TY - JOUR
T1 - Post-Transformation IGHV-IGHD-IGHJ Mutations in Chronic Lymphocytic Leukemia B Cells
T2 - Implications for Mutational Mechanisms and Impact on Clinical Course
AU - Bagnara, Davide
AU - Tang, Catherine
AU - Brown, Jennifer R.
AU - Kasar, Siddha
AU - Fernandes, Stacey
AU - Colombo, Monica
AU - Vergani, Stefano
AU - Mazzarello, Andrea N.
AU - Ghiotto, Fabio
AU - Bruno, Silvia
AU - Morabito, Fortunato
AU - Rai, Kanti R.
AU - Kolitz, Jonathan E.
AU - Barrientos, Jacqueline C.
AU - Allen, Steven L.
AU - Fais, Franco
AU - Scharff, Matthew D.
AU - MacCarthy, Thomas
AU - Chiorazzi, Nicholas
N1 - Funding Information:
DB received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No 794075. JB was supported by funding from the NIH’s National Cancer Institute through the R01 grant CA 213442. NC and KRR thank the Karches Family, The Nash Family Foundation, The Marks Foundation, and the Jean Walton Fund for Leukemia, Lymphoma, and Myeloma Research for their support of the Feinstein Institutes’ CLL Research & Treatment Program. MS and TM are supported by a Multi-PI grant 1R01AI132507-01A1 from NIAID.
Publisher Copyright:
© Copyright © 2021 Bagnara, Tang, Brown, Kasar, Fernandes, Colombo, Vergani, Mazzarello, Ghiotto, Bruno, Morabito, Rai, Kolitz, Barrientos, Allen, Fais, Scharff, MacCarthy and Chiorazzi.
PY - 2021/5/25
Y1 - 2021/5/25
N2 - Analyses of IGHV gene mutations in chronic lymphocytic leukemia (CLL) have had a major impact on the prognostication and treatment of this disease. A hallmark of IGHV-mutation status is that it very rarely changes clonally over time. Nevertheless, targeted and deep DNA sequencing of IGHV-IGHD-IGHJ regions has revealed intraclonal heterogeneity. We used a DNA sequencing approach that achieves considerable depth and minimizes artefacts and amplification bias to identify IGHV-IGHD-IGHJ subclones in patients with prolonged temporal follow-up. Our findings extend previous studies, revealing intraclonal IGHV-IGHD-IGHJ diversification in almost all CLL clones. Also, they indicate that some subclones with additional IGHV-IGHD-IGHJ mutations can become a large fraction of the leukemic burden, reaching numerical criteria for monoclonal B-cell lymphocytosis. Notably, the occurrence and complexity of post-transformation IGHV-IGHD-IGHJ heterogeneity and the expansion of diversified subclones are similar among U-CLL and M-CLL patients. The molecular characteristics of the mutations present in the parental, clinically dominant CLL clone (CDC) differed from those developing post-transformation (post-CDC). Post-CDC mutations exhibit significantly lower fractions of mutations bearing signatures of activation induced deaminase (AID) and of error-prone repair by Polη, and most of the mutations were not ascribable to those enzymes. Additionally, post-CDC mutations displayed a lower percentage of nucleotide transitions compared with transversions that was also not like the action of AID. Finally, the post-CDC mutations led to significantly lower ratios of replacement to silent mutations in VH CDRs and higher ratios in VH FRs, distributions different from mutations found in normal B-cell subsets undergoing an AID-mediated process. Based on these findings, we propose that post-transformation mutations in CLL cells either reflect a dysfunctional standard somatic mutational process or point to the action of another mutational process not previously associated with IG V gene loci. If the former option is the case, post-CDC mutations could lead to a lesser dependence on antigen dependent BCR signaling and potentially a greater influence of off-target, non-IG genomic mutations. Alternatively, the latter activity could add a new stimulatory survival/growth advantage mediated by the BCR through structurally altered FRs, such as that occurring by superantigen binding and stimulation.
AB - Analyses of IGHV gene mutations in chronic lymphocytic leukemia (CLL) have had a major impact on the prognostication and treatment of this disease. A hallmark of IGHV-mutation status is that it very rarely changes clonally over time. Nevertheless, targeted and deep DNA sequencing of IGHV-IGHD-IGHJ regions has revealed intraclonal heterogeneity. We used a DNA sequencing approach that achieves considerable depth and minimizes artefacts and amplification bias to identify IGHV-IGHD-IGHJ subclones in patients with prolonged temporal follow-up. Our findings extend previous studies, revealing intraclonal IGHV-IGHD-IGHJ diversification in almost all CLL clones. Also, they indicate that some subclones with additional IGHV-IGHD-IGHJ mutations can become a large fraction of the leukemic burden, reaching numerical criteria for monoclonal B-cell lymphocytosis. Notably, the occurrence and complexity of post-transformation IGHV-IGHD-IGHJ heterogeneity and the expansion of diversified subclones are similar among U-CLL and M-CLL patients. The molecular characteristics of the mutations present in the parental, clinically dominant CLL clone (CDC) differed from those developing post-transformation (post-CDC). Post-CDC mutations exhibit significantly lower fractions of mutations bearing signatures of activation induced deaminase (AID) and of error-prone repair by Polη, and most of the mutations were not ascribable to those enzymes. Additionally, post-CDC mutations displayed a lower percentage of nucleotide transitions compared with transversions that was also not like the action of AID. Finally, the post-CDC mutations led to significantly lower ratios of replacement to silent mutations in VH CDRs and higher ratios in VH FRs, distributions different from mutations found in normal B-cell subsets undergoing an AID-mediated process. Based on these findings, we propose that post-transformation mutations in CLL cells either reflect a dysfunctional standard somatic mutational process or point to the action of another mutational process not previously associated with IG V gene loci. If the former option is the case, post-CDC mutations could lead to a lesser dependence on antigen dependent BCR signaling and potentially a greater influence of off-target, non-IG genomic mutations. Alternatively, the latter activity could add a new stimulatory survival/growth advantage mediated by the BCR through structurally altered FRs, such as that occurring by superantigen binding and stimulation.
KW - activation-induced deaminase
KW - chronic lymphocytic leukemia
KW - immunoglobulin genes
KW - mutation mechanisms
KW - somatic mutations
UR - http://www.scopus.com/inward/record.url?scp=85107424458&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85107424458&partnerID=8YFLogxK
U2 - 10.3389/fonc.2021.640731
DO - 10.3389/fonc.2021.640731
M3 - Article
AN - SCOPUS:85107424458
SN - 2234-943X
VL - 11
JO - Frontiers in Oncology
JF - Frontiers in Oncology
M1 - 640731
ER -