Genomics

The costs of competition: high social status males experience accelerated epigenetic aging in wild baboons

1. Jordan A. Anderson
2. Rachel A. Johnston
3. Amanda J. Lea
4. Fernando A. Campos
5. Tawni N. Voyles
6. Mercy Y. Akinyi
7. Susan C. Alberts
8. Elizabeth A. Archie
9. Jenny Tung

• Curated by eLife

  Evaluation Summary:

  In this paper, the authors collect epigenomic data from a well-studied wild baboon community, which they use to construct an epigenetic clock, a method of measuring "biological age" that is increasingly used as a tool in human aging research. The authors find that deviations between biological and chronological age can in part be explained by social phenomena. In particular, for male baboons, maintaining social dominance may play an important role in accelerating the dimension of aging indexed by this measure. This is a foundational study for social-biological-health 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 #1 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms

1. Bas B. Oude Munnink
2. Reina S. Sikkema
3. David F. Nieuwenhuijse
4. Robert Jan Molenaar
5. Emmanuelle Munger
6. Richard Molenkamp
7. Arco van der Spek
8. Paulin Tolsma
9. Ariene Rietveld
10. Miranda Brouwer
11. Noortje Bouwmeester-Vincken
12. Frank Harders
13. Renate Hakze-van der Honing
14. Marjolein C.A. Wegdam-Blans
15. Ruth J. Bouwstra
16. Corine GeurtsvanKessel
17. Annemiek A. van der Eijk
18. Francisca C. Velkers
19. Lidwien A.M. Smit
20. Arjan Stegeman
21. Wim H.M. van der Poel
22. Marion P.G. Koopmans

Reviewed by ScreenIT, NCRC

Evolution of cytokine production capacity in ancient and modern European populations

1. Jorge Domínguez-Andrés
2. Yunus Kuijpers
3. Olivier B Bakker
4. Martin Jaeger
5. Cheng-Jian Xu
6. Jos WM Van der Meer
7. Mattias Jakobsson
8. Jaume Bertranpetit
9. Leo AB Joosten
10. Yang Li
11. Mihai G Netea

• Curated by eLife

  Evaluation Summary:

  Dominguez-Andrés et al. collect a large amount of immune-related trait association data from a cohort made up of 534 individuals of Western European ancestry. The goal was to track the evolutionary trajectories of cytokine production capacity over time in a number of patients with different exposure to infectious organisms, infectious disease, autoimmune and inflammatory diseases, using the 500 Functional Genomics cohort of the Human Functional Genomics Project. From this analysis it was hypothesized that the Neolithic transition was characterized by strong changes in the adaptive response to pathogens in human biology. Overall, the manuscript is interesting but could be improved by significant enhancements to statistical methodology.

  (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

Improving oligo-conjugated antibody signal in multimodal single-cell analysis

1. Terkild Brink Buus
2. Alberto Herrera
3. Ellie Ivanova
4. Eleni Mimitou
5. Anthony Cheng
6. Ramin Sedaghat Herati
7. Thales Papagiannakopoulos
8. Peter Smibert
9. Niels Ødum
10. Sergei B. Koralov

Reviewed by eLife

In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

1. Juan Carlos Jado
2. Michelle Dow
3. Krypton Carolino
4. Adam Klie
5. Gregory J. Fonseca
6. Trey Ideker
7. Hannah Carter
8. Elizabeth A. Winzeler

• Curated by eLife

  Summary: The authors examined the genomic basis of resistance evolution in human chronic myelogenous leukemia (CML) near-haploid cell lines to 5 separate chemotherapeutic agents.

  Using either whole genome or whole exome analysis, they found numerous instances of single nucleotide polymorphisms and copy number variants, including amplifications and deletions, among lines. They then used subsequent knockdown or knockout experiments to confirm that these variants, in fact, lead to increased resistance in these lines.

  The work is interesting, timely, and has potential clinical implications. For example, the resistance alleles identified here could be closely examined in future studies in order to develop treatment strategies. However, the experimental design has certain limitations, advances in understanding chemotherapy resistance mechanisms is currently modest, and the presentation of results can be improved. We feel overall that these could be addressed, but that they will require significant extra experimental work.

Reviewed by eLife

Mendelian randomization identifies folliculin expression as a mediator of diabetic retinopathy

1. Andrew D. Skol
2. Segun C. Jung
3. Ana Marija Sokovic
4. Siquan Chen
5. Sarah Fazal
6. Olukayode Sosina
7. Poulami Borkar
8. Amy Lin
9. Maria Sverdlov
10. Dingcai Cao
11. Anand Swaroop
12. Ionut Bebu
13. DCCT/ EDIC Study group
14. Barbara E. Stranger
15. Michael A. Grassi

Reviewed by eLife

Gene expression variability in human and chimpanzee populations share common determinants

1. Benjamin J. Fair
2. Lauren E. Blake
3. Abhishek Sarkar
4. Bryan J. Pavlovic
5. Claudia Cuevas
6. Yoav Gilad

Reviewed by eLife

Large-scale analysis of DNA methylation identifies cellular alterations in blood from psychosis patients and molecular biomarkers of treatment-resistant schizophrenia

1. Eilis Hannon
2. Emma L Dempster
3. Georgina Mansell
4. Joe Burrage
5. Nick Bass
6. Marc M Bohlken
7. Aiden Corvin
8. Charles J Curtis
9. David Dempster
10. Marta Di Forta
11. Timothy G Dinan
12. Gary Donohoe
13. Fiona Gaughran
14. Michael Gill
15. Amy Gillespie
16. Cerisse Gunasinghe
17. Hilleke E Hulshoff
18. Christina M Hultman
19. Viktoria Johansson
20. Rene S Kahn
21. Jaakko Kaprio
22. Gunter Kenis
23. Kaarina Kowalec
24. James MacCabe
25. Colm McDonald
26. Andew McQuillin
27. Derek W Morris
28. Kieran C Murphy
29. Collette Mustard
30. Igor Nenadic
31. Michael C O’Donovan
32. Diego Quattrone
33. Alexander L Richards
34. Bart PF Rutten
35. David St Clair
36. Sebastian Therman
37. Timothea Toulopoulou
38. Jim Van Os
39. John L Waddington
40. Wellcome Trust Case Control Consortium 2
41. CREeTable AR consortium
42. Patrick Sullivan
43. Evangelos Vassos
44. Gerome Breen
45. David Andrew Collier
46. Robin Murray
47. Leonard S Schalkwyk
48. Jonathan Mill

Reviewed by eLife

Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

1. Jun Yao
2. Douglas C. Wu
3. Ryan M. Nottingham
4. Alan M. Lambowitz

Reviewed by eLife

Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions

1. Carlos Farkas
2. Francisco Fuentes-Villalobos
3. José Luis Garrido
4. Jody J Haigh
5. María Inés Barría

Reviewed by ScreenIT, PeerJ