Single-cell RNA Sequencing Coupled to TCR Profiling of Large Granular Lymphocyte Leukemia T Cells

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Apr 12

PMID 35411048

Authors

Shouguo Gao

Zhijie Wu

Bradley Arnold

Carrie Diamond

Sai Batchu

Valentina Giudice

Lemlem Alemu

Diego Quinones Raffo

Xingmin Feng

Sachiko Kajigaya

John Barrett

Sawa Ito

Neal S Young

Affiliations

Soon will be listed here.

Abstract

T-cell large granular lymphocyte leukemia (T-LGLL) is a lymphoproliferative disease and bone marrow failure syndrome which responds to immunosuppressive therapies. We show single-cell TCR coupled with RNA sequencing of CD3 T cells from 13 patients, sampled before and after alemtuzumab treatments. Effector memory T cells and loss of T cell receptor (TCR) repertoire diversity are prevalent in T-LGLL. Shared TCRA and TCRB clonotypes are absent. Deregulation of cell survival and apoptosis gene programs, and marked downregulation of apoptosis genes in CD8 clones, are prominent features of T-LGLL cells. Apoptosis genes are upregulated after alemtuzumab treatment, especially in responders than non-responders; baseline expression levels of apoptosis genes are predictive of hematologic response. Alemtuzumab does not attenuate TCR clonality, and TCR diversity is further skewed after treatment. Inferences made from analysis of single cell data inform understanding of the pathophysiologic mechanisms of clonal expansion and persistence in T-LGLL.

Citing Articles

TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes.

Luo T, Shen W, Zhang C, Song D, Zhang X, Guo A Database (Oxford). 2025; 2025.

PMID: 40036846 PMC: 11885782. DOI: 10.1093/database/baaf012.

Comprehensive Analysis of TCR and BCR Repertoires: Insights into Methodologies, Challenges, and Applications.

Seo K, Choi J Genomics Inform. 2025; 23(1):6.

PMID: 39994831 PMC: 11853700. DOI: 10.1186/s44342-024-00034-z.

A single-cell RNA sequencing dataset of peripheral blood cells in long COVID patients on herbal therapy.

Prazanowska K, Kim T, Kang J, Jin Y, Kwon S, Lim S Sci Data. 2025; 12(1):177.

PMID: 39885244 PMC: 11782672. DOI: 10.1038/s41597-025-04510-1.

T cell receptor-centric perspective to multimodal single-cell data analysis.

Mullan K, Ha M, Valkiers S, de Vrij N, Ogunjimi B, Laukens K Sci Adv. 2024; 10(48):eadr3196.

PMID: 39612336 PMC: 11606500. DOI: 10.1126/sciadv.adr3196.

Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3.

Chuang H, Li R, Huang H, Liu S, Wan C, Chaudhuri S BMC Genomics. 2024; 25(1):1127.

PMID: 39574011 PMC: 11583680. DOI: 10.1186/s12864-024-11036-0.

References

Dumitriu B, Ito S, Feng X, Stephens N, Yunce M, Kajigaya S . Alemtuzumab in T-cell large granular lymphocytic leukaemia: interim results from a single-arm, open-label, phase 2 study. Lancet Haematol. 2016; 3(1):e22-9. PMC: 4721315. DOI: 10.1016/S2352-3026(15)00227-6. View

Lamy T, Moignet A, Loughran Jr T . LGL leukemia: from pathogenesis to treatment. Blood. 2017; 129(9):1082-1094. DOI: 10.1182/blood-2016-08-692590. View

Shah M, Zhang R, Irby R, Kothapalli R, Liu X, Arrington T . Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes. Blood. 2008; 112(3):770-81. PMC: 2481553. DOI: 10.1182/blood-2007-11-121871. View

Giudice V, Feng X, Lin Z, Hu W, Zhang F, Qiao W . Deep sequencing and flow cytometric characterization of expanded effector memory CD8CD57 T cells frequently reveals T-cell receptor Vβ oligoclonality and CDR3 homology in acquired aplastic anemia. Haematologica. 2018; 103(5):759-769. PMC: 5927970. DOI: 10.3324/haematol.2017.176701. View

Sandberg Y, Kallemeijn M, Dik W, Tielemans D, Wolvers-Tettero I, van Gastel-Mol E . Lack of common TCRA and TCRB clonotypes in CD8(+)/TCRαβ(+) T-cell large granular lymphocyte leukemia: a review on the role of antigenic selection in the immunopathogenesis of CD8(+) T-LGL. Blood Cancer J. 2014; 4:e172. PMC: 3913939. DOI: 10.1038/bcj.2013.70. View

Clemente M, Przychodzen B, Jerez A, Dienes B, Afable M, Husseinzadeh H . Deep sequencing of the T-cell receptor repertoire in CD8+ T-large granular lymphocyte leukemia identifies signature landscapes. Blood. 2013; 122(25):4077-85. PMC: 3862272. DOI: 10.1182/blood-2013-05-506386. View

Redmond D, Poran A, Elemento O . Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med. 2016; 8(1):80. PMC: 4962388. DOI: 10.1186/s13073-016-0335-7. View

Han A, Glanville J, Hansmann L, Davis M . Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat Biotechnol. 2014; 32(7):684-92. PMC: 4337815. DOI: 10.1038/nbt.2938. View

Andor N, Simonds E, Czerwinski D, Chen J, Grimes S, Wood-Bouwens C . Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints. Blood. 2018; 133(10):1119-1129. PMC: 6405336. DOI: 10.1182/blood-2018-08-862292. View

10.

Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg H, Dufort M, Murray S . Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4 T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. J Immunol. 2017; 199(1):323-335. PMC: 5499675. DOI: 10.4049/jimmunol.1700172. View

11.

Azizi E, Carr A, Plitas G, Cornish A, Konopacki C, Prabhakaran S . Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Cell. 2018; 174(5):1293-1308.e36. PMC: 6348010. DOI: 10.1016/j.cell.2018.05.060. View

12.

Zemmour D, Zilionis R, Kiner E, Klein A, Mathis D, Benoist C . Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nat Immunol. 2018; 19(3):291-301. PMC: 6069633. DOI: 10.1038/s41590-018-0051-0. View

13.

Sant S, Grzelak L, Wang Z, Pizzolla A, Koutsakos M, Crowe J . Single-Cell Approach to Influenza-Specific CD8 T Cell Receptor Repertoires Across Different Age Groups, Tissues, and Following Influenza Virus Infection. Front Immunol. 2018; 9:1453. PMC: 6030351. DOI: 10.3389/fimmu.2018.01453. View

14.

Guo X, Zhang Y, Zheng L, Zheng C, Song J, Zhang Q . Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat Med. 2018; 24(7):978-985. DOI: 10.1038/s41591-018-0045-3. View

15.

Savas P, Virassamy B, Ye C, Salim A, Mintoff C, Caramia F . Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. Nat Med. 2018; 24(7):986-993. DOI: 10.1038/s41591-018-0078-7. View

16.

Yost K, Satpathy A, Wells D, Qi Y, Wang C, Kageyama R . Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med. 2019; 25(8):1251-1259. PMC: 6689255. DOI: 10.1038/s41591-019-0522-3. View

17.

Zhang Y, Zheng L, Zhang L, Hu X, Ren X, Zhang Z . Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients. Sci Data. 2019; 6(1):131. PMC: 6656756. DOI: 10.1038/s41597-019-0131-5. View

18.

Jang J, Juran B, Cunningham K, Gupta V, Son Y, Yang J . Single-cell mass cytometry on peripheral blood identifies immune cell subsets associated with primary biliary cholangitis. Sci Rep. 2020; 10(1):12584. PMC: 7387528. DOI: 10.1038/s41598-020-69358-4. View

19.

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R . Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018; 36(5):411-420. PMC: 6700744. DOI: 10.1038/nbt.4096. View

20.

Leek J, Johnson W, Parker H, Jaffe A, Storey J . The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012; 28(6):882-3. PMC: 3307112. DOI: 10.1093/bioinformatics/bts034. View