Cancer Biology

CNN-based learning of single-cell transcriptomes reveals a blood-detectable multi-cancer signature of brain metastasis

1. Ryan Lusby
2. Debojyoti Chowdhury
3. Sarah Carl
4. Vijay K Tiwari

• Curated by eLife

  eLife Assessment

  This important study describes a deep learning framework that analyzes single-cell RNA data to identify a tumor-agnostic gene signature associated with brain metastases. The identified signature uncovers key molecular mechanisms, highlights potential therapeutic targets, and demonstrates a metastasis-specific transcriptional signal in circulating platelets, suggesting its promise for non-invasive diagnostics through liquid biopsy. The evidence supporting the findings is solid, utilizing interpretable deep learning methodologies and large-scale datasets across multiple cancer types, though some aspects may benefit from additional analysis and validation.

Reviewed by eLife

Androgen deprivation triggers a cytokine signaling switch to induce immune suppression and prostate cancer recurrence

1. Kai Sha
2. Renyuan Zhang
3. Aerken Maolake
4. Shalini Singh
5. Gurkamal Chatta
6. Kevin H Eng
7. Kent L Nastiuk
8. John J Krolewski

• Curated by eLife

  eLife Assessment

  This potentially valuable work aimed at a better understanding of the mechanisms of response and resistance to androgen deprivation therapy in prostate cancer using genetically engineered mouse models. A key observation relates to the timing of TNF blockage therapy and the concept of a "TNF switch." The solid data were collected using conventional approaches and the conclusions are mostly justified, particularly with the inclusion of more detailed statistics in the revision. The work will be of interest to the prostate cancer research community.

Reviewed by eLife

Role of tankyrase scaffolding in the β-catenin destruction complex and WNT signaling

1. Qian Wang
2. Liping Li
3. Lin You
4. Shuai Wang
5. Lei Han
6. Bingnan Wang
7. Liping Yao
8. Yong Lu
9. Ilgen Mender
10. Ann M Flusche
11. Chiho Kim
12. Nageswari Yarravarapu
13. Andrew Lemoff
14. Lawrence Lum
15. Jerry W Shay
16. Yonghao Yu
17. Chuo Chen

• Curated by eLife

  eLife Assessment

  This important study reports the development of the first tankyrase degrader and demonstrates its enhanced ability to inhibit β-catenin signaling compared to conventional tankyrase inhibitors. The evidence supporting the conclusions is comprehensive and convincing, based on rigorous biochemical and cellular analyses. The findings will be of broad interest to researchers studying Wnt signaling, protein degradation, and cancer biology.

Reviewed by eLife

Transcriptional subtypes on immune microenvironment and predicting postoperative recurrence and metastasis in human pheochromocytoma and paraganglioma

1. Yang Liu
2. Xu Yan
3. Yibo Zhang
4. Zhenfu Gao
5. Fengrui Nan
6. Siyu Shi
7. Jingyun Chen
8. Lingyu Li

• Curated by eLife

  eLife Assessment

  This is a valuable study describing transcriptome-based pheochromocytoma and paraganglioma (PPGL) subtypes and exploring the mutations, immune correlates and disease progression of cases in each subtype. The cohort is a reasonable size and a second cohort is included from the Cancer Genome Atlas (TCGA). One of the key premises of the study is that identification of driver mutations in PPGL is not complete and that compromises characterisation for prognostic purposes. This is a solid starting point on which to base characterisation using different methods.

Reviewed by eLife

Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers

1. Richard C Centore
2. Luis MM Soares
3. Salih Topal
4. Rishi G Vaswani
5. Kana Ichikawa
6. Zhifang Li
7. Hong Fan
8. Jeremy W Setser
9. David L Lahr
10. Laura E Zawadzke
11. Xueying Chen
12. Kimberly D Barnash
13. Jordana Muwanguzi
14. Neville Anthony
15. Gabriel J Sandoval
16. Katharine Feldman
17. GiNell Elliott
18. Ammar Adam
19. David Huang
20. Yunji Davenport
21. Shawn Schiller
22. Kevin J Wilson
23. Johannes Voigt
24. Lan Xu
25. Martin Hentemann
26. David S Millan
27. Ho Man Chan
28. Carl P Decicco
29. Ryan G Kruger
30. Gromoslaw A Smolen
31. Steven F Bellon

• Curated by eLife

  eLife Assessment

  This study constitutes a fundamental advance for the uveal melanoma research field that might be exploited to target this deadly cancer and more generally for targeting transcriptional dependency in cancers. This work substantially advances our understanding of pharmacological inhibition of SWI/SNF as a therapeutic approach for cancer. The study is well written and provides compelling evidence, including comprehensive datasets, compound screens, gene expression analysis, epigenetics, as well as animal studies.

Reviewed by eLife

Single-Cell Atlas of AML Reveals Age-Related Gene Regulatory Networks in t(8;21) AML

1. Jessica Whittle
2. Stefan Meyer
3. Georges Lacaud
4. Syed Murtuza Baker
5. Mudassar Iqbal

• Curated by eLife

  eLife Assessment

  This manuscript provides a single-cell transcriptomic atlas for AML (222 samples comprising 748,679 cells) integrating data from multiple studies. They use this dataset to investigate t(8;21) AML, and they reconstruct the Gene Regulatory Network and enhancer Gene Regulatory Network, which allowed identification of interesting targets. This aggregation is important and can help infer differences in genetic regulatory modules based on the age of disease onset. Their compelling effort may help explain age-related variations in prognosis and disease development in subtype-specific manner.

Reviewed by eLife

Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

1. Adrien Tourneur
2. Joel Rodrigues Vitória
3. Manuel Saiselet
4. Ligia Craciun
5. Denis Larsimont
6. Anne Lefort
7. Frederick Libert
8. Carine Maenhaut
9. Sabine Costagliola
10. Maxime Tarabichi
11. Mirian Romitti
12. Vincent Detours

Reviewed by Review Commons

Therapeutic benefits of maintaining CDK4/6 inhibitors and incorporating CDK2 inhibitors beyond progression in breast cancer

1. Jessica Armand
2. Sungsoo Kim
3. Kibum Kim
4. Eugene Son
5. Minah Kim
6. Kevin Kalinsky
7. Hee Won Yang

• Curated by eLife

  eLife Assessment

  This study presents fundamental insights into overcoming resistance in hormone receptor-positive breast cancer by demonstrating that sustained CDK4/6 inhibitor treatment, either alone or in combination with CDK2 inhibitors, significantly suppresses the growth of drug-resistant cancer cells. The findings are supported by compelling evidence from both in vitro cell line experiments and in vivo mouse models, highlighting the therapeutic potential of maintaining CDK4/6 inhibitors beyond disease progression. Additionally, the identification of cyclin E overexpression as a key driver of resistance offers a target that will be of value for future therapeutic strategies, potentially improving outcomes for patients with advanced breast cancer.

Reviewed by eLife

The G protein-coupled receptor TBXA2R activates ERMs to control cell motility and invasion of triple-negative breast cancer cells.

1. Kevin Leguay
2. Omaima Naffati
3. Yu Yan He
4. Mireille Rogue
5. Chloe Tesniere
6. Melania Gombos
7. Hellen Kuasne
8. Louis Gaboury
9. Christian Le Gouill
10. Sylvain Meloche
11. Michel Bouvier
12. Sebastien Carreno

Reviewed by Review Commons

Multi-gradient permutation survival analysis identifies mitosis and immune signatures steadily associated with cancer patient prognosis

1. Xinlei Cai
2. Yi Ye
3. Xiaoping Liu
4. Zhaoyuan Fang
5. Luonan Chen
6. Fei Li
7. Hongbin Ji

• Curated by eLife

  eLife Assessment

  This paper contains valuable ideas for methodology concerned with the identification of genes associated with disease prognosis in a broad range of cancers. However, there are concerns that the statistical properties of MEMORY are incompletely investigated and described. Further, more precise details about the implementation of the method would increase the replicability of the findings by other researchers.

Reviewed by eLife