Ludwig H, Boccadoro M, Moreau P, San-Miguel J, Cavo M, Pawlyn C, et al. Recommendations for vaccination in multiple myeloma: a consensus of the European Myeloma Network. Leukemia. 2021;35:31–44.

Article  PubMed  Google Scholar 

Fendler A, Au L, Shepherd STC, Byrne F, Cerrone M, Boos LA, et al. Functional antibody and T cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study. Nat Cancer. 2021;2:1321–37.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fendler A, Shepherd STC, Au L, Wilkinson KA, Wu M, Byrne F, et al. Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: The CAPTURE study. Nat Cancer. 2021;2:1321–37.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ehmsen S, Asmussen A, Jeppesen SS, Nilsson AC, Osterlev S, Vestergaard H, et al. Antibody and T cell immune responses following mRNA COVID-19 vaccination in patients with cancer. Cancer Cell. 2021;39:1034–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Abdul-Jawad S, Bau L, Alaguthurai T, Del Molino Del Barrio I, Laing AG, Hayday TS, et al. Acute Immune Signatures and Their Legacies in Severe Acute Respiratory Syndrome Coronavirus-2 Infected Cancer Patients. Cancer Cell. 2021;39:257–75. e6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Monin L, Laing AG, Munoz-Ruiz M, McKenzie DR, Del Molino Del Barrio I, Alaguthurai T, et al. Safety and immunogenicity of one versus two doses of the COVID-19 vaccine BNT162b2 for patients with cancer: interim analysis of a prospective observational study. Lancet Oncol. 2021;22:765–78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thakkar A, Gonzalez-Lugo JD, Goradia N, Gali R, Shapiro LC, Pradhan K, et al. Seroconversion rates following COVID-19 vaccination among patients with cancer. Cancer Cell. 2021. https://doi.org/10.1016/j.ccell.2021.06.002.

Mittelman M, Magen O, Barda N, Dagan N, Oster HS, Leader A, et al. Effectiveness of the BNT162b2mRNA COVID-19 vaccine in patients with hematological neoplasms in a nationwide mass vaccination setting. Blood. 2022;139:1439–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Enßle JC, Campe J, Schwenger A, Wiercinska E, Hellstern H, Dürrwald R, et al. Severe impairment of T-cell responses to BNT162b2 immunization in patients with multiple myeloma. Blood. 2022;139:137–42.

Article  PubMed  Google Scholar 

Enssle JC, Campe J, Büchel S, Moter A, See F, Grießbaum K, et al. Enhanced but variant-dependent serological and cellular immune responses to third-dose BNT162b2 vaccination in patients with multiple myeloma. Cancer Cell. 2022. https://doi.org/10.1016/J.CCELL.2022.05.003.

Van Oekelen O, Gleason CR, Agte S, Srivastava K, Beach KF, Aleman A, et al. Highly variable SARS-CoV-2 spike antibody responses to two doses of COVID-19 RNA vaccination in patients with multiple myeloma. Cancer Cell. 2021. https://doi.org/10.1016/j.ccell.2021.06.014.

Aleman A, Van Oekelen O, Upadhyaya B, Beach K, Kogan Zajdman A, Alshammary H, et al. Augmentation of humoral and cellular immune responses after third-dose SARS-CoV-2 vaccination and viral neutralization in myeloma patients. Cancer Cell. 2022. https://doi.org/10.1016/J.CCELL.2022.03.013.

Langerbeins P, Hallek M. COVID-19 in patients with hematologic malignancy. Blood. 2022;140:236–52.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nooka AK, Shanmugasundaram U, Cheedarla N, Verkerke H, Edara VV, Valanparambil R, et al. Determinants of Neutralizing Antibody Response After SARS CoV-2 Vaccination in Patients With Myeloma. J Clin Oncol. 2022;40:3057–64.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keppler-Hafkemeyer A, Greil C, Wratil PR, Shoumariyeh K, Stern M, Hafkemeyer A, et al. Potent high-avidity neutralizing antibodies and T cell responses after COVID-19 vaccination in individuals with B cell lymphoma and multiple myeloma. Nat Cancer. 2022;4:81–95.

PubMed  PubMed Central  Google Scholar 

Pagano L, Salmanton-García J, Marchesi F, Blennow O, Gomes da Silva M, Glenthøj A, et al. Breakthrough COVID-19 in vaccinated patients with hematologic malignancies: results from the EPICOVIDEHA survey. Blood. 2022;140:2773–87.

Article  CAS  PubMed  Google Scholar 

Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, et al. Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med. 2021;27:904–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, et al. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat Commun. 2022;13:1–23.

Article  Google Scholar 

Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, et al. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med. 2020;26:1070–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee JS, Park S, Jeong HW, Ahn JY, Choi SJ, Lee H, et al. Immunophenotyping of covid-19 and influenza highlights the role of type i interferons in development of severe covid-19. Sci Immunol. 2020;5:1554.

Article  Google Scholar 

Jarisch A, Wiercinska E, Daqiq-Mirdad S, Hellstern H, Ajib S, Cremer A, et al. SARS-CoV-2-specific T cells are generated in less than half of allogeneic HSCT recipients failing to seroconvert after COVID-19 vaccination. Eur J Immunol. 2022;52:1194–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, et al. MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data. Genome Biol. 2020;21:111.

Article  PubMed  PubMed Central  Google Scholar 

Traag VA, Waltman L, van Eck NJ. From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep. 2019;9:1–12.

Article  CAS  Google Scholar 

Dann E, Henderson NC, Teichmann SA, Morgan MD, Marioni JC. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat Biotechnol. 2021;40:245–53.

Article  PubMed  Google Scholar 

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

R Core Team RF for SC. R: A Language and Environment for Statistical Computing. 2020. https://www.R-project.org/.

Triana S, Vonficht D, Jopp-Saile L, Raffel S, Lutz R, Leonce D, et al. Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. Nat Immunol. 2021;22:1577–89.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Björkström NK, Strunz B, Ljunggren HG. Natural killer cells in antiviral immunity. Nat Rev Immunol. 2021;22:112–23.

Article  PubMed  PubMed Central  Google Scholar 

Maucourant C, Filipovic I, Ponzetta A, Aleman S, Cornillet M, Hertwig L, et al. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol. 2020;5:6832.

Article  Google Scholar 

Witkowski M, Tizian C, Ferreira-Gomes M, Niemeyer D, Jones TC, Heinrich F, et al. Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells. Nat 2021. 2021;600:295–301.

CAS  Google Scholar 

Smith SL, Kennedy PR, Stacey KB, Worboys JD, Yarwood A, Seo S, et al. Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. Blood Adv. 2020;4:1388–406.

Article  CAS  PubMed  PubMed Central  Google Scholar 

GeurtsvanKessel CH, Geers D, Schmitz KS, Mykytyn AZ, Lamers MM, Bogers S, et al. Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Sci Immunol. 2022;7:eabo2202.

Article  CAS  PubMed  Google Scholar 

Rodda LB, Morawski PA, Pruner KB, Fahning ML, Howard CA, Franko N, et al. Imprinted SARS-CoV-2-specific memory lymphocytes define hybrid immunity. Cell. 2022;185:1588–1601.e14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Minervina AA, Pogorelyy MV, Kirk AM, Crawford JC, Allen EK, Chou CH, et al. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells. Nat Immunol. 2022;23:781–90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O’Rourke P, de Silva AD, et al. Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Sci Immunol. 2018;3. https://doi.org/10.1126/SCIIMMUNOL.AAN8664/SUPPL_FILE/AAN8664_TABLE_S9.XLSX.

Juno JA, Bockel D van, Kent SJ, Kelleher AD, Zaunders JJ, Munier CML Cytotoxic CD4 T Cells-Friend or Foe during Viral Infection? Front Immunol. 2017;8. https://doi.org/10.3389/FIMMU.2017.00019.

Brown DM, Lee S, Garcia-Hernandez M, de la L, Swain SL. Multifunctional CD4 cells expressing gamma interferon and perforin mediate protection against lethal influenza virus infection. J Virol. 2012;86:6792–803.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Watson AM, Lam LKM, Klimstra WB, Ryman KD. The 17D-204 Vaccine Strain-Induced Protection against Virulent Yellow Fever Virus Is Mediated by Humoral Immunity and CD4+ but not CD8+ T Cells. PLoS Pathog. 2016;12:e1005786.

Article  PubMed  PubMed Central  Google Scholar 

Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, et al. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19. Cell. 2020;183:1340–1353.e16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brown DM, Lampe AT, Workman AM. The differentiation and protective function of cytolytic CD4 T cells in influenza infection. Front Immunol. 2016;7:185278.