eLife

Latest preprint reviews

1. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion

   This article has 4 authors:

   1. Davin Jeong
   2. Guang Shi
   3. Xin Li
   4. D Thirumalai

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study, of interest for students of the biology of genomes, uses simulations in combination with published data to examine how many TADs remain after cohesin depletion. The authors suggest that a significant subset of chromosome conformations do not require cohesin, and that knowledge of specific epigenetic states can be used to identify regions of the genome that still interact in the absence of cohesin. The theoretical approaches and quantitative analysis are state-of-the-art, and the data quality and strength of the conclusions are convincing, but it is unfortunately still unclear whether physical boundaries (of domains?) in the model appear to be a consequence of preserved TADs, or whether preserved TADs are caused by the physical boundaries.

   Reviewed by eLife

2. Polymorphisms in intron 1 of HLA-DRA differentially associate with type 1 diabetes and celiac disease and implicate involvement of complement system genes C4A and C4B

   This article has 15 authors:

   1. Ozkan Aydemir
   2. Jeffrey A Bailey
   3. Daniel Agardh
   4. Åke Lernmark
   5. Janelle A Noble
   6. Agnes Andersson Svärd
   7. Elizabeth P Blankenhorn
   8. Hemang M Parikh
   9. Anette-G Ziegler
   10. Jorma Toppari
   11. Beena Akolkar
   12. William A Hagopian
   13. Marian J Rewers
   14. John P Mordes
   15. TEDDY Study Group

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents valuable findings on genetic risk factors for type 1 diabetes and celiac disease using a large cohort from the Environmental Determinants of Diabetes in the Young (TEDDY) study. The evidence supporting the claims of the authors is solid, although the inclusion of the genetic effect of this locus on individuals with different genetic backgrounds would have strengthened the study. The work will be of interest to population geneticists working on diabetes and celiac disease.

   Reviewed by eLife

3. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers

   This article has 2 authors:

   1. Jose Mario Bello Pineda
   2. Robert K Bradley

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable finding on the association between DUX4 expression with features of immune evasion in human tissue and clinical outcomes in patients with advanced urothelial cancer. The evidence supporting the claims of the authors is convincing, using a range of corroborative statistical techniques. Compared to an earlier version, the quality of the manuscript has been enhanced, for example Figure 5 now illustrates the key features of survival probability estimates over time for patients assigned to with the test or training set.

   Reviewed by eLife

4. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers

   This article has 2 authors:

   1. Jose Mario Bello Pineda
   2. Robert K Bradley

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable finding on the association between DUX4 expression with features of immune evasion in human tissue and clinical outcomes in patients with advanced urothelial cancer. The evidence supporting the claims of the authors is convincing, using a range of corroborative statistical techniques. Compared to an earlier version, the quality of the manuscript has been enhanced, for example Figure 5 now illustrates the key features of survival probability estimates over time for patients assigned to with the test or training set.

   Reviewed by eLife

5. Single-cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

   This article has 6 authors:

   1. Seo-Gyeong Bae
   2. Guo Nan Yin
   3. Jiyeon Ock
   4. Jun-Kyu Suh
   5. Ji-Kan Ryu
   6. Jihwan Park

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors provide important insights into the pathogenesis of erectile dysfunction (ED) in patients with diabetes. The authors present compelling evidence, using single-cell transcriptomic analysis in both mouse and human cavernous tissues, to support their claims regarding the key roles of pericytes in diabetic ED. The identification of LBH as a potential pericyte-specific marker in both mouse and human tissues further strengthens their findings. This well-written manuscript offers novel and significant contributions to the field, identifying potential therapeutic targets for further investigation.

   Reviewed by eLife

6. Single-cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

   This article has 6 authors:

   1. Seo-Gyeong Bae
   2. Guo Nan Yin
   3. Jiyeon Ock
   4. Jun-Kyu Suh
   5. Ji-Kan Ryu
   6. Jihwan Park

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors provide important insights into the pathogenesis of erectile dysfunction (ED) in patients with diabetes. The authors present compelling evidence, using single-cell transcriptomic analysis in both mouse and human cavernous tissues, to support their claims regarding the key roles of pericytes in diabetic ED. The identification of LBH as a potential pericyte-specific marker in both mouse and human tissues further strengthens their findings. This well-written manuscript offers novel and significant contributions to the field, identifying potential therapeutic targets for further investigation.

   Reviewed by eLife

7. Septin 7 interacts with Numb to preserve sarcomere structural organization and muscle contractile function

   This article has 12 authors:

   1. Rita De Gasperi
   2. Laszlo Csernoch
   3. Beatrix Dienes
   4. Monika Gonczi
   5. Jayanta K Chakrabarty
   6. Shahar Goeta
   7. Abdurrahman Aslan
   8. Carlos A Toro
   9. David Karasik
   10. Lewis M Brown
   11. Marco Brotto
   12. Christopher P Cardozo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This convincing study demonstrates a potentially important role for the factor Numb in skeletal muscle excitation-contraction coupling, since a Numb knockout reduced contractile force. The authors thus demonstrate a novel role for Numb in calcium release in skeletal muscle.

   Reviewed by eLife

8. Systematic Analysis of Network-driven Adaptive Resistance to CDK4/6 and Estrogen Receptor Inhibition using Meta-Dynamic Network Modelling

   This article has 3 authors:

   1. Anthony Hart
   2. Sung-Young Shin
   3. Lan K. Nguyen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript presents a useful method for a comprehensive numerical simulation to systematically characterise the effect of heterogeneity in either the initial conditions or the biophysical parameters on the dynamic behaviour of protein signalling networks. Nevertheless, the presentation and detail of their model appear incomplete to fully support the main claims of the manuscript.

   Reviewed by eLife

9. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2301.00759

10. Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer’s disease dataset

    This article has 3 authors:

    1. Alan E Murphy
    2. Nurun Fancy
    3. Nathan Skene

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This paper reports a useful finding on the impact of choices of quality control and differential analysis methods on the discovery of disease-associated gene expression signatures. The study provides a solid comparison of the data process by re-analysis of a large-scale snRNA-seq dataset for Alzheimer's Disease. This paper would be of interest to the community as to rigorous analyses for large-scale single cell datasets.

    Reviewed by eLife