Genomics

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma

1. Olivia G Waltner
2. April A Apfelbaum
3. Emma D Wrenn
4. Shruti S Bhise
5. Sami B Kanaan
6. Rula Green Gladden
7. Mark A Mendoza
8. Roger Volden
9. Zev Kronenberg
10. Anand Patel
11. Michael Dyer
12. Jay F Sarthy
13. Elizabeth R Lawlor
14. Scott N Furlan

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of the gene regulatory networks that contribute to tumour heterogeneity and tumor plasticity in Ewing sarcoma, with key implications for other fusion-driven sarcomas. The authors employed compelling orthogonal approaches, including single-cell sequencing and xenografts, to reveal the existence and plasticity of specific gene regulatory networks (e.g., TGF-beta signaling) within Ewing sarcoma, as well as significant differences that exist between cell lines and patient tumors.

Reviewed by eLife

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

1. Fiona Teltscher
2. Petra Korlević
3. Edel Sheerin
4. Alex Makunin
5. Mara K N Lawniczak

Reviewed by GigaScience

Systematic identification of oscillatory gene expression in single cell types

1. Alexis Weinreb
2. Manasa Basavaraju
3. Marc Hammarlund
4. Maxwell G. Heiman

Reviewed by Review Commons

Evolutionary remodeling of non-canonical ORF translation in mammals

1. Yue Chang
2. Tianyu Lei
3. Feng Zhou
4. Jiawen Jiang
5. Yu Huang
6. Ziyang Zhu
7. Hong Zhang

• Curated by eLife

  eLife Assessment

  This study presents a large, systematically curated catalog of non-canonical open reading frames (ncORFs) in human and mouse through the reanalysis of nearly 400 Ribo-seq datasets using a standardized pipeline; the resulting atlas consolidates ncORF annotations across tissues and provides a valuable resource for investigating non-canonical translation and ORF emergence. The main conclusions are supported by consistent data processing and multiple computational measures of translation and conservation. While the pipeline is transparent and technically robust, some analytical criteria and dataset limitations could be described more explicitly, and several downstream conclusions would benefit from more cautious interpretation, some evolutionary inferences are primarily correlative; dataset heterogeneity, uneven tissue representation, and limited experimental validation also constrain the strength of a subset of the findings. Overall, the evidence is solid, and the resource is likely to be broadly beneficial to the community.

Reviewed by eLife, Arcadia Science