Cancer Biology

Comprehensive and unbiased multiparameter high-throughput screening by compaRe finds effective and subtle drug responses in AML models

1. Morteza Chalabi Hajkarim
2. Ella Karjalainen
3. Mikhail Osipovitch
4. Konstantinos Dimopoulos
5. Sandra L Gordon
6. Francesca Ambri
7. Kasper Dindler Rasmussen
8. Kirsten Grønbæk
9. Kristian Helin
10. Krister Wennerberg
11. Kyoung-Jae Won

• Curated by eLife

  Evaluation Summary:

  This paper aims to address the current gap in the efficient analysis of large-scale multiparameter flow cytometry and other datasets. The authors offer a software toolkit with an efficient algorithm for comparing numerous samples at once. The study is well presented and is relevant to single cell analysis research.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations

1. H Nayanga Thirimanne
2. Feinan Wu
3. Derek H Janssens
4. Jherek Swanger
5. Ahmed Diab
6. Heather M Feldman
7. Robert A Amezquita
8. Raphael Gottardo
9. Patrick J Paddison
10. Steven Henikoff
11. Bruce E Clurman

• Curated by eLife

  Evaluation Summary:

  FBXW7 is a CRL controlling the abundance of numerous transcription factors through targeted degradation. The authors use isogenic cancer and normal cell lines that differ only in the functional status of FBXW7 to examine the genome-wide effects of FBXW7. The authors demonstrate that null and missense mutations have similar large-scale effects on gene expression and chromatin modification status of many loci at intergenic and intronic regions, but that there are substantial differences in affected loci between the mutant backgrounds. This study represents the first such systematic evaluation of the impact of FBXW7 functional variation on global gene expression.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Identification of two cancer stem cell-like populations in triple-negative breast cancer xenografts

1. Jun Nakayama
2. Hiroko Matsunaga
3. Koji Arikawa
4. Takuya Yoda
5. Masahito Hosokawa
6. Haruko Takeyama
7. Yusuke Yamamoto
8. Kentaro Semba

Reviewed by Review Commons

Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors

1. Gökçe Senger
2. Stefano Santaguida
3. Martin H Schaefer

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to the cancer biology community. The study leverages high-throughput genomic and proteomic data to evaluate the role of aneuploidy on functional pathway changes in cancer.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Reprogramming and redifferentiation of mucosal-associated invariant T cells reveal tumor inhibitory activity

1. Chie Sugimoto
2. Yukie Murakami
3. Eisuke Ishii
4. Hiroyoshi Fujita
5. Hiroshi Wakao

• Curated by eLife

  Evaluation Summary:

  This paper describes a reprogramming platform for studying mucosal-associated invariant T (MAIT) cells that can overcome the current technology limitations in studying MAITs. With more detailed elucidation the identity of reprogrammed MAIT cells compared to endogenous MAITs, this paper will of broad interest to those studying the role of these cells in tumor immunity.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Proton export drives the Warburg Effect

1. Shonagh Russell
2. Liping Xu
3. Yoonseok Kam
4. Dominique Abrahams
5. Daniel Verduzco
6. Joseph Johnson
7. Tamir Epstein
8. Epifanio Ruiz
9. Mark C. Lloyd
10. Jonathan Wojtkowiak
11. Alex S. Lopez
12. Marilyn M. Bui
13. Robert J. Gillies
14. Pawel Swietach
15. Bryce Ordway

• Curated by eLife

  Evaluation Summary:

  This manuscript addresses a phenomenon of great interest to researchers in cell metabolism and cancer biology: namely, why do cancer cells often secrete high levels of lactate, despite the presence of abundant oxygen to power nutrient oxidation (Warburg effect). The authors propose that lactate export and subsequent extracellular acidification provides a selective advantage and the concomitant rise in intracellular pH is sufficient to drive flux through glycolysis, thereby sustaining the Warburg effect. This is an intriguing hypothesis that ties together many published observations, but it would require further support both from the technical and conceptual side.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

JAMMIT Analysis Defines 2 Semi-Independent Immune Processes Common to 29 Solid Tumors

1. Emory Zitello
2. Michael Vo
3. Shaoqiu Chen
4. Scott Bowler
5. Vedbar Khadka
6. Thomas Wenska
7. Peter Hoffmann
8. Gordon Okimoto
9. Youping Deng

• Curated by eLife

  Evaluation Summary:

  This study provides a sound and novel algorithm to analyze the massive cancer data and its findings greatly help inform novel cancer immunotherapy across various cancer types. Moreover, a 3-gene signature was established based upon Tc1, Tc17, and immune cold tumors to estimate the abundance of monocytic infiltrates that could potentially impact on the overall survival of cancer patients. It might be of great interest to the general audience of cancer biologists, immunologists and computational biologists.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewer remained anonymous to the authors.)

Reviewed by eLife

Ras/MAPK signalling intensity defines subclonal fitness in a mouse model of hepatocellular carcinoma

1. Anthony Lozano
2. Francois-Régis Souche
3. Carine Chavey
4. Valérie Dardalhon
5. Christel Ramirez
6. Serena Vegna
7. Guillaume Desandre
8. Anaïs Riviere
9. Amal Zine El Aabidine
10. Philippe Fort
11. Leila Akkari
12. Urszula Hibner
13. Damien Grégoire

Reviewed by Review Commons

The extracellular matrix supports cancer cell growth under amino acid starvation by promoting tyrosine catabolism

1. Mona Nazemi
2. Bian Yanes
3. Montserrat Llanses Martinez
4. Heather Walker
5. Frederic Bard
6. Elena Rainero

Reviewed by Review Commons, ASAPbio crowd review

Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells

1. David J Hosfield
2. Sandra Weber
3. Nan-Sheng Li
4. Madline Sauvage
5. Carstyn F Joiner
6. Govinda R Hancock
7. Emily A Sullivan
8. Estelle Ndukwe
9. Ross Han
10. Sydney Cush
11. Muriel Lainé
12. Sylvie C Mader
13. Geoffrey L Greene
14. Sean W Fanning

• Curated by eLife

  Evaluation Summary:

  This paper will be of broad interest to many fields, including drug discovery, cancer biology, and structure biology. It makes a significant advance in understanding the mechanism of action of hormone therapies for breast cancer, and how resistance driving mutations alter drug responses. The structural biology data has clear potential for strong impact though some additional analysis might be needed.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife