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3003 A Multi-Omic Study Unveils a Clonal Population of TET2-Mutated Infiltrating T-Cells in Germinal Center B Cell Lymphomas (DLBCL and FL)

Program: Oral and Poster Abstracts
Session: 621. Lymphomas: Translational—Molecular and Genetic: Poster II
Hematology Disease Topics & Pathways:
Research, Translational Research, Lymphomas, B Cell lymphoma, bioinformatics, Diseases, Lymphoid Malignancies, Technology and Procedures
Sunday, December 10, 2023, 6:00 PM-8:00 PM

Sofia Huerga1*, Beñat Ariceta2*, Paula Aguirre-Ruiz3*, Patxi San-Martin2*, Sarai Sarvide2*, Marta Abengozar-Muela, MD4*, Diego Alignani2*, Rocio Figueroa, MD, PhD1*, Carlos Grande, MD, PhD1*, Alvaro Lopez-Janeiro, MD5*, Emma Muiños-Lopez, PhD3*, Juan Roberto Rodriguez-Madoz, PhD2*, Amaia Vilas-Zornoza2*, Felipe Prosper, MD, PhD1 and Miguel Canales6*

1Hematology and Cell Therapy Department, Clínica Universidad de Navarra, Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Cancer Center Clinica Universidad de Navarra (CCUN) and Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Pamplona, Spain
2Hematology and Oncology Program, Centre for Applied Medical Research (CIMA), Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
3Hematology and Oncology Program, Centre for Applied Medical Research (CIMA), Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain, Pamplona, Spain
4Department of Pathology, Clinica Universidad de Navarra (CUN), Pamplona, Spain
5Departament of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
6Clinica Universidad de Navarra Cancer Center (CCUN), Pamplona, Spain


Follicular lymphomas (FL) and diffuse large B cell lymphomas (DLBCL) share a common germinal center (GC) B cell precursor. Nevertheless, these lymphomas appear to originate from different developmental stages, through distinct pathogenetic mechanisms and their clinical behavior varies significantly, even among FL or DLBCL patients. To understand the molecular and transcriptional heterogeneity underlying this clinical diversity we conducted a multi-omic study in GC B cell lymphomas.


Our study comprised 3 DLBCL patients (1 non-GCB (germinal center B), 1 non-GCB CD5+, and 1 GCB) and 2 FL (1 with no transformation (ntFL) and 1 patient with transformation (tFL)) at diagnosis. We performed single-cell multiome-sequencing (scDNA-seq + scProtein) (Tapestri platform -Mission Bio-) and single cell RNA-sequencing (scRNA-seq) (Chromium system -10xGenomics-) from cell suspensions and spatial transcriptomics (Visium technology -10xGenomics-) from paraffin blocks.


Genotyping data were available for 19,700 cells. A total of 311 variants across the 5 samples passed all quality controls. We selected probably pathogenic and pathogenic variants for downstream analysis. Germline variants were discarded.

In 3 of 5 patients, we detected 1 somatic and nonsynonymous variant defining the first clone (variants in KMT2D and NOTCH2 mutated in 6-38% of the cells) and another somatic and nonsynonymous variant, defining a subclone (variants in KMT2D, ATM, EZH2 mutated in 1-15% of the cells). In 1 of 5 patients (ntFL), we detected up to 4 mutations, acquired linearly (B2M, GNA13, EZH2, RHOA mutated clone represents 8% of the cells). Remarkably, all patients showed the same pathogenic variant in TET2 (1-2% of the cells), as an independent clone. The highest molecular similarity was observed between the GCB DLBCL patient and the tFL patient. Both had the same variant in KMT2D as the first hit (later GCB-DLBCL acquired ATM, while tFL acquired EZH2 as a second hit). ATM and EZH2 mutations have been described in “bulk” studies conducted on DLBCL and FL patients, respectively.

Regarding protein expression, there was a good correlation between GCB and non-GCB phenotypes studied by immunohistochemistry and scProtein (the expression of CD10 by proteomics was lower in non-GCB patients). TET2 clones described by scDNA-seq were enriched in CD5+ and CD19- cells, suggesting they belong to the T-lymphoid lineage. The other clones and subclones were enriched in CD19+ and CD5- cells (Figure 1).

Data from 54,024 single cells were obtained for scRNA-seq analysis, with an average of 10,805 cells (7,335-18,205) for each sample. Cell type annotation was performed based on the expression of canonical markers. We identified 13 different clusters, the main ones being: GC B cells, post-GC B cells, naïve B cells, myeloid cells, CD8+ cytotoxic T cells, CD4+ naïve T cells, CD4+ reg T cells, CD4+ helper T cells.

All samples contained subpopulations of both GC and post-GC B cell clusters. However, GCB DLBCL and FL patients were significantly enriched in GC B cells (63.2 vs 22.2%; p<0.01), whereas non-GCB patients were significantly enriched in post-GC B cells (35.5 vs 2.9%; p<0.01). Part of the normal B-cell transcriptional function was preserved in all samples (Figure 2). The analysis of the infiltrating T cells revealed that the CD4+/CD8+ T cells ratio progressively increased from ntFL (1.14) to tFL (2.25) and DLBCL (2.58). Furthermore, we estimated the exhaustion status of T cells by the expression of these five markers (TIGIT, LAG3, CTLA4, HAVCR2, PDCD1). Exhaustion T cell markers were highly expressed in CD8+ cytotoxic T cells and cycling T cells and lower expressed in CD4+ reg T cells. Both DLBCL and tFL have a stronger pattern of exhaustion than ntFL.

Finally, by the spatial transcriptomics analysis, we have identified distinct cell type proportions according to their matched single-cell RNA data.


Our results confirm the intra and intertumor heterogeneity in GC B cell lymphomas. Notably, the greatest molecular and transcriptional similarities are observed between the GCB DLBCL and tFL patients at diagnosis. Moreover, our findings support the critical role of the tumor microenvironment for the persistence and development of the tumor clone. The finding of a TET2 mutated clone in the infiltrating T cells of all the patients is particularly noteworthy, as it may suggest the possible presence of clonal lymphopoiesis.

Disclosures: Grande: AbbVie: Other: Advisory Board. Canales: Beigene: Consultancy; BMS: Consultancy; Incyte: Consultancy; Janssen: Consultancy; Karyopharm: Consultancy; Kite: Consultancy; Kyowa: Consultancy; Lilly: Consultancy; Roche: Consultancy; Takeda: Consultancy; Incyte: Speakers Bureau; Janssen: Speakers Bureau; Kite: Speakers Bureau; Kyowa: Speakers Bureau; Roche: Speakers Bureau; Takeda: Speakers Bureau.

*signifies non-member of ASH