal muscle in thermogenesis in mice, with potential significance for the field. The overall approach is innovative but on balance the evidence for the claim is incomplete, as cast immobilization, while innovative, is likely stressful, may impact muscle and BAT directly, and imposes an energetic cost of motion on the animal that is not accounted for. Further experiments are also needed to directly assess the role of adipose-derived BCAAs in thermogenesis. The authors have done a good job of textually editing their manuscript to clarify the findings and limitations of the study.

   Reviewed by eLife

9. Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms

   This article has 13 authors:

   1. Hebin Liao
   2. Xiaodan Yan
   3. Chenyi Wang
   4. Chun Huang
   5. Wei Zhang
   6. Leyi Xiao
   7. Jun Jiang
   8. Yongjia Bao
   9. Tao Huang
   10. Hanbo Zhang
   11. Chunming Guo
   12. Yufeng Zhang
   13. Yingying Pu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This work describes how the toxin-antitoxin (TA) system, which uses the cyclic di-GMP as an antitoxin, controls both the persistence of antibiotics linked to biofilms and the integrity of the bacterial genome. The authors present solid evidence linking cyclic di-GMP and the toxin HipH. The work is valuable because it establishes the relationship between bacterial persistence and biofilm resilience, which lays a strong basis for future research on the formation of bacterial biofilms and antibiotic resistance.

   Reviewed by eLife

10. Super-enhancer-driven ZFP36L1 promotes PD-L1 expression in infiltrative gastric cancer

    This article has 10 authors:

    1. Xujin Wei
    2. Jie Liu
    3. Jia Cheng
    4. Wangyu Cai
    5. Wen Xie
    6. Kang Wang
    7. Lingyun Lin
    8. Jingjing Hou
    9. Jianchun Cai
    10. Huiqin Zhuo

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      The authors provide useful data to support the existence of a regulatory pathway starting with SPI1-driven ZFP36L1 expression, that goes on to downregulate HDAC3 expression at the transcript level, leading to PD-L1 upregulation due to implied enhanced acetylation of its promoter region. This is therefore an interesting pathway that adds to our understanding of how PD-L1 expression is controlled in gastric cancer. However, this is likely one of many possible pathways that impact PD-L1 expression, and the data are currently incomplete to support the claims made.

    Reviewed by eLife