eLife

Latest preprint reviews

1. Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features

   This article has 21 authors:

   1. Dominic WH Shayler
   2. Kevin Stachelek
   3. Linda Cambier
   4. Sunhye Lee
   5. Jinlun Bai
   6. Bhavana Bhat
   7. Mark W Reid
   8. Daniel J Weisenberger
   9. Jennifer G Aparicio
   10. Yeha Kim
   11. Mitali Singh
   12. Maxwell Bay
   13. Matthew E Thornton
   14. Eamon K Doyle
   15. Zachary Fouladian
   16. Stephan G Erberich
   17. Brendan H Grubbs
   18. Michael A Bonaguidi
   19. Cheryl Mae Craft
   20. Hardeep P Singh
   21. David Cobrinik

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this important paper, the authors use single-cell RNA sequencing to understand post-mitotic cone and rod developmental states and identify cone-specific features that contribute to retinoblastoma genesis. The authors report findings that have practical implications for retinal development, gene expression, and cell fate specification. The evidence is compelling as the experimental design and analysis are exceptionally rigorous.

   Reviewed by eLife

2. Cdhr1a and pcdh15b may link photoreceptor outer segments with calyceal processes revealing a potential mechanism for cone-rod dystrophy

   This article has 3 authors:

   1. Meet K Patel
   2. Warlen Pereira Piedade
   3. Jakub K Famulski

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study investigates the interaction of two integral membrane proteins (Cdhr1a and Pcdh15b) and their roles in cone-rod dystrophy. Convincing evidence using loss-of-function mutants demonstrates clearly that both proteins are required for cone maintenance and survival. Although some evidence (Western blots and cell aggregation assays) demonstrates Cdhr1a and Pcdh15b can physically interact, there is insufficient evidence to support the subcellular localization and the proposed heterodimeric interaction of the two proteins from distinct subcellular compartments in cone photoreceptors.

   Reviewed by eLife

3. Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal

   This article has 10 authors:

   1. Carley N Gray
   2. Manickam Ashokkumar
   3. Derek H Janssens
   4. Jennifer L Kirchherr
   5. Brigitte Allard
   6. Emily Hsieh
   7. Terry L Hafer
   8. Nancie M Archin
   9. Edward P Browne
   10. Michael Emerman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Using multiple techniques previously validated by the authors, this study identified INTS12, a component of the Integrator complex involved in 3' processing of small nuclear RNAs U1 and U2, as a factor promoting HIV-1 latency. The work is valuable, based on a sound strategy for screening targets to activate HIV latency and the solid mechanistic insights it provides on INTS12 repression of transcriptional elongation. Future studies are needed to explore INTS12 as a drug target against HIV/AIDS.

   Reviewed by eLife

4. Molecular consequences of acute versus chronic CDK12 loss in prostate carcinoma nominates distinct therapeutic strategies

   This article has 21 authors:

   1. Sander Frank
   2. Thomas Persse
   3. Ilsa Coleman
   4. Armand Bankhead
   5. Dapei Li
   6. Navonil De-Sarkar
   7. Divin Wilson
   8. Dmytro Rudoy
   9. Manasvita Vashisth
   10. Patty Galipeau
   11. Michael Yang
   12. Brian Hanratty
   13. Ruth Dumpit
   14. Colm Morrissey
   15. Eva Corey
   16. R Bruce Montgomery
   17. Michael C Haffner
   18. Colin C Pritchard
   19. Valeri Vasioukhin
   20. Gavin Ha
   21. Peter S Nelson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The paper is a fundamental study examining the role of CDK12 loss in prostate cancer. While previous studies have suggested that CDK12 loss confers HRD phenotypes, clinical trials using PARPi in CDK12 altered patients have not demonstrated significant benefit. This work investigates these mechanisms in depth and provides compelling evidence. A comprehensive genomic analysis serves an excellent resource to the field, showing that biallelic CDK12 alterations do not have genomic features of HRd. Moreover, the study explored both acute and chronic deletion of CDK12, with data suggestive of CDK12-altered cells being uniquely sensitive to CDK13 inhibition. While some minor weaknesses have been previously noted by the reviewers, the authors have adequately addressed these concerns with appropriate rigor.

   Reviewed by eLife

5. Enhanced bacterial chemotaxis in confined microchannels occurs at lane widths matching circular swimming radius

   This article has 4 authors:

   1. Caijuan Yue
   2. Chi Zhang
   3. Rongjing Zhang
   4. Junhua Yuan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work examines the effects of side-wall confinement on chemotaxis of swimming bacteria in a shallow microfluidic channel. The authors present convincing experimental evidence, combined with geometric analysis and numerical simulations of simplified models, showing that chemotaxis is enhanced when the distance between the side walls is comparable to the intrinsic radius of chiral circular swimming near open surfaces. This study should be of interest to scientists specializing in bacteria-surface interactions.

   Reviewed by eLife

6. Increased bone inflammation in type 2 diabetes and obesity correlates with Wnt signaling downregulation and reduced bone strength

   This article has 15 authors:

   1. Giulia Leanza
   2. Malak Faraj
   3. Francesca Cannata
   4. Viola Viola
   5. Niccolò Pellegrini
   6. Flavia Tramontana
   7. Claudio Pedone
   8. Gianluca Vadalà
   9. Alessandra Piccoli
   10. Rocky Strollo
   11. Francesca Zalfa
   12. Roberto Civitelli
   13. Mauro Maccarrone
   14. Rocco Papalia
   15. Nicola Napoli

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a convincing paper that addresses topics important in our understanding of how inflammatory markers are modulated in both obesity and type 2 diabetes and their effects on Wnt signaling mediators in human bone. There are changes in bone at the tissue level in these 2 common metabolic disorders that ultimately lead to compromised bone strength. These data will be critical to our understanding of the pathophysiology of skeletal fragility in obesity and diabetes.

   Reviewed by eLife

7. STAMBPL1 activates the GRHL3/HIF1A/VEGFA axis through interaction with FOXO1 to promote angiogenesis in triple-negative breast cancer

   This article has 8 authors:

   1. Huan Fang
   2. Huichun Liang
   3. Chuanyu Yang
   4. Dewei Jiang
   5. Qianmei Luo
   6. Wen-Ming Cao
   7. Huifeng Zhang
   8. Ceshi Chen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study conducted by Fang et al. offers significant and fundamental insights, notably enhancing our understanding of angiogenesis. While some of the claims are supported by convincing experimental approaches, others lack sufficient validation. Additionally, there are instances where critical experimental controls appear to be absent.

   Reviewed by eLife

8. Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson’s disease

   This article has 10 authors:

   1. Zachary Gaertner
   2. Cameron Oram
   3. Amanda Schneeweis
   4. Elan Schonfeld
   5. Cyril Bolduc
   6. Chuyu Chen
   7. Daniel Dombeck
   8. Loukia Parisiadou
   9. Jean-Francois Poulin
   10. Rajeshwar Awatramani

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study combines single nucleus transcriptional profiling with spatial transcriptomics to identify and map heterogeneity among dopamine neurons in the mouse ventral midbrain. The compelling results separate dopamine neurons into three broad families that have unique (yet overlapping) spatial distribution within the ventral tegmental area and substantia nigra, and also identify population-specific changes in a LRRK2 mouse model of Parkinson's Disease. The creation of a public-facing app where the snRNA-seq data can be investigated by anyone is a major strength.

   Reviewed by eLife

9. HIF1A-mediated pathways promote euploid cell survival in chromosomally mosaic embryos

   This article has 3 authors:

   1. Estefania Sanchez-Vasquez
   2. Marianne E Bronner
   3. Magdalena Zernicka-Goetz

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Sanchez-Vasquez et al establish an innovative approach to induce aneuploidy in preimplantation embryos. This important study extends the author's previous publications evaluating the consequences of aneuploidy in the mammalian embryo. In this work, the authors investigate the developmental potential of aneuploid embryos and characterize changes in gene expression profiles under normoxic and hypoxic culture conditions. Using a solid methodology they identify sensitivity to Hif1alpha loss in aneuploid embryos, and in further convincing experiments they assess how levels of DNA damage and DNA repair are altered under hypoxic and normoxic conditions.

   Reviewed by eLife, preLights

10. An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity

    This article has 7 authors:

    1. Xiaodan Yan
    2. Hebin Liao
    3. Chenyi Wang
    4. Chun Huang
    5. Wei Zhang
    6. Chunming Guo
    7. Yingying Pu

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This work introduces an important new method for depleting ribosomal RNA from bacterial single-cell RNA sequencing libraries, demonstrating its applicability for studying heterogeneity in microbial biofilms. The findings provide convincing evidence for a distinct subpopulation of cells at the biofilm base that upregulates PdeI expression. Future studies exploring the functional relationship between PdeI and c-di-GMP levels, along with the roles of co-expressed genes within the same cluster, could further enhance the depth and impact of these conclusions.

    Reviewed by eLife