Immunology

The 1000+ mouse project: large-scale spatiotemporal parametrization and modeling of preclinical cancer immunotherapies

1. Adam L Kenet
2. Sooraj Achar
3. Alka Dwivedi
4. John Buckley
5. Marie Pouzolles
6. Haiying Qin
7. Christopher Chien
8. Naomi Taylor
9. Grégoire Altan-Bonnet

• Curated by eLife

  eLife Assessment

  The authors developed a fundamental computational method, which is intended to automatically process bioluminescence imaging-derived tumour images across anatomical regions and over time. This allows quantitative analysis of such data, and the authors applied it to describe the spatiotemporal distribution of tumour cells in response to CD19-targeted CAR-T cells that contained either CD28 or 4-1BB costimulatory domains. Some operational limitations were identified, which relate to the pipeline's reliance on predefined regions of interest instead of aligning signal sites with anatomical information, scaling, and not taking animal pose into account. Overall, the authors provide compelling evidence for the functionality of their computational approach towards automated analysis of bioluminescence imaging data, while applying it to a current topic of wide interest in cell therapy research.

Reviewed by eLife

Aurora kinase A promotes trained immunity via regulation of endogenous S-adenosylmethionine metabolism

1. Mengyun Li
2. Huan Jin
3. Yongxiang Liu
4. Zining Wang
5. Lin Li
6. Tiantian Wang
7. Xiaojuan Wang
8. Hongxia Zhang
9. Bitao Huo
10. Tiantian Yu
11. Shoujie Wang
12. Wei Zhao
13. Jinyun Liu
14. Peng Huang
15. Jun Cui
16. Xiaojun Xia

• Curated by eLife

  eLife Assessment

  The authors use a range of techniques to examine the role of Aurora Kinase A (AurA) in trained immunity. The study is hypothesis driven, it uses solid experimental approaches, and the data are presented in a logical manner. The findings are valuable to the trained immunity field because they provide an in-depth look at a common inducer of trained immunity, beta-glucan.

Reviewed by eLife

Newly discovered and conserved role of IgM against viral infection in an early vertebrate

1. Weiguang Kong
2. Xinyou Wang
3. Guangyi Ding
4. Peng Yang
5. Yong Shi
6. Chang Cai
7. Xinyi Yang
8. Gaofeng Cheng
9. Fumio Takizawa
10. Zhen Xu

• Curated by eLife

  eLife Assessment

  The manuscript is an important study which aims to demonstrate the conserved and crucial role of IgM in both systemic and mucosal antiviral immunity in teleost, challenging the established differential roles of IgT and IgM. The strength of the evidence is solid and supported by a combination of in vivo studies, viral infection models, and complementary in vitro assays. In the current version, authors validate the MoAb against IgM

Reviewed by eLife

Single-cell analysis of signalling and transcriptional responses to type I interferons

1. Rachel E. Rigby
2. Kevin Rue-Albrecht
3. David Sims
4. Jan Rehwinkel

Reviewed by Review Commons

scRNA+TCR-seq Reveals the Proportion and Characteristics of Dual TCR Treg Cells in Mouse Lymphoid and Non-lymphoid Tissues

1. Yuanyuan Xu
2. Qi Peng
3. Xiaoping Lu
4. Long Ma
5. Jun Li
6. Xinsheng Yao

• Curated by eLife

  eLife Assessment

  This study reanalyzed previously published scRNA-seq and TCR-seq data to examine the proportion and characteristics of dual-TCR-expressing Treg cells in mice, presenting some useful insights into TCR diversity and immune regulation. However, the evidence is incomplete, particularly with respect to data interpretation, statistical rigor, and the functionality of dual -TCR Treg cells. The study is potentially of interest to immunologists studying T-cell biology.

Reviewed by eLife

Correlates of protection against African swine fever virus identified by a systems immunology approach

1. Kirill Lotonin
2. Francisco Brito
3. Kemal Mehinagic
4. Obdulio García-Nicolás
5. Matthias Liniger
6. Noelle Donzé
7. Sylvie Python
8. Stephanie Talker
9. Tosca Ploegaert
10. Nicolas Ruggli
11. Charaf Benarafa
12. Artur Summerfield

• Curated by eLife

  eLife Assessment

  This study provides valuable findings regarding potential correlates of protection against the African swine fever virus. The evidence supporting the claims is solid, although analysis using a higher number of animals and other virus strains will be required to further evaluate the relevance of the immune parameters associated to protection. The work will be of broad interest to veterinary immunologists, and particularly those working on African swine fever.

Reviewed by eLife

Thrifty wide-context models of B cell receptor somatic hypermutation

1. Kevin Sung
2. Mackenzie M Johnson
3. Will Dumm
4. Noah Simon
5. Hugh Haddox
6. Julia Fukuyama
7. Frederick A Matsen

• Curated by eLife

  eLife Assessment

  This study provides an important method to model the statistical biases of hypermutations during the affinity maturation of antibodies. The authors show convincingly that their model outperforms previous methods with fewer parameters; this is made possible by the use of machine learning to expand the context dependence of the mutation bias. They also show that models learned from nonsynonymous mutations and from out-of-frame sequences are different, prompting new questions about germinal center function. Strengths of the study include an open-access tool for using the model, a careful curation of existing datasets, and a rigorous benchmark; it is also shown that current machine-learning methods are currently limited by the availability of data, which explains the only modest gain in model performance afforded by modern machine learning.

Reviewed by eLife

Single molecule imaging of transcription dynamics, RNA localization and fate in human T cells

1. M. Valeria Lattanzio
2. Nikolina Šoštarić
3. Nandhini Kanagasabesan
4. Branka Popović
5. Antonia Bradarić
6. Leyma Wardak
7. Aurélie Guislain
8. Philipp Savakis
9. Evelina Tutucci
10. Monika C. Wolkers

Reviewed by Review Commons

A pair of congenic mice for imaging of transplants by positron emission tomography using anti-transferrin receptor nanobodies

1. Thomas Balligand
2. Claire Carpenet
3. Sergi Olivé Palau
4. Tom Jaspers
5. Pavana Suresh
6. Xin Liu
7. Himadri Medhi
8. Yoon Ho Lee
9. Mohammad Rashidian
10. Bart De Strooper
11. Hidde L Ploegh
12. Maarten Dewilde

• Curated by eLife

  eLife Assessment

  In this highly innovative study, Carpenet C et al explore the use of nanobody-based PET imaging to track proliferative cells after in vivo transplantation in mice, in a fully immunocompetent setting. The development of a unique set of PET tracers and mouse strains to track genetically-unmodified transplanted cells in vivo is an important novel asset that could potentially facilitate cell tracking in different research fields. The evidence provided is compelling as the new method proposed might facilitate overcoming certain limitations of alternative approaches, such as full sized immunoglobulins and small molecules.

Reviewed by eLife