theobinfwiki - Immunology Journal Club

Schedule

See the schedule on the Utrecht Center for Quantitative Immunology website

Links to interesting websites

Watch conference talks online from the KITP Quantative Immunology conference (February 2016)

Conferences/Workshops

Date	Name and link	Location	Abstract deadline	Registration deadline	Note

List of discussed papers (a.k.a. the OCD list)

Date	Title	Presentor	Comments (optional)
2018
10/04/2018	Martin et al., Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1, J Clin Invest (3 Apr 2018)	Can
20/03/2018	Zemmour et al., Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR, Nature Immunology (12 Feb 2018)	Eduardo
13/03/2018	Leitman et al., Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape, JEM (6 Nov 2017)	Juliane
27/02/2018	Helft et al., Dendritic Cell Lineage Potential in Human Early Hematopoietic Progenitors, Cell (Jul 2017)	Abhinandan
13/02/2018	Park et al., Local proliferation maintains a stable pool of tissue-resident memory T cells after antiviral recall responses, Nature Immunol (Feb 2018)	Peter
30/01/2018	Marty et al., MHC-I Genotype Restricts the Oncogenic Mutational Landscape, Cell (2017)	Wanissa
23/01/2018	Alculumbre et al., Diversification of human plasmacytoid predendritic cells in response to a single stimulus, Nature Immunology (2018)	Nila
16/01/2018	Ramsuran et al., Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells, Science (Jan 2018)	Chris	see also Apps et al. (2013)
2017
19/12/2017	Villani et al., Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors, Science (Apr 2017)	WeiYang
28/11/2017	Farlik et al., DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation, Cell Stem Cell (Dec 2016)	Abhinandan
21/11/2017	Estes et al., Defining total-body AIDS-virus burden with implications for curative strategies, Nature Med. (Nov 2017)	Anet
7/11/2017	Glasner et al., Zika Virus Escapes NK Cell Detection by Upregulating Major Histocompatibility Complex Class I Molecules, J Virol (Oct 2017)	Can
31/10/2017	Dash et al., Quantifiable predictive features define epitope-specific T cell receptor repertoires, Nature (July 2017)	Ewald
24/10/2017	Kakaradov et al., Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing, Nat Immunol (April 2017)	Aridaman
17/10/2017	Cho et al., TCR Signal Quality Modulates Fate Decisions of Single CD4+ T Cells in a Probabilistic Manner, Cell Rep (Jul 2017)	Rob
10/10/2017	Gorin et al., HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes, PLOS Pathogens (August 2017)	Chris
26/09/2017	Bettini et al., Cutting Edge: CD3 ITAM Diversity Is Required for Optimal TCR Signaling and Thymocyte Development, J Immunol (Sep 2017)	Koichi
19/09/2017	Human fetal dendritic cells promote prenatal McGovern et al., T-cell immune suppression through arginase-2, Nature (June 2017)	Dieter
12/09/2017	Descours et al., CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses, Nature (March 2017)	Juliane
11/07/2017	Glanville et al., Identifying specificity groups in the T cell receptor repertoire, Nature (Jul 2017)	Eduardo	see also Dash et al.
04/07/2017	Velten et al., Human haematopoietic stem cell lineage commitment is a continuous process, Nature (Feb 2017)	Abhinandan
27/06/2017	Byrareddy et al., Sustained virologic control in SIV+ macaques after antiretroviral and α4β7 antibody therapy, Science (Oct 2016)	Anet
20/06/2017	Elemans et al., HIV-1 adaptation to NK cell-mediated immune pressure, PLOS Pathogens (June 2017)	Can	see Alter et al. (IJC 28/09/2011 :-)
13/06/2017	Yu et al., Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation, Nature Immunology (March 2017)	Aridaman
30/05/2017	Ahmed et al., Human Stem Cell-like Memory T Cells Are Maintained in a State of Dynamic Flux, Cell Rep. (December 2016)	Esther
23/05/2017	Goncalves et al., A new mechanism shapes the naïve CD8+ T cell repertoire: the selection for full diversity, Mol Immunol (May 2017)	Rob
09/05/2017	Rieckmann et al., Social network architecture of human immune cells unveiled by quantitative proteomics, Nature (May 2017)	WeiYang
25/04/2017	Sun et al., Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization, Front Immunol (April 2017)	Eduardo
18/04/2017	Bouziat et al., Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease, Science (2017)	Dieter
11/04/2017	Kamphorst et al., Rescue of exhausted CD8 T cells by PD-1-targeted therapies is CD28-dependent, Science (March 2017)	Joep	cf. Im et al. (27/09/2016)
04/04/2017	Doud et al., Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin, Viruses (2016)	Chris
21/03/2017	Davoli et al., Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy, Science (Jan 2017)	Ianthe
07/03/2017	Song et al., Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope, Nat Struct Mol Biol (Feb 2017)	Bram
14/02/2017	Novkovic et al., Topological Small-World Organization of the Fibroblastic Reticular Cell Network Determines Lymph Node Functionality, PLOS Biology (July 2016)	Kasper	Primer by Textor et al.
07/02/2017	Flerin et al., TCR Clonotype-specific Differences in Inhibitory Activity of HIV-1 Cytotoxic T Cell Clones is Not Mediated by TCR Alone, J Virol. (Jan 2017)	Ewald
24/01/2017	F. Zanini, In-vivo mutation rates and fitness landscape of HIV-1, arXiv (Jul 2016)	Chris
17/01/2017	S. Heinzel et al., A Myc-dependent division timer complements a cell-death timer to regulate T cell and B cell responses, Nat Immunol. (Jan 2017)	Rob	How lymphocytes add up
2016
20/12/2016	De Simone et al., Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells, Immunity (Nov 2016)	Abhinandan
15/11/2016	Boritz et al., Multiple Origins of Virus Persistence during Natural Control of HIV Infection, Cell (Aug 2016)	Aridaman
01/11/2016	Oberle et al., A Minimum Epitope Overlap between Infections Strongly Narrows the Emerging T Cell Repertoire, Cell Rep. (Oct 2016)	Ester
19/10/2016	Sharon et al., Genetic variation in MHC proteins is associated with T cell receptor expression biases, Nat Genet (Sept 2016)	Ewald
04/10/2016	Lambert Emo et al., Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen, PLOS Pathogens (Sept 2016)	Chris	cf. Lim et al. (29/09/2015)
27/09/2016	Im et al.,Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy, Nature (Aug 2016)	Rob
20/09/2016	Notta et al., Distinct routes of lineage development reshape the human blood hierarchy across ontogeny, Science (Jan 2016)	Aridaman
13/09/2016	Stadinski et al., Hydrophobic CDR3 residues promote the development of self-reactive T cells, Nat Immunol (Aug 2016)	Can
30/08/2016	Pulko et al., Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses, Nature Immunology (Aug 2016)	Peter
21/06/2016	Wang er al., Inhibition of T cell receptor signaling by cholesterol sulfate, a naturally occurring derivative of membrane cholesterol, Nature (May 2016)	Marten
24/05/2016	Ruibal et al., Unique human immune signature of Ebola virus disease in Guinea, Nature (May 2016)	Chris
17/05/2016	Beura et al., Normalizing the environment recapitulates adult human immune traits in laboratory mice, Nature (Apr 2016)	Martijn
10/05/2016	Rubelt et al., Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells, Nat Commun (Mar 2016)	Bram
03/05/2016	McGranahan et al., Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade, Science (Mar 2016)	Ewald
12/04/2016	Halle et al., In Vivo Killing Capacity of Cytotoxic T Cells Is Limited and Involves Dynamic Interactions and T Cell Cooperativity, Immunity (Feb 2016)	Rob
29/03/2016	Jozwick et al., RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection, Nat. Commun. (Dec 2015)	Can
08/03/2016	van de Sandt et al., Differential Recognition of Influenza A Viruses by M158-66 Epitope-Specific CD8+ T Cells Is Determined by Extraepitopic Amino Acid Residues, J. Virol. (November 2015)	Chris
22/02/2016	Tubo et al., Most microbe-specific naïve CD4+ T cells produce memory cells during infection, Science (January 2016)	Aridaman
02/02/2016	Desponds et al., Fluctuating fitness shapes the clone-size distribution of immune repertoires, PNAS (January 2016)	Peter
19/01/2016	Maiuri et al., Actin flows mediate a universal coupling between cell speed and cell persistence, Cell (April 2015)	Martijn
2015
15/12/2015	Sewald et al., Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection, Science (October 2015)	Ewald
01/12/2015	McDonald et al., Crossreactive ab T Cell Receptors Are the Predominant Targets of Thymocyte Negative Selection, Immunity (November 2015)	Bram
17/11/2015	Ndhlovu et al., Magnitude and Kinetics of CD8(+) T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point, Immunity (September 2015)	Chris
03/11/2015	van Allen et al., Genomic correlates of response to CTLA4 blockade in metastatic melanoma, Science (September 2015)	Can
20/10/2015	Moreau et al., Signal strength regulates antigen-mediated T-cell deceleration by distinct mechanisms to promote local exploration or arrest, PNAS (September 2015)	Sanket
29/09/2015	Lim et al., Neutrophil trails guide influenza-specific CD8+ T cells in the airways, Science 340 (4 September 2015)	Rob
16/06/2015	Cohn et al., HIV-1 integration landscape during latent and active infection, Cell (January 2015)	Aridaman
09/06/2015	Wroblewski et al., Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz, PLOS Biol. (May 2015)	Can
28/04/2015	Claiborne et al., Replicative fitness of transmitted HIV-1 drives acute immune activation, proviral load in memory CD4+ T cells, and disease progression, PNAS (March 2015)	Chris
31/03/2015	Mohan et al. Antigenic Subversion: A Novel Mechanism of Host Immune Evasion by Ebola Virus (December 2012)	Paola
24/03/2015	Roberts et al., Structured observations reveal slow HIV-1 CTL escape, PLOS Genetics (February 2015)	Sai
24/02/2015	Nelson et al., T Cell Receptor Cross-Reactivity between Similar Foreign and Self Peptides Influences Naive Cell Population Size and Autoimmunity, Immunity (December 2014)	Bram
17/02/2015	Varble et al., Influenza A virus transmission bottlenecks are defined by infection route and recipient host, Cell, Host & Microbe (November 2014)	Rutger W
27/01/2015	Penaloza-MacMaster et al., Vaccine-elicited CD4 T cells induce immunopathology after chronic LCMV infection, Science (January 2015)	Aridaman
13/01/2015	Acton et al., Dendritic cells control fibroblastic reticular network tension and lymph node expansion, Nature 514, 498–502 (23 October 2014)	Johannes
06/01/2015	Becattini et al., Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines, Science (December 2014)	Rob

Immunology Journal Club

Schedule

Links to interesting websites

Conferences/Workshops

List of discussed papers (a.k.a. the OCD list)

Date

Title

Presentor

Comments (optional)