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Recombination junctions from antibody isotype switching classify immune and DNA repair dysfunction

Class switch recombination (CSR) is a process contributing to antibody diversity and generating characteristic genomic junctions that reflect DNA double-strand break repair efficiency. Here authors present a platform to profile the repertoire of CSR junction patterns; long-read-sequenced PCR products from blood-derived lymphocytes are analysed by a dedicated bioinformatic pipeline to accurately detect immunodeficiencies and DNA repair defects.

Clara Vázquez García
Benedikt Obermayer
Kathrin de la Rosa
ResearchOpen Access19 Dec 2025
Nature Communications

Volume: 16, P: 1-15
Tracing tumorigenesis in a solid tumor model at single-cell resolution

Understanding tumour development at a granular level is a challenge in solid tumours. Here, the authors provide a cell atlas across tumour development in a genetic model of salivary gland squamous cell carcinoma using single-cell transcriptome and epitope profiling.

Samantha D. Praktiknjo
Benedikt Obermayer
Nikolaus Rajewsky
ResearchOpen Access20 Feb 2020
Nature Communications

Volume: 11, P: 1-12
Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19

The immune response is key in determining disease severity of COVID19. Here Nouailles et al., apply bulk proteomics and scRNA-Seq of lung and blood samples of SARS-CoV-2 infected Syrian hamsters and provide a temporal atlas of the systemic and pulmonary cellular responses.

Geraldine Nouailles
Emanuel Wyler
Martin Witzenrath
ResearchOpen Access11 Aug 2021
Nature Communications

Volume: 12, P: 1-18
Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19

Infection with SARS-CoV-2 has been linked with substantive inflammation, lung pathology and development of COVID-19. Here the authors spatially associate CCL18 and CCL21 in distinct tissue niches with lung pathology of severe COVID-19.

Ronja Mothes
Anna Pascual-Reguant
Anja E. Hauser
ResearchOpen Access11 Feb 2023
Nature Communications

Volume: 14, P: 1-16
CD4⁺ T cell calibration of antigen-presenting cells optimizes antiviral CD8⁺ T cell immunity

Bedoui and colleagues describe a sequential process of integration of innate and CD40-delivered signals in APCs, which optimizes their capacity to drive antiviral CD8⁺ T cell responses.

Elise Gressier
Jonas Schulte-Schrepping
Sammy Bedoui
Research15 May 2023
Nature Immunology

Volume: 24, P: 979-990
Detecting actively translated open reading frames in ribosome profiling data

RiboTaper quantifies the three-nucleotide periodicity in Ribo-seq data to find translated open reading frames (ORFs). The de novo inferred set of ORFs comprehensively defines the cellular proteome across a wide expression range and comprises few additional translated noncoding regions.

Lorenzo Calviello
Neelanjan Mukherjee
Uwe Ohler
Research14 Dec 2015
Nature Methods

Volume: 13, P: 165-170
Human alveolar progenitors generate dual lineage bronchioalveolar organoids

The GSK3 inhibitor CHIR99021 is required to maintain the alveolar lineage in alveolar progenitors grown in airway media or AT2 cells become plastic, with the observed effects acting outside of its role as a GSK3B inhibitor.

Karen Hoffmann
Benedikt Obermayer
Mirjana Kessler
ResearchOpen Access25 Aug 2022
Communications Biology

Volume: 5, P: 1-17
Author Correction: Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses

Swetha Rajasekaran
Jalal Siddiqui
Wayne Miles
Amendments and CorrectionsOpen Access30 Sept 2021
Communications Biology

Volume: 4, P: 1
Transcriptomic comparison of primary human lung cells with lung tissue samples and the human A549 lung cell line highlights cell type specific responses during infections with influenza A virus

Wilhelm Bertrams
Katja Hönzke
Andreas C. Hocke
ResearchOpen Access29 Nov 2022
Scientific Reports

Volume: 12, P: 1-11
Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma

Philip Bischoff
Alexandra Trinks
Frederick Klauschen
ResearchOpen Access18 Oct 2021
Oncogene

Volume: 40, P: 6748-6758
Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses

Swetha Rajasekaran et al. integrate transcriptional, proteomic, and metabolomic data to explore how cells adapt to inactivation of RB1, a hallmark of cancer. Combined with their genetic analyses in a Drosophila model, the authors identify key metabolic pathways that may be involved in the growth of RB1-depleted cancer cells.

Swetha Rajasekaran
Jalal Siddiqui
Wayne Miles
ResearchOpen Access17 Aug 2021
Communications Biology

Volume: 4, P: 1-13
Mixed messages: Re-initiation factors regulate translation of animal mRNAs

When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5′ untranslated region (5′ UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation.

Benedikt Obermayer
Nikolaus Rajewsky
Research Highlights22 Aug 2014
Cell Research

Volume: 24, P: 1383-1384

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