scholarly journals A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets

2018 ◽  
Vol 215 (3) ◽  
pp. 761-771 ◽  
Author(s):  
Ángel F. Álvarez-Prado ◽  
Pablo Pérez-Durán ◽  
Arantxa Pérez-García ◽  
Alberto Benguria ◽  
Carlos Torroja ◽  
...  

Activation-induced deaminase (AID) initiates antibody diversification in germinal center (GC) B cells through the deamination of cytosines on immunoglobulin genes. AID can also target other regions in the genome, triggering mutations or chromosome translocations, with major implications for oncogenic transformation. However, understanding the specificity of AID has proved extremely challenging. We have sequenced at very high depth >1,500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. We have also identified the most highly mutated hotspot for AID activity described to date. Furthermore, integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets. We also have found that base excision repair and mismatch repair back up each other to faithfully repair AID-induced lesions. Finally, our data establish a novel link between AID mutagenic activity and lymphomagenesis.

PLoS Genetics ◽  
2020 ◽  
Vol 16 (12) ◽  
pp. e1008960
Author(s):  
Pilar Delgado ◽  
Ángel F. Álvarez-Prado ◽  
Ester Marina-Zárate ◽  
Isora V. Sernandez ◽  
Sonia M. Mur ◽  
...  

Most B cell lymphomas originate from B cells that have germinal center (GC) experience and bear chromosome translocations and numerous point mutations. GC B cells remodel their immunoglobulin (Ig) genes by somatic hypermutation (SHM) and class switch recombination (CSR) in their Ig genes. Activation Induced Deaminase (AID) initiates CSR and SHM by generating U:G mismatches on Ig DNA that can then be processed by Uracyl-N-glycosylase (UNG). AID promotes collateral damage in the form of chromosome translocations and off-target SHM, however, the exact contribution of AID activity to lymphoma generation and progression is not completely understood. Here we show using a conditional knock-in strategy that AID supra-activity alone is not sufficient to generate B cell transformation. In contrast, in the absence of UNG, AID supra-expression increases SHM and promotes lymphoma. Whole exome sequencing revealed that AID heavily contributes to lymphoma SHM, promoting subclonal variability and a wider range of oncogenic variants. Thus, our data provide direct evidence that UNG is a brake to AID-induced intratumoral heterogeneity and evolution of B cell lymphoma.


2020 ◽  
Author(s):  
Pilar Delgado ◽  
Ángel F Álvarez-Prado ◽  
Ester Marina-Zárate ◽  
Isora V Sernandez ◽  
Sonia M Mur ◽  
...  

ABSTRACTMost B cell lymphomas originate from B cells that have germinal center (GC) experience and bear chromosome translocations and numerous point mutations. GCs B cells remodel their immunoglobulin (Ig) genes by somatic hypermutation (SHM) and class switch recombination (CSR) in their immunoglobulin (Ig) genes. Activation Induced Deaminase (AID) initiates CSR and SHM by generating U:G mismatches on Ig DNA that can then be processed by Uracyl-N-glycosylase (UNG). AID promotes collateral damage in the form of chromosome translocations and off-target SHM, however, the exact contribution of AID activity to lymphoma generation and progression is not completely understood. Here we show using a conditional knock-in strategy that AID supraactivity alone is not sufficient to generate B cell transformation. In contrast, in the absence of UNG, AID supra-expression increases SHM and promotes lymphoma. Whole exome sequencing revealed that AID heavily contributes to lymphoma SHM, promoting subclonal variability and a wider range of oncogenic variants. Thus, our data provide direct evidence that UNG is a brake to AID-induced intratumoral heterogeneity and evolution of B cell lymphoma.


2020 ◽  
Author(s):  
Yuqing Feng ◽  
Conglei Li ◽  
Jessica Stewart ◽  
Philip Barbulescu ◽  
Noe Seija Desivo ◽  
...  

Activation-induced cytidine deaminase (AID) catalyzes the deamination of deoxycytidines within Immunoglobulin (Ig) genes to induce somatic hypermutation (SHM) and class switch recombination (CSR). AID-induced deoxyuracils within Ig loci are recognized and processed by subverted base excision and mismatch repair pathways that ensure a mutagenic outcome in B lymphocytes. However, it is unclear why DNA repair pathways that remove deoxyuracil from DNA are not efficient at faithfully repairing AID-induced lesions. Here, we identified through a genome-wide CRISPR screen that FAM72A, a protein with no ascribed function, is a major determinant for the error-prone processing of deoxyuracil. Fam72a-deficient CH12F3-2 B cells and primary B cells from Fam72a-/- mice have reduced CSR and SHM frequencies. The SHM spectrum in B cells from Fam72a-/- mice is opposite to that observed in Ung2-/- mice, suggesting that UNG2 is hyperactive in FAM72A-deficient cells. Indeed, FAM72A binds to UNG2 resulting in reduced UNG2 activity, and significantly reduced protein levels in the G1 phase, coinciding with peak AID activity. This effect leads to increased genome-wide deoxyuracils in B cells. By antagonizing UNG2, FAM72A therefore increases U:G mispairs that engage mutagenic mismatch repair promoting error-prone processing of AID-induced deoxyuracils. This work shows that FAM72A bridges base-excision repair and mismatch repair to modulate antibody maturation.


2021 ◽  
Author(s):  
Carmen Gomez-Escolar ◽  
Alvaro Serrano-Navarro ◽  
Alberto Benguria ◽  
Ana Dopazo ◽  
Fatima Sanchez-Cabo ◽  
...  

Germinal centers (GC) are microstructures where B cells that have been activated by antigen can improve the affinity of their B cell receptors and differentiate into memory B cells (MBCs) or antibody secreting plasma cells. Activation Induced Deaminase (AID) initiates antibody diversification in GCs by somatic hypermutation and class switch recombination. Here we have addressed the role of AID in the terminal differentiation of GC B cells by combining single cell transcriptome and immunoglobulin clonal analysis in a mouse model that traces AID-experienced cells. We identified 8 transcriptional clusters that include dark zone and light zone GC subsets, plasmablasts/plasma cells (PB), 4 subsets of MBCs and a novel prePB subset, which shares the strongest clonal relationships with PBs. Mice lacking AID have various alterations in the size and expression profiles of these transcriptional clusters. We find that AID deficiency leads to a reduced proportion of prePB cells and severely impairs transitions between the prePB and the PB subsets. Thus, AID shapes the differentiation fate of GC B cells by enabling PB generation from a prePB state.


Author(s):  
Mahnoush Bahjat ◽  
Maria Stratigopoulou ◽  
Bas Pilzecker ◽  
Tijmen P. van Dam ◽  
Simon Mobach ◽  
...  

ABSTRACTIn B cells, the error-prone repair of activation-induced cytidine deaminase (AID)-induced lesions in immunoglobulin variable genes cause somatic hypermutation (SHM) of antibody genes. Due to clonal selection in the germinal centers (GC) this active mutation process provides the molecular basis for antibody affinity maturation. AID deaminates cytosine (C) to create uracil (U) in DNA. Typically, the short patch base excision repair (spBER) effectively restores genomic U lesions. We here demonstrate that GC B cells actively degrade DNA polymerase β (Polβ), resulting in the inactivation of the gap-filling step of spBER. Consequently, lesions instigated by AID, and likely other base damages, are channeled towards mutagenic non-canonical mismatch repair (mncMMR), responsible for the vast majority of mutations at adenine and thymine (A:T) bases. Apparently, GC B cells prohibit faithful spBER, thereby favoring A:T mutagenesis during SHM. Lastly, our data suggest that the loss of Polβ relates to hypoxia that characterizes the GC microenvironment.


2018 ◽  
Vol 115 (19) ◽  
pp. 4921-4926 ◽  
Author(s):  
Eddy Sanchai Thientosapol ◽  
Daniel Bosnjak ◽  
Timothy Durack ◽  
Igor Stevanovski ◽  
Michelle van Geldermalsen ◽  
...  

Activation-induced deaminase (AID) initiates hypermutation of Ig genes in activated B cells by converting C:G into U:G base pairs. G1-phase variants of uracil base excision repair (BER) and mismatch repair (MMR) then deploy translesion polymerases including REV1 and Pol η, which exacerbates mutation. dNTP paucity may contribute to hypermutation, because dNTP levels are reduced in G1 phase to inhibit viral replication. To derestrict G1-phase dNTP supply, we CRISPR-inactivated SAMHD1 (which degrades dNTPs) in germinal center B cells. Samhd1 inactivation increased B cell virus susceptibility, increased transition mutations at C:G base pairs, and substantially decreased transversion mutations at A:T and C:G base pairs in both strands. We conclude that SAMHD1’s restriction of dNTP supply enhances AID’s mutagenicity and that the evolution of Ig hypermutation included the repurposing of antiviral mechanisms based on dNTP starvation.


2012 ◽  
Vol 209 (7) ◽  
pp. 1379-1389 ◽  
Author(s):  
Pablo Pérez-Durán ◽  
Laura Belver ◽  
Virginia G. de Yébenes ◽  
Pilar Delgado ◽  
David G. Pisano ◽  
...  

Secondary diversification of antibodies through somatic hypermutation (SHM) and class switch recombination (CSR) is a critical component of the immune response. Activation-induced deaminase (AID) initiates both processes by deaminating cytosine residues in immunoglobulin genes. The resulting U:G mismatch can be processed by alternative pathways to give rise to a mutation (SHM) or a DNA double-strand break (CSR). Central to this processing is the activity of uracil-N-glycosylase (UNG), an enzyme normally involved in error-free base excision repair. We used next generation sequencing to analyze the contribution of UNG to the resolution of AID-induced lesions. Loss- and gain-of-function experiments showed that UNG activity can promote both error-prone and high fidelity repair of U:G lesions. Unexpectedly, the balance between these alternative outcomes was influenced by the sequence context of the deaminated cytosine, with individual hotspots exhibiting higher susceptibility to UNG-triggered error-free or error-prone resolution. These results reveal UNG as a new molecular layer that shapes the specificity of AID-induced mutations and may provide new insights into the role of AID in cancer development.


2005 ◽  
Vol 201 (4) ◽  
pp. 637-645 ◽  
Author(s):  
Teresa M. Wilson ◽  
Alexandra Vaisman ◽  
Stella A. Martomo ◽  
Patsa Sullivan ◽  
Li Lan ◽  
...  

Activation-induced cytidine deaminase deaminates cytosine to uracil (dU) in DNA, which leads to mutations at C:G basepairs in immunoglobulin genes during somatic hypermutation. The mechanism that generates mutations at A:T basepairs, however, remains unclear. It appears to require the MSH2–MSH6 mismatch repair heterodimer and DNA polymerase (pol) η, as mutations of A:T are decreased in mice and humans lacking these proteins. Here, we demonstrate that these proteins interact physically and functionally. First, we show that MSH2–MSH6 binds to a U:G mismatch but not to other DNA intermediates produced during base excision repair of dUs, including an abasic site and a deoxyribose phosphate group. Second, MSH2 binds to pol η in solution, and endogenous MSH2 associates with the pol in cell extracts. Third, MSH2–MSH6 stimulates the catalytic activity of pol η in vitro. These observations suggest that the interaction between MSH2–MSH6 and DNA pol η stimulates synthesis of mutations at bases located downstream of the initial dU lesion, including A:T pairs.


Author(s):  
Almudena Ramiro ◽  
Bernardo Reina San‐Martin ◽  
Kevin McBride ◽  
Mila Jankovic ◽  
Vasco Barreto ◽  
...  

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2793-2793 ◽  
Author(s):  
James A.L. Fenton ◽  
David Gonzalez ◽  
Andy C. Rawstron ◽  
Gareth J. Morgan ◽  
Andrew S. Jack ◽  
...  

Abstract Analysis of immunoglobulin heavy chain (IgH) rearrangements in B-CLL differentiates subgroups of patients with significantly different clinical outcomes. Cases can be categorised according to mutational status of the variable (V) segment with unmutated VH regions linked to a worse prognosis. A restricted pattern of use of specific VH, DH and JH gene segments has also been reported in B-CLL. It has been hypothesised that B-CLL originates as a clonal expansion of B-cells that have been selected and activated by contact with self or foreign antigens, leading to those small clones to proliferate, mutate their IGH genes, acquire genetic lesions and eventually become malignant. B-CLL cells normally express low levels of Ig on the surface, normally IgM, although a proportion of patients express IgG or IgA, following the class-switch recombination (CSR) process. We have analysed the pattern of SHM and gene segment usage in this particular subgroup for 44 patients with IgG B-CLL. Successful PCR amplification of recombined Smu-Sgamma switch region DNA was achieved in 40 patients, confirming the presence of IgG class-switching. Mutational analysis of IgH V genes revealed 80% of patients contained more than 2% somatic hypermutation (SHM), with 63% of samples having a greater than 5% SHM rate. For VH gene segment usage, a significant predominance of the VH4 family was seen in 22 cases (50%), followed by VH3 in 17 cases (39%), while VH1 family was found in only 3 of 44 samples, this differs from classical IgM B-CLL where VH3 family usage predominates. Overall, VH4-34 was the most frequently used gene segment (34%), followed by VH3-07 (14%) and VH4-39 (9%). DH6-13 was the most frequently used DH segment (21%), followed by DH6-19 (13%). JH gene segment usage did not differ from normal B-cells, with JH4 being the most frequently used, followed by JH6 and JH5. There was a significant association between VH4-39, DH6-13 and JH5 in three samples all containing unmutated sequence. Together this data reveals a distinct pattern of IGH VDJ rearrangements in IgG B-CLL compared to classical IgM B-CLL. Firstly, the rate of SHM in IgG B-CLL (80%) is significantly higher than the 50% observed in IgM B-CLL. Secondly, VH segment usage pattern differs between the two subgroups with a significant under-representation of VH1 as well as an over-representation of VH4 family members in the IgG subgroup. Finally, there is a striking association between VH4-39 and DH6-13/JH5 in the very few unmutated rearrangements. This could be indicative of a different clonal history of these particular B cells in B-CLL. Together with recent published data, this latter finding suggests that this is a further sub-category exclusive to IgG B-CLL, where selection of a specific antigen receptor may have lead to B-CLL development in such cases. We conclude that class-switched IgG B-CLL contains different molecular features in the IgH genes compared with classical IgM B-CLL, and other B-cell malignancies. The clinical implications of these differences, especially the relationship between the mutational status of the VH genes and outcome in IgG B-CLL, will be further investigated.


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