Preprint Club
A cross-institutional Journal Club Initiative
2023 - January
Human intestinal epithelial cells can internalize luminal fungi via LC3-associated phagocytosis.
Cohen-Kedar, S. et al. (BioRxiv) doi:10.1101/2022.12.14.520372
Immunogenicity of non-canonical HLA-I tumor ligands identified through proteogenomics
Lozano-Rabella, M. et al. (BioRxiv) DOI: 10.1101/2022.11.07.514886
2022 - November
B cell depletion attenuates CD27 signaling of T helper cells in multiple sclerosis
Ulutekin, C. et al. (medRxiv) doi:10.1101/2022.10.17.22281079
Cystatin F (Cst7) drives sex-dependent changes in microglia in an amyloid-driven model of Alzheimer’s Disease
Daniels, M.J.D. et al. (BioRxiv) doi: 10.1101/2022.11.18.516922
Enhanced STAT5a activation rewires exhausted CD8 T cells during chronic stimulation to acquire a hybrid durable effector like state
Beltra, J-C. et al. (BioRxiv) doi: 10.1101/2022.10.03.509766
2022 - October
Release of the pre-assembled naRNA-LL37 composite DAMP re-defines neutrophil extracellular traps (NETs) as intentional DAMP webs
Bork, F. et al. (BioRxiv) doi: 10.1101/2022.07.26.499571
Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendrocytes
Garza, R. et al. (BioRxiv) doi: 10.1101/2022.09.07.506982
Eradication of tumors with pre-existing antigenic heterogeneity by vaccine-mediated co-engagement of CAR T and endogenous T-cells
Ma, Y. et al. (BioRxiv) doi: 10.1101/2022.10.05.511036
2022 - September
Long-term retention of antigens in germinal centres is controlled by the spatial organisation of the follicular dendritic cell network
Martinez-Riano, A. et al. (BioRxiv) doi: 10.1101/2022.09.06.506650
2022 - June
A unique epigenomic landscape defines CD8+ tissue-resident memory T cells
Buquicchio, F. et al. (BioRxiv) doi: 10.1101/2022.05.04.490680
GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology
Earley, Z. et al. (BioRxiv) doi: 10.1101/2021.10.28.466194
Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation
Dikiy, S. et al. (BioRxiv) doi: 10.1101/2022.05.16.492030
2022 - May
Integrated protein and transcriptome high-throughput spatial profiling
Ben-Chetrit N. et al. (BioRxiv) doi: 10.1101/2022.03.15.484516
Induction of a CD8 T cell intrinsic DNA damage and repair response isassociated with clinical response to PD-1 blockade in uterine cancer
Muroyama, Y. et al. (BioRxiv) doi: 10.1101/2022.04.16.488552
Unaltered T cell responses to common antigens in individuals with Parkinson’s disease
Williams, G.P. et al. (BioRxiv) doi: 10.1101/2022.04.05.487195
Sex differences in NK cells mediated by the X-linked epigenetic regulator UTX
Cheng, M. et al. (BioRxiv) doi: 10.1101/2022.04.21.489076
Brain resident memory T cells rapidly expand and initiate neuroinflammatory responses following CNS injury and viral infection
Ayasoufi, K. et al. (BioRxiv) doi: 10.1101/2022.04.08.487707
Distinct gene expression by expanded clones of quiescent memory CD4+ T cells harboring intact latent HIV-1 proviruses
Weymar, G.H.J. et al. (BioRxiv) doi: 10.1101/2022.03.02.482683
2022 - April
Immune checkpoint blockade induces gut microbiota translocation that augments extraintestinal anti-tumor immunity
Choi, Y. et al. (BioRxiv) doi: 10.1101/2022.01.26.477865
STING controls T cell memory fitness during infection through Tcell intrinsic and IDO dependent mechanisms
Quaney, M.J. et al. (BioRxiv) doi: 10.1101/2022.03.19.484992
Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates
Giles, J.R. et al. (BioRxiv) doi: 10.1101/2022.03.27.485974
In Utero Activation of NK Cells in Congenital CMV Infection
Vabeen, A.V. et al. (BioRxiv) doi: 10.1101/2022.04.04.487059
The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity.
Ho, P. et al. (BioRxiv) doi: 10.1101/2022.03.21.485049
Nuclear envelope disruption triggers hallmarks of aging in lung alveolar macrophages
De Silva, N.S. et al. (BioRxiv) doi: 10.1101/2022.02.17.480837
Microbial Energy Metabolism Fuels a CSF2-dependent Intestinal Macrophage Niche within Tertiary Lymphoid Organs
Chiaranunt, P. et al. (BioRxiv) doi: 10.1101/2022.03.23.485563
2022 - March
Three functionally distinct classes of cGAS proteins in nature revealed by self-DNA-induced interferon responses
Mosallanejad, K. et al. (BioRxiv) doi: 10.1101/2022.03.09.483681
Germinal center block exacerbates extrafollicular responses and accelerates autoimmune disease progression in a murine lupus model
Voss, L.F. et al. (BioRxiv) doi: 10.1101/2022.03.04.482991
Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC
Baer, J.M. et al. (BioRxiv) doi: 10.1101/2022.02.09.479745
2022 - February
Divergent clonal differentiation trajectories of T cell exhaustion
Daniel, B. et al. (BioRxiv) doi: 10.1101/2021.12.16.472900
Microenvironmental Sensing by Fibroblasts Controls Macrophage Population Size
Zhou, X., Franklin, R. et al. (BioRxiv) doi: 10.1101/2022.01.18.476683
2022 - January
Structurally and functionally distinct early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response
Chakraborty, S. et al. (BioRxiv) doi: 10.1101/2021.05.25.445649
The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanisms
Willett, B.J. et al. (medRxiv) doi: 10.1101/2022.01.03.21268111
Overactive STAT3 drives accumulation of disease-associated CD21low B cells
Masle-Farquhar, E. et al. (BioRxiv) doi: 10.1101/2021.12.20.473595
IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α
Van Dis, E. et al. (BioRxiv) doi: 10.1101/2021.12.16.473015
Differentiation of a CD4+/CD8ab+ Double Positive T cell Population From the CD8 Pool is Sufficient To mediate Graft-vs-Host Disease but not Graft-vs-Leukemia Effects
Hess, N.J. et al. (BioRxiv) doi: 10.1101/2022.01.11.475845
2021 - December
Antigen presentation by type 3 innate lymphoid cells instructs the differentiation of gut microbiota-specific regulatory T cells
Kedmi, R. et al. (BioRxiv) doi: 10.1101/2021.11.19.469318
γδ T cells are effectors of immune checkpoint blockade in mismatch repair-deficient colon cancers with antigen presentation defects
de Vries, N.L. et al. (BioRxiv) doi: 10.1101/2021.01.14.464229
Inhibition of microbial deconjugation of micellar bile acids protects against intestinal permeability and liver injury
Li, D.K. et al. (BioRxiv) doi: 10.1101/2021.03.24.436896
Tertiary lymphoid structures induced by CXCL13-producing CD4+ T cells increase tumor infiltrating CD8+ T cells and B cells in ovarian cancer
Ukita, M. et al. (BioRxiv) doi: 10.1101/2021.12.01.470493
2021 - November
Microbiome-specific T follicular helper cells drive tertiary lumphoid structures and anti-tumor immunity against colorectal cancer
Overacre-Delgoffe, A.E. et al. (BioRxiv) doi: 10.1101/2021.01.27.428417
Commensal bacteria promote type I interferon signalling to maintain immune tolerance
Vasques Ayala, A. et al. (BioRxiv) doi: 10.1101/2021.10.21.464743
Pan-cancer mapping of single T cell profiles reveals a TCF1:CXCR6-CXCL16 regulatory axis essential for effective anti-tumor immunity
Jerby-Arnon, L. et al. (BioRxiv) doi: 10.1101/2021.10.31.466532
2021 - October
Hematopoietic stem and progenitor cells integrate Bacteroides-derived innate immune signals to promote gut tissue repair
Hayashi, Y. et al. (BioRxiv) doi: 10.1101/2021.10.05.463122
Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer
Kersten, K. et al. (BioRxiv) doi: 10.1101/2021.09.27.461866
Predictive framework of macrophage activation
Sanin, D.E. et al. (BioRxiv) doi: 10.1101/2021.08.02.454825
2021 - September
Induction of transposable element expression is central to innate sensing
Rookhuizen DC et al. (BioRxiv) doi:10.1101/2021.09.10.457789
SARS-CoV-2 mRNA vaccination elicits robust and persistent T follicular helper cell response in humans
Mudd PA et al. (BioRxiv) doi:10.1101/2021.09.08.459485
Excess dietary sugar impairs colonic epithelial regeneration 1 in response to damage
Burr et al. (BioRxiv) doi: 10.1101/2021.08.18.456840
2021 - June
Signatures of mast cell activation are associated with severe COVID-19
Tan J. et al. (MedRxiv) DOI: 10.1101/2021.05.31.21255594
The extracellular ATP receptor P2RX7 imprints a pro-memory transcriptional signature in effector CD8+ T cells
Vardam-Kaur, T. et al. (BioRxiv) DOI: 10.1101/2021.05.25.445679
2021 - May
Active Surveillance Characterizes Human Intratumoral T Cell Exhaustion
You, R. et al. (BioRxiv) DOI: 10.1101/2021.05.06.443033
The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair
McCowan, J. et al. (BioRxiv) DOI: 10.1101/2021.05.06.442095
Differentiation of exhausted CD8 T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory
Tonnerre, P. et al. (BioRxiv) DOI: 10.1101/2021.04.03.437705
Hematopoietic stem cell requirement for macrophage regeneration is tissue-specific
Eddins, D.J. et al. (BioRxiv) DOI: 10.1101/2021.04.08.439077
2021 - April
When killers become thieves: trogocytosed PD-1 inhibits NK cells in cancer
Hasim, M.S. et al. (BioRxiv) DOI: 10.1101/2020.06.26.174342
Alveolar macrophages strictly rely on GM-CSF from alveolar epithelial type 2 cells before and after birth
Gschwend, J. et al. (BioRxiv) DOI: 10.1101/2021.04.01.438051
Extracellular Delivery of Functional Mitochondria Reverses the Dysfunction of CD4+ T Cells in Aging
Headley, C.A. et al. (BioRxiv) DOI: 10.1101/2021.02.21.432151
2021 - March
Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees
Tarke, A. et al. (BioRxiv) DOI: 10.1101/2021.02.27.433180
Selected Nature Reviews Immunology Highlight
The skin environment controls local dendritic cell differentiation and function through innate IL-13
Mayer, J.U. et al. (BioRxiv) DOI: 10.1101/2021.01.05.425466
Murine ex vivo cultured alveolar macrophages provide a novel tool to study tissue-resident macrophage behavior and function
Gorki, A.D. et al. (BioRxiv) DOI: 10.1101/2021.02.11.430791
Sting orchestrates the crosstalk between polyunsaturated fatty acids metabolism and inflammatory responses
Vila, I.K. et al. (BioRxiv) DOI: 10.1101/2020.12.22.423950
CINS: Cell Interaction Network inference from Single cell expression data
Yuan, Y. et al. (BioRxiv) DOI: 10.1101/2021.02.22.432206
2021 - February
Maternal infection promotes offspring tissue-specific immune fitness
Lim, A.I. et al (BioRxiv). DOI: 10.1101/2021.01.13.426542
Novel gut pathobionts confound results in a widely used model of human inflammatory disease
Forster, S.C. et al. (BioRxiv) DOI: 10.1101/2021.02.09.430393
MTHFD2 is a Metabolic Checkpoint Controlling Effector and Regulatory T Cell Fate and Function
Sugiura, A. et al. (BioRxiv) DOI: 10.1101/2021.02.03.428939
Combining an alarmin HMGN1 peptide with PD-L1 blockade facilitates stem-like CD8+ T cell expansion and results in robust anti-tumor effects
Chen, C.Y. et al. (BioRxiv) DOI: 10.1101/2020.12.15.422990
A reservoir of stem-like CD8 T cells in the tumor-draining lymph node maintains the ongoing anti-tumor immune response
Connolly, KA. et al. (BioRxiv) DOI: 10.1101/2021.01.27.428467
Altered basal lipid metabolism underlies the functional impairment of naive CD8+ T cells in elderly humans
Nicoli, F. et al. (BioRxiv) DOI: 10.1101/2020.09.24.311704
2021 - January
Multi-antigen recognition circuits overcome challenges of specificity, heterogeneity, and durability in T cell therapy for glioblastoma
Choe, JH. et al. (BioRxiv) DOI: 10.1101/2021.01.07.425632
Diverse Functional Autoantibodies in Patients with COVID-19
Wang, E.Y. et al. (MedRxiv) DOI: 10.1101/2020.12.10.20247205
Neoantigen driven B cell and CD4+ T follicular helper cell collaboration promotes robust anti-tumor CD8+ T cell responses
Cui, C. et al. (BioRxiv) DOI: 10.1101/2020.12.23.424168
2020 - December
A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro
Cheng, M.H. et al. (BioRxiv) DOI: 10.1101/2020.11.24.395079
Selected Nature Reviews Immunology Highlight
ADAR1 interaction with Z-RNA promotes editing of endogenous double-stranded RNA and prevents MDA5-dependent immune activation
De Reuver et al. (BioRxiv) DOI: 10.1101/2020.12.04.411702
Vaccination reshapes the virus-specific T cell repertoire in unexposed adults
Pan*, Y.G., Aiamkitsumrit, B. et al. (BioRxiv) DOI: 10.1101/2020.10.01.322958