Wouters MCA, Nelson BH. Prognostic significance of tumor-infiltrating B cells and plasma cells in human cancer. Clin Cancer Res. 2018;24:6125–35.

Article  CAS  PubMed  Google Scholar 

Fridman WH, Petitprez F, Meylan M, Chen TWW, Sun CM, Roumenina LT, et al. B cells and cancer: To B or not to B? J Exp Med. 2021;218:e20200851.

Article  CAS  PubMed  Google Scholar 

Petitprez F, de Reyniès A, Keung EZ, Chen TWW, Sun CM, Calderaro J, et al. B cells are associated with survival and immunotherapy response in sarcoma. Nature 2020;577:556–60.

Article  CAS  PubMed  Google Scholar 

Vanhersecke L, Brunet M, Guégan JP, Rey C, Bougouin A, Cousin S, et al. Mature tertiary lymphoid structures predict immune checkpoint inhibitor efficacy in solid tumors independently of PD-L1 expression. Nat Cancer. 2021;2:794–802.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cabrita R, Lauss M, Sanna A, Donia M, Skaarup Larsen M, Mitra S, et al. Tertiary lymphoid structures improve immunotherapy and survival in melanoma. Nature 2020;577:561–5.

Article  CAS  PubMed  Google Scholar 

Helmink BA, Reddy SM, Gao J, Zhang S, Basar R, Thakur R, et al. B cells and tertiary lymphoid structures promote immunotherapy response. Nature 2020;577:549–55.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ling Y, Zhong J, Weng Z, Lin G, Liu C, Pan C, et al. The prognostic value and molecular properties of tertiary lymphoid structures in oesophageal squamous cell carcinoma. Clin Transl Med. 2022;12:e1074.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li R, Huang X, Yang W, Wang J, Liang Y, Zhang T, et al. Tertiary lymphoid structures favor outcome in resected esophageal squamous cell carcinoma. J Pathol Clin Res. 2022;8:422–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yao C, Yu H, Zhou G, Xu J, Gu D, Yin L, et al. Tumor-infiltrating plasma cells are the promising prognosis marker for esophageal squamous cell carcinoma. Esophagus. 2021;18:574–84.

Article  PubMed  Google Scholar 

Vitale I, Shema E, Loi S, Galluzzi L. Intratumoral heterogeneity in cancer progression and response to immunotherapy. Nat Med. 2021;27:212–24.

Article  CAS  PubMed  Google Scholar 

Yan T, Cui H, Zhou Y, Yang B, Kong P, Zhang Y, et al. Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma. Nat Commun. 2019;10:1670.

Article  PubMed  PubMed Central  Google Scholar 

Dinh HQ, Pan F, Wang G, Huang QF, Olingy CE, Wu ZY, et al. Integrated single-cell transcriptome analysis reveals heterogeneity of esophageal squamous cell carcinoma microenvironment. Nat Commun. 2021;12:7335.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang X. Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis. Nat Commun. 2021;12:5291.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng Y, Chen Z, Han Y, Han L, Zou X, Zhou B, et al. Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment. Nat Commun. 2020;11:6268.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jia Y, Zhang B, Zhang C, Kwong DL, Chang Z, Li S, et al. Single‐cell transcriptomic analysis of primary and metastatic tumor ecosystems in esophageal squamous cell carcinoma. Adv Sci 2023;10:2204565.

Article  CAS  Google Scholar 

Fugmann SD, Lee AI, Shockett PE, Villey IJ, Schatz DG. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu Rev Immunol. 2000;18:495–527.

Article  CAS  PubMed  Google Scholar 

Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000;102:553–63.

Article  CAS  PubMed  Google Scholar 

Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 2015;31:3356–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Z, Cheng Z, Lu S, Chard Dunmall LS, Wang J, Guo Y, et al. Characterization of the intra-tumoral B cell immunoglobulin repertoire is of prognostic value for esophageal squamous cell carcinoma. Front Immunol. 2022;13:896627.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang C, Huang H, Miao Y, Xiong H, Lu Z. Clonal distribution and intratumour heterogeneity of the B-cell repertoire in oesophageal squamous cell carcinoma. J Pathol. 2018;246:323–30.

Article  CAS  PubMed  Google Scholar 

Song Y, Yan S, Fan W, Zhang M, Liu W, Lu H, et al. Identification and validation of the immune subtypes of lung adenocarcinoma: implications for immunotherapy. Front Cell Dev Biol. 2020;8:550.

Article  PubMed  PubMed Central  Google Scholar 

Carlson CS, Emerson RO, Sherwood AM, Desmarais C, Chung MW, Parsons JM, et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat Commun. 2013;4:2680.

Article  PubMed  Google Scholar 

Zhang W, Feng Q, Wang C, Zeng X, Du Y, Lin L, et al. Characterization of the B Cell Receptor Repertoire in the Intestinal Mucosa and of Tumor-Infiltrating Lymphocytes in Colorectal Adenoma and Carcinoma. J Immunol. 2017;198:3719–28.

Article  CAS  PubMed  Google Scholar 

Hao D, Han G, Sinjab A, Gomez-Bolanos LI, Lazcano R, Serrano A, et al. The single-cell immunogenomic landscape of B and plasma cells in early-stage lung adenocarcinoma. Cancer Discov. 2022;12:2626–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu Q, Hong Y, Qi P, Lu G, Mai X, Xu S, et al. Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling. Nat Commun. 2021;12:2186.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods. 2015;12:380–1.

Article  CAS  PubMed  Google Scholar 

Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021;18:627–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benítez R, Yu K, Sirota M, Malats N, Pineda S. Characterization of the tumor-infiltrating immune repertoire in muscle invasive bladder cancer. Front Immunol. 2023;14:986598.

Article  PubMed  PubMed Central  Google Scholar 

Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, et al. Comprehensive characterizations of immune receptor repertoire in tumors and cancer immunotherapy studies. Cancer Immunol Res. 2022;10:788–99.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andreani T, Slot LM, Gabillard S, Strübing C, Reimertz C, Yaligara V, et al. Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data. NAR Genom Bioinform. 2022;4:lqac049.

Article  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21.

Article  CAS  PubMed  Google Scholar 

Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–9.

Article  CAS  PubMed  Google Scholar 

Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JNH, et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013;4:358.

Article  PubMed  PubMed Central  Google Scholar 

Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SH. Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. Proc Natl Acad Sci USA. 2019;116:22664–72.

Article