Immunology

Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming

1. Magdalena L Russell
2. Noah Simon
3. Philip Bradley
4. Frederick A Matsen

• Curated by eLife

  eLife assessment

  Russel et al. study and reveal compelling evidence for potential sequence-based factors that may drive VDJ trimming, a mechanism involved in VDJ recombination that shapes adaptive immune repertoire generation. The work is based on a rigorous statistical comparison of logistic regression models to reveal the role and function of cutting enzymes in shaping T- and B-cell receptor diversity. It could provide fundamental new insights into these processes with some claims being currently incomplete.

Reviewed by eLife

BCR-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics

1. Luqman O. Awoniyi
2. Alexey V. Sarapulov
3. Sara Hernández-Pérez
4. Marika Runsala
5. Diogo M. Cunha
6. Blanca Tejeda-González
7. Vid Šustar
8. M. Özge Balci
9. Petar Petrov
10. Pieta K. Mattila

Reviewed by Review Commons

Maintained imbalance of triglycerides, apolipoproteins, energy metabolites and cytokines in long-term COVID-19 syndrome patients

1. Georgy Berezhnoy
2. Rosi Bissinger
3. Anna Liu
4. Claire Cannet
5. Hartmut Schäfer
6. Katharina Kienzle
7. Michael Bitzer
8. Helene Häberle
9. Siri Göpel
10. Christoph Trautwein
11. Yogesh Singh

Reviewed by PeerRef

ATRAP - Accurate T cell Receptor Antigen Pairing through data-driven filtering of sequencing information from single-cells

1. Helle Rus Povlsen
2. Amalie Kai Bentzen
3. Mohammad Kadivar
4. Leon Eyrich Jessen
5. Sine Reker Hadrup
6. Morten Nielsen

• Curated by eLife

  eLife assessment

  This paper is of interest to immunologists conducting single-cell analyses of T-cell recognition. It provides a means of curating datasets to ensure T cell-antigen pairs are identified. The data generated through this method often suffers from a relatively high background, so the authors present a computational approach to enhance the signal-to-noise of this type of analysis. At this stage, it is unclear if the thresholds and filtering steps described by the authors can be generally applied to other datasets of different qualities than the one used here.

Reviewed by eLife

Nirmatrelvir treatment of SARS‐CoV‐2‐infected mice blunts antiviral adaptive immune responses

1. Valeria Fumagalli
2. Pietro Di Lucia
3. Micol Ravà
4. Davide Marotta
5. Elisa Bono
6. Stefano Grassi
7. Lorena Donnici
8. Rolando Cannalire
9. Irina Stefanelli
10. Anastasia Ferraro
11. Francesca Esposito
12. Elena Pariani
13. Donato Inverso
14. Camilla Montesano
15. Serena Delbue
16. Stanley Perlman
17. Enzo Tramontano
18. Raffaele De Francesco
19. Vincenzo Summa
20. Luca G Guidotti
21. Matteo Iannacone

Reviewed by Review Commons

Cellular and molecular dynamics in the lungs of neonatal and juvenile mice in response to E. coli

1. Sharon A McGrath-Morrow
2. Jarrett Venezia
3. Roland Ndeh
4. Nigel Michki
5. Javier Perez
6. Benjamin David Singer
7. Raffaello Cimbro
8. Mark Soloski
9. Alan L Scott

• Curated by eLife

  eLife assessment

  This study examines the inflammatory and immune response to live E. coli bacterial infection in neonatal and juvenile mice. Important information is described on the roles of Class II MHC and interferon responsive genes in regulating the host response to infection. This study will inform future efforts to further elucidate the impact of bacterial infections on lung development.

Reviewed by eLife

Germinal center B cells that acquire nuclear proteins are specifically suppressed by follicular regulatory T cells

1. Fang Ke
2. Zachary L Benet
3. Mitra P Maz
4. Jianhua Liu
5. Alexander L Dent
6. Joanne Michelle Kahlenberg
7. Irina L Grigorova

• Curated by eLife

  eLife assessment

  It is well known that Tfr cells have the capacity to preferentially suppress autoimmune antibody responses, but it is not known why such specificity exists. This important work provides new information as to how self-reactive antibody responses are regulated and has significant implications to the fields of autoimmunity and vaccine design. The overall experimental designs and the data quality are largely convincing, but the authors should include more careful controls.

Reviewed by eLife

Liver type 1 innate lymphoid cells lacking IL-7 receptor are a native killer cell subset fostered by parenchymal niches

1. Takuma Asahi
2. Shinya Abe
3. Guangwei Cui
4. Akihiro Shimba
5. Tsukasa Nabekura
6. Hitoshi Miyachi
7. Satsuki Kitano
8. Keizo Ohira
9. Johannes M Dijkstra
10. Masaki Miyazaki
11. Akira Shibuya
12. Hiroshi Ohno
13. Koichi Ikuta

• Curated by eLife

  eLife assessment

  This study provides important insights on the developmental process and functional heterogeneity of liver ILC1s, especially how IL-7R+ and IL-7R- ILC1s are generated. Authors present compelling evidence on the dependence of ILC1s on IL-7R- precursor and their reliance on IL-15 to develop cytotoxic functions. The work will be of broad interest to immunologists and liver biologists.

Reviewed by eLife

Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

1. Niels JM Verstegen
2. Sabrina Pollastro
3. Peter-Paul A Unger
4. Casper Marsman
5. George Elias
6. Tineke Jorritsma
7. Marij Streutker
8. Kevin Bassler
9. Kristian Haendler
10. Theo Rispens
11. Joachim L Schultze
12. Anja ten Brinke
13. Marc Beyer
14. S Marieke van Ham

• Curated by eLife

  eLife assessment

  In this work, Verstegen and colleagues established an in vitro system and describe human B cell differentiation pathways via germinal center B cells towards plasma cells by performing single-cell analysis of in vitro stimulated human B cells. The study provides solid evidence toward establishment of in vitro model for B cell differentiation. This study may be valuable in differentiation of primary naive B cells into ASC ex vivo and will be of interest for immunologists with emphasis in B cell biology.

Reviewed by eLife

Homeostatic activation of aryl hydrocarbon receptor by dietary ligands dampens cutaneous allergic responses by controlling Langerhans cells migration

1. Adeline Cros
2. Alba De Juan
3. Renaud Leclère
4. Julio L Sampaio
5. Mabel San Roman
6. Mathieu Maurin
7. Sandrine Heurtebise-Chrétien
8. Elodie Segura

Reviewed by Review Commons