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Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer.
Yousuf S, Qiu M, Voith von Voithenberg L, Hulkkonen J, Macinkovic I, Schulz AR, Hartmann D, Mueller F, Mijatovic M, Ibberson D, AlHalabi KT, Hetzer J, Anders S, Brüne B, Mei HE, Imbusch CD, Brors B, Heikenwälder M, Gaida MM, Büchler MW, Weigert A, Hackert T, Roth S. Yousuf S, et al. Gastroenterology. 2023 Oct;165(4):891-908.e14. doi: 10.1053/j.gastro.2023.05.036. Epub 2023 May 30. Gastroenterology. 2023. PMID: 37263303 Free article.
We determined prognostic associations of immune signatures and performed a meta-analysis of the immune microenvironment in PDAC and lung adenocarcinoma on single-cell level. RESULTS: We provided a spatially resolved fine map of the immune landscape in PDAC. We substantiate …
We determined prognostic associations of immune signatures and performed a meta-analysis of the immune microenvironment in PDAC and l …
A multi-omic analysis of human naive CD4+ T cells.
Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. Mitchell CJ, et al. BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4. BMC Syst Biol. 2015. PMID: 26542228 Free PMC article.
Here, we report the first multi-omic analysis of human primary naive CD4+ T cells isolated from a single individual. ...In addition, we carried out a multi-omic comparative analysis of naive with …
Here, we report the first multi-omic analysis of human primary naive CD4+ T cells is …
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Chen L, et al. Cell. 2016 Nov 17;167(5):1398-1414.e24. doi: 10.1016/j.cell.2016.10.026. Cell. 2016. PMID: 27863251 Free PMC article.
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cel …
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human ge …
Single-cell multi-omics analysis reveals IFN-driven alterations in T lymphocytes and natural killer cells in systemic lupus erythematosus.
Trzupek D, Lee M, Hamey F, Wicker LS, Todd JA, Ferreira RC. Trzupek D, et al. Wellcome Open Res. 2022 May 12;6:149. doi: 10.12688/wellcomeopenres.16883.2. eCollection 2021. Wellcome Open Res. 2022. PMID: 35509371 Free PMC article.
Furthermore, we identified additional alterations consistent with increased immune activation in this patient, most notably a shift towards terminally differentiated CD57 (+) CD8 (+) T cell and CD16 (+) NK (dim) phenotypes, and the presence of a subset of recently-activated na …
Furthermore, we identified additional alterations consistent with increased immune activation in this patient, most notably a shift towards …
CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation.
Zhang W, Morris AB, Peek EV, Karadkhele G, Robertson JM, Kissick HT, Larsen CP. Zhang W, et al. Front Immunol. 2021 Apr 15;12:620386. doi: 10.3389/fimmu.2021.620386. eCollection 2021. Front Immunol. 2021. PMID: 33936035 Free PMC article.
Our detailed exploration of the distribution, phenotype, TCR repertoire and transcriptome of CD4+ T cells within CMV seropositive healthy individuals using high-dimensional flow cytometry and single cell multi-omics sequencing reveals that CMV seroposi …
Our detailed exploration of the distribution, phenotype, TCR repertoire and transcriptome of CD4+ T cells within CMV se …
Short-Chain Fatty Acids Augment Differentiation and Function of Human Induced Regulatory T Cells.
Hu M, Alashkar Alhamwe B, Santner-Nanan B, Miethe S, Harb H, Renz H, Potaczek DP, Nanan RK. Hu M, et al. Int J Mol Sci. 2022 May 20;23(10):5740. doi: 10.3390/ijms23105740. Int J Mol Sci. 2022. PMID: 35628549 Free PMC article.
Regulatory T cells (Tregs) control immune system activity and inhibit inflammation. ...Our target was to identify the potential phenotypic markers best characterizing human iTregs. Naive non-Treg CD4(+) cells were isolated from the peripheral bl …
Regulatory T cells (Tregs) control immune system activity and inhibit inflammation. ...Our target was to identify the potentia …
Immunogenomic correlates of immune-related adverse events for anti-programmed cell death 1 therapy.
Zhang L, Shi Y, Han X. Zhang L, et al. Front Immunol. 2022 Nov 25;13:1032221. doi: 10.3389/fimmu.2022.1032221. eCollection 2022. Front Immunol. 2022. PMID: 36505471 Free PMC article.
Further predictive accuracy was achieved by DC and TMB in combination with CD4(+) naive T-cells abundance, and then validated in the small cell lung cancer cohort. Additionally, global screening of multiomics data identified 11 novel predictors …
Further predictive accuracy was achieved by DC and TMB in combination with CD4(+) naive T-cells abundance, and t …
Dynamics of Type I and Type II Interferon Signature Determines Responsiveness to Anti-TNF Therapy in Rheumatoid Arthritis.
Iwasaki T, Watanabe R, Ito H, Fujii T, Okuma K, Oku T, Hirayama Y, Ohmura K, Murata K, Murakami K, Yoshitomi H, Tanaka M, Matsuda S, Matsuda F, Morinobu A, Hashimoto M. Iwasaki T, et al. Front Immunol. 2022 Jun 6;13:901437. doi: 10.3389/fimmu.2022.901437. eCollection 2022. Front Immunol. 2022. PMID: 35734167 Free PMC article.
The factors influencing long-term responses to a tumor necrosis factor inhibitor (TNFi) in rheumatoid arthritis (RA) patients currently remain unknown. Therefore, we herein conducted a multi-omics analysis of TNFi responses in a Japanese RA cohort. Blood samples wer …
The factors influencing long-term responses to a tumor necrosis factor inhibitor (TNFi) in rheumatoid arthritis (RA) patients currently rema …
Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.
Chen L, Yang R, Kwan T, Tang C, Watt S, Zhang Y, Bourque G, Ge B, Downes K, Frontini M, Ouwehand WH, Lin JW, Soranzo N, Pastinen T, Chen L. Chen L, et al. Sci Data. 2020 Nov 9;7(1):376. doi: 10.1038/s41597-020-00719-4. Sci Data. 2020. PMID: 33168820 Free PMC article.
To better access these effects, we carried out both ribosomal RNA-depleted and poly(A)-selected RNA-seq for CD4(+) T naive cells isolated from 40 healthy individuals from the Blueprint Project. ...This dataset offers a unique opportunity to understand how library co …
To better access these effects, we carried out both ribosomal RNA-depleted and poly(A)-selected RNA-seq for CD4(+) T naive cel …