Somatic hypermutation

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Somatic hypermutation (or SHM) is a cellular mechanism by which the immune system adapts to the new foreign elements that confront it (e.g. microbes), as seen during class switching. A major component of the process of affinity maturation, SHM diversifies B cell receptors used to recognize foreign elements (antigens) and allows the immune system to adapt its response to new threats during the lifetime of an organism. [1] Somatic hypermutation involves a programmed process of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only an organism's individual immune cells, and the mutations are not transmitted to the organism's offspring. [2] Because this mechanism is merely selective and not precisely targeted, somatic hypermutation has been strongly implicated in the development of B-cell lymphomas [3] and many other cancers. [4] [5]

Contents

Targeting

Simplistic overview of V(D)J recombination and somatic hypermutations at the immunoglobulin heavy chain variable region. Abbreviation of the regions: C = constant, D = diversity, J = joining, V = variable, L = light, H = heavy, FW = frame work, CDR = complementarity-determining regions, N = junctional diversity sequence. SMH wiki v5.png
Simplistic overview of V(D)J recombination and somatic hypermutations at the immunoglobulin heavy chain variable region. Abbreviation of the regions: C = constant, D = diversity, J = joining, V = variable, L = light, H = heavy, FW = frame work, CDR = complementarity-determining regions, N = junctional diversity sequence.

When a B cell recognizes an antigen, it is stimulated to divide (or proliferate). During proliferation, the B-cell receptor locus undergoes an extremely high rate of somatic mutation that is at least 105–106 fold greater than the normal rate of mutation across the genome. [2] Variation is mainly in the form of single-base substitutions, with insertions and deletions being less common. These mutations occur mostly at "hotspots" in the DNA, which are concentrated in hypervariable regions. These regions correspond to the complementarity-determining regions; the sites involved in antigen recognition on the immunoglobulin. [6] The "hotspots" of somatic hypermutation vary depending on the base that is being mutated. RGYW for a G, WRCY for a C, WA for an A and TW for a T. [7] [8] The overall result of the hypermutation process is achieved by a balance between error-prone and high fidelity repair. [9] This directed hypermutation allows for the selection of B cells that express immunoglobulin receptors possessing an enhanced ability to recognize and bind a specific foreign antigen. [1]

Mechanisms

Cytosine Cytosine chemical structure.svg
Cytosine
Uracil Uracil.svg
Uracil

The mechanism of SHM involves deamination of cytosine to uracil in DNA by the enzyme activation-induced cytidine deaminase, or AID. [10] [11] A cytosine:guanine pair is thus directly mutated to a uracil:guanine mismatch. Uracil residues are not normally found in DNA, therefore, to maintain the integrity of the genome, most of these mutations must be repaired by high-fidelity Base excision repair enzymes. The uracil bases are removed by the repair enzyme, uracil-DNA glycosylase. [11] Error-prone DNA polymerases are then recruited to fill in the gap and create mutations. [10] [12]

The synthesis of this new DNA involves error-prone DNA polymerases, which often introduce mutations at the position of the deaminated cytosine itself or neighboring base pairs. During B cell division the immunoglobulin variable region DNA is transcribed and translated. The introduction of mutations in the rapidly proliferating population of B cells ultimately culminates in the production of thousands of B cells, possessing slightly different receptors and varying specificity for the antigen, from which the B cell with highest affinities for the antigen can be selected. The B cells with the greatest affinity will then be selected to differentiate into plasma cells producing antibody and long-lived memory B cells contributing to enhanced immune responses upon reinfection. [2]

The hypermutation process also utilizes cells that auto-select against the 'signature' of an organism's own cells. It is hypothesized that failures of this auto-selection process may also lead to the development of an auto-immune response. [13]

Models

Developments on the viability of the two main competing molecular models on the mechanism of somatic hypermutation (SHM) since 1987 have now reached a resolution, particular molecular data published since 2000. Much of this early phase data has been reviewed by Teng and Papavasiliou [10] and additionally outlined by Di Noia and Maul, [14] [15] and the SHM field data reviewed in Steele [16] [17] and additionally outlined in these papers. [4] [5] [17] [18] [19] [20] [21] [ excessive citations ]

DNA deamination model

This can be labelled the DNA-based model. It is enzymatically focused solely on DNA substrates. The modern form, outlined in previous sections is the Neuberger "DNA deamination model" based on activation-induced cytidine deaminase (AID) and short-patch error-prone DNA repair by DNA polymerase-eta operating around AID C-to-U lesions [10] [14] [15] This model only partially explains the origins of the full spectrum of somatic mutations at A:T and G:C base pairs observed in SHM in B lymphocytes in vivo during an antigen-driven immune response. It also does not logically explain how strand biased mutations may be generated. A key feature is its critical dependence on the gap-filling error prone DNA repair synthesis properties of DNA polymerase-eta targeting A:T base pairs at AID-mediated C-to-U lesions or ssDNA nicks. [22] [23] [24] This error-prone DNA polymerase is the only known error-prone polymerase involved in SHM in vivo. [24] What is often ignored in these studies is that this Y family DNA polymerase enzyme is also an efficient reverse transcriptase as demonstrated in in vitro assays. [20]

Reverse transcriptase model

Adenosine Adenosine chemical structure.svg
Adenosine
Inosine Inosine chemical structure.svg
Inosine

The more controversial competing mechanism is an RNA/RT-based mechanism (reverse transcriptase model of SHM) which attempts to explain the production of the full spectrum of strand-biased mutations at A:T and G:C base pairs whereby mutations of A are observed to exceed mutations of T (A>>>T) and mutations of G are observed to exceed mutations of C (G>>>C). This involves error-prone cDNA synthesis via an RNA-dependent DNA polymerase copying the base modified Ig pre-mRNA template and integrating the now error-filled cDNA copy back into the normal chromosomal site. The errors in the Ig pre-mRNA are a combination of adenosine-to-inosine (A-to-I) RNA editing [18] [19] and RNA polymerase II transcription elongation complex copying uracil and abasic sites (arising as AID-mediated lesions) into the nascent pre-mRNA using the transcribed (TS) DNA as the copying template strand. [21] The modern form of this mechanism thus critically depends on AID C-to-U DNA lesions and long tract error-prone cDNA synthesis of the transcribed strand by DNA polymerase-eta acting as a reverse transcriptase. [16]

The evidence for and against each mechanism is critically evaluated in Steele [16] showing that all the molecular data on SHM published since 1980 supports directly or indirectly this RNA/RT-based mechanism. Recently Zheng et al. [25] have supplied critical independent validation by showing that Adenosine Deaminase enzymes acting on RNA (ADARs) can A-to-I edit both the RNA and DNA moieties of RNA:DNA hybrids in biochemical assays in vitro. RNA:DNA hybrids of about 11 nucleotides in length are transient structures formed at transcription bubbles in vivo during RNA polymerase II elongation.[ citation needed ]

A preliminary analysis of the implications of the Zheng et al. data has been submitted as formal paper to a refereed journal by Steele and Lindley. [26] The Zheng et al. [25] data strongly imply that the RNA moiety would need to be first A-to-I RNA edited then reverse transcribed and integrated to generate the strong A>>>T strand biased mutation signatures at A:T base pairs observed in all SHM and cancer hypermutation data sets. [4] [5] [16] [21] Editing (A-to-I) of the DNA moiety at RNA:DNA hybrids in vivo cannot explain the A>>T strand bias because such direct DNA modifications would result in T>>>A strand bias which is not observed in any SHM or cancer data set in vivo. [4] [5] [16] [21] In this regard Robyn Lindley has also recently discovered that the Ig-SHM-like strand-biased mutations in cancer genome protein-coding genes are also in "codon-context". Lindley has termed this process targeted somatic mutation (TSM) to highlight that somatic mutations are far more targeted than previously thought in somatic tissues associated with disease. [27] [28] The TSM process implies an "in-frame DNA reader" whereby DNA and RNA deaminases at transcribed regions are guided in their mutagenic action, by the codon reading frame of the DNA. [27] [28]

See also

Related Research Articles

Deamination is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases.

<span class="mw-page-title-main">DNA repair</span> Cellular mechanism

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in tens of thousands of individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages. This can eventually lead to malignant tumors, or cancer as per the two hit hypothesis.

Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA contained within each cell nucleus of a eukaryotic organism. It encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. It adheres to Mendelian inheritance, with information coming from two parents, one male and one female—rather than matrilineally as in mitochondrial DNA.

DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC 3.2.2. Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced. DNA glycosylases catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond.

In immunology, affinity maturation is the process by which TFH cell-activated B cells produce antibodies with increased affinity for antigen during the course of an immune response. With repeated exposures to the same antigen, a host will produce antibodies of successively greater affinities. A secondary response can elicit antibodies with several fold greater affinity than in a primary response. Affinity maturation primarily occurs on membrane immunoglobulin of germinal center B cells and as a direct result of somatic hypermutation (SHM) and selection by TFH cells.

<span class="mw-page-title-main">DNA mismatch repair</span> System for fixing base errors of DNA replication

DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

<span class="mw-page-title-main">Base excision repair</span> DNA repair process

Base excision repair (BER) is a cellular mechanism, studied in the fields of biochemistry and genetics, that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky helix-distorting lesions. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication. BER is initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites. These are then cleaved by an AP endonuclease. The resulting single-strand break can then be processed by either short-patch or long-patch BER.

<span class="mw-page-title-main">Activation-induced cytidine deaminase</span> Enzyme that creates mutations in DNA

Activation-induced cytidine deaminase, also known as AICDA, AID and single-stranded DNA cytosine deaminase, is a 24 kDa enzyme which in humans is encoded by the AICDA gene. It creates mutations in DNA by deamination of cytosine base, which turns it into uracil. In other words, it changes a C:G base pair into a U:G mismatch. The cell's DNA replication machinery recognizes the U as a T, and hence C:G is converted to a T:A base pair. During germinal center development of B lymphocytes, AID also generates other types of mutations, such as C:G to A:T. The mechanism by which these other mutations are created is not well understood. It is a member of the APOBEC family.

Hypergammaglobulinemia is a medical condition with elevated levels of gamma globulin. It is a type of immunoproliferative disorder.

V(D)J recombination is the mechanism of somatic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation. It results in the highly diverse repertoire of antibodies/immunoglobulins and T cell receptors (TCRs) found in B cells and T cells, respectively. The process is a defining feature of the adaptive immune system.

Missense mRNA is a messenger RNA bearing one or more mutated codons that yield polypeptides with an amino acid sequence different from the wild-type or naturally occurring polypeptide. Missense mRNA molecules are created when template DNA strands or the mRNA strands themselves undergo a missense mutation in which a protein coding sequence is mutated and an altered amino acid sequence is coded for.

<span class="mw-page-title-main">Immunoglobulin class switching</span> Biological mechanism

Immunoglobulin class switching, also known as isotype switching, isotypic commutation or class-switch recombination (CSR), is a biological mechanism that changes a B cell's production of immunoglobulin from one type to another, such as from the isotype IgM to the isotype IgG. During this process, the constant-region portion of the antibody heavy chain is changed, but the variable region of the heavy chain stays the same. Since the variable region does not change, class switching does not affect antigen specificity. Instead, the antibody retains affinity for the same antigens, but can interact with different effector molecules.

<span class="mw-page-title-main">POLD1</span> Protein-coding gene in the species Homo sapiens

The gene polymerase delta 1 (POLD1) encodes the large, POLD1/p125, catalytic subunit of the DNA polymerase delta (Polδ) complex. The Polδ enzyme is responsible for synthesizing the lagging strand of DNA, and has also been implicated in some activities at the leading strand. The POLD1/p125 subunit encodes both DNA polymerizing and exonuclease domains, which provide the protein an important second function in proofreading to ensure replication accuracy during DNA synthesis, and in a number of types of replication-linked DNA repair following DNA damage.

<span class="mw-page-title-main">POLQ</span> Protein-coding gene in the species Homo sapiens

DNA polymerase theta is an enzyme that in humans is encoded by the POLQ gene. This polymerase plays a key role in one of the three major double strand break repair pathways: theta-mediated end joining (TMEJ). Most double-strand breaks are repaired by non-homologous end joining (NHEJ) or homology directed repair (HDR). However, in some contexts, NHEJ and HR are insufficient and TMEJ is the only solution to repair the break. TMEJ is often described as alternative NHEJ, but differs in that it lacks a requirement for the Ku heterodimer, and it can only act on resected DNA ends. Following annealing of short regions on the DNA overhangs, DNA polymerase theta catalyzes template-dependent DNA synthesis across the broken ends, stabilizing the paired structure.

<span class="mw-page-title-main">SMUG1</span> Protein-coding gene in the species Homo sapiens

Single-strand selective monofunctional uracil DNA glycosylase is an enzyme that in humans is encoded by the SMUG1 gene. SMUG1 is a glycosylase that removes uracil from single- and double-stranded DNA in nuclear chromatin, thus contributing to base excision repair.

<span class="mw-page-title-main">DNA polymerase eta</span> Protein-coding gene in the species Homo sapiens

DNA polymerase eta, is a protein that in humans is encoded by the POLH gene.

Genome instability refers to a high frequency of mutations within the genome of a cellular lineage. These mutations can include changes in nucleic acid sequences, chromosomal rearrangements or aneuploidy. Genome instability does occur in bacteria. In multicellular organisms genome instability is central to carcinogenesis, and in humans it is also a factor in some neurodegenerative diseases such as amyotrophic lateral sclerosis or the neuromuscular disease myotonic dystrophy.

<span class="mw-page-title-main">Kataegis</span>

In molecular biology, kataegis describes a pattern of localized hypermutations identified in some cancer genomes, in which a large number of highly patterned basepair mutations occur in a small region of DNA. The mutational clusters are usually several hundred basepairs long, alternating between a long range of C→T substitutional pattern and a long range of G→A substitutional pattern. This suggests that kataegis is carried out on only one of the two template strands of DNA during replication. Compared to other cancer-related mutations, such as chromothripsis, kataegis is more commonly seen; it is not an accumulative process but likely happens during one cycle of replication.

Mutational signatures are characteristic combinations of mutation types arising from specific mutagenesis processes such as DNA replication infidelity, exogenous and endogenous genotoxin exposures, defective DNA repair pathways, and DNA enzymatic editing.

<span class="mw-page-title-main">Nina Papavasiliou</span> Immunologist

Nina Papavasiliou is an immunologist and Helmholtz Professor in the Division of Immune Diversity at the German Cancer Research Center in Heidelberg, Germany. She is also an adjunct professor at the Rockefeller University, where she was previously associate professor and head of the Laboratory of Lymphocyte Biology. She is best known for her work in the fields of DNA and RNA editing.

References

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  2. 1 2 3 Oprea, M. (1999) Antibody Repertoires and Pathogen Recognition: Archived 2008-09-06 at the Wayback Machine The Role of Germline Diversity and Somatic Hypermutation (Thesis) University of Leeds.
  3. ↑ Odegard V.H.; Schatz D.G. (2006). "Targeting of somatic hypermutation". Nat. Rev. Immunol. 6 (8): 573–583. doi:10.1038/nri1896. PMID   16868548. S2CID   6477436.
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  5. 1 2 3 4 Lindley, R.A.; Steele, E.J. (2013). "Critical analysis of strand-biased somatic mutation signatures in TP53 versus Ig genes, in genome -wide data and the etiology of cancer". ISRN Genomics. 2013 Article ID 921418: 18 pages.
  6. ↑ Li, Z.; Wool, C.J.; Iglesias-Ussel; M.D., Ronai, D.; Scharff, M.D. (2004). "The generation of antibody diversity through somatic hypermutation and class switch recombination". Genes & Development. 18 (1): 1–11. doi: 10.1101/gad.1161904 . PMID   14724175.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ↑ Dunn-Walters, DK; Dogan, A; Boursier, L; MacDonald, CM; Spencer, J (1998). "Base-specific sequences that bias somatic hypermutation deduced by analysis of out of frame genes". J. Immunol. 160: 2360–64. doi: 10.4049/jimmunol.160.5.2360 . S2CID   23647692.
  8. ↑ Spencer, J; Dunn-Walters, DK (2005). "Hypermutation at A-T base pairs: The A nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences around A and T nucleotides". J. Immunol. 175 (8): 5170–77. doi: 10.4049/jimmunol.175.8.5170 . PMID   16210621.
  9. ↑ Liu, M.; Schatz, D.G. (2009). "Balancing AID and DNA repair during somatic hypermutation". Trends in Immunology. 30 (4): 173–181. doi:10.1016/j.it.2009.01.007. PMID   19303358.
  10. 1 2 3 4 Teng, G.; Papavasiliou, F.N. (2007). "Immunoglobulin Somatic Hypermutation". Annu. Rev. Genet. 41: 107–120. doi:10.1146/annurev.genet.41.110306.130340. PMID   17576170.
  11. 1 2 Larson, E.D.; Maizels, N. (2004). "Transcription-coupled mutagenesis by the DNA deaminase AID". Genome Biol. 5 (3): 211. doi:10.1186/gb-2004-5-3-211. PMC   395756 . PMID   15003109.
  12. ↑ Bachl, J.; Ertongur, I.; Jungnickel, B. (2006). "Involvement of Rad18 in somatic hypermutation". Proc. Natl. Acad. Sci. USA. 103 (32): 12081–86. Bibcode:2006PNAS..10312081B. doi: 10.1073/pnas.0605146103 . PMC   1567700 . PMID   16873544.
  13. ↑ Metzger, T.C. (2011). "Control of Central and Peripheral Tolerance by Aire". Immunological Reviews. 241 (1): 89–103. doi:10.1111/j.1600-065X.2011.01008.x. PMC   3093413 . PMID   21488892.
  14. 1 2 Di Noia, J. M.; Neuberger, M. S. (2007). "Molecular mechanisms of somatic hypermutation". Annu. Rev. Biochem. 76: 1–22. doi:10.1146/annurev.biochem.76.061705.090740. PMID   17328676.
  15. 1 2 Maul, R. W.; Gearhart, P. J. (2010). AID and Somatic Hypermutation. pp. 159–191. doi:10.1016/S0065-2776(10)05006-6. ISBN   9780123813022. PMC   2954419 . PMID   20510733.{{cite book}}: |journal= ignored (help)
  16. 1 2 3 4 5 Steele, E.J. (2016). "Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures". DNA Repair. 45: 1–24. doi:10.1016/j.dnarep.2016.07.001. PMID   27449479.
  17. 1 2 Steele, E.J.; Pollard, J.W. (1987). "Hypothesis : Somatic Hypermutation by gene conversion via the error prone DNA-to-RNA-to-DNA information loop". Mol. Immunol. 24 (6): 667–673. doi:10.1016/j.dnarep.2016.07.001. PMID   2443841.
  18. 1 2 Steele, E.J.; Lindley, R.A.; Wen, J; Weiler, G.F. (2006). "Computational analyses show A-to-G mutations correlate with nascent mRNA hairpins at somatic hypermutation hotspots". DNA Repair. 5 (11): 1346–1363. doi:10.1016/j.dnarep.2006.06.002. PMID   16884961.
  19. 1 2 Steele, E.J.; Franklin, A; Blanden, R.V. (2004). "Genesis of the strand biased signature in somatic hypermutation of rearranged immunoglobulin variable genes". Immunol. Cell Biol. 82 (2): 208–218. doi:10.1046/j.0818-9641.2004.01224.x. PMID   15061776. S2CID   23764779.
  20. 1 2 Franklin, A.; Milburn, P. J.; Blanden, R.V.; Steele, E. J. (2004). "Human DNA polymerase-eta an A-T mutator in somatic hypermutation of rearranged immunoglobulin genes, is a reverse transcriptase". Immunol. Cell Biol. 82 (2): 219–225. doi:10.1046/j.0818-9641.2004.01221.x. PMID   15061777. S2CID   24370183.
  21. 1 2 3 4 Steele, E.J. (2009). "Mechanism of somatic hypermutation: Critical analysis of strand biased mutation signatures at A:T and G:C base pairs". Mol. Immunol. 46 (3): 305–320. doi:10.1016/j.molimm.2008.10.021. PMID   19062097.
  22. ↑ Zeng, X; Winter, D.B.; Kasmer, C; Kraemer, K.H.; Lehmann, A.R.; Gearhart, P.J. (2001). "DNA polymerase-eta is an A-T mutator in somatic hypermutation of immunoglobulin variable genes". Nat. Immunol. 2 (6): 537–541. doi:10.1038/88740. PMID   11376341. S2CID   6213513.
  23. ↑ Wilson, T.M.; Vaisman, A; Martomo, S.A.; Sullivan, P; Lan, L.; Hanaoka, F.; Yasui, A.; Woodgate, R.; Gearhart, P.J. (2005). "MSH2-MSH6 stimulates DNA polymerase eta, suggesting a role for A:T mutations in antibody genes". J. Exp. Med. 201 (4): 637–645. doi:10.1084/jem.20042066. PMC   2213055 . PMID   15710654.
  24. 1 2 Delbos, F; Aoufouchi, S; Faili, A; Weill, J-C; Reynaud, C-A (2007). "DNA polymerase-eta is the sole contributor of A/T modifications during immunoglobulin gene hypermutation in the mouse". J. Exp. Med. 204 (2007): 17–23. doi:10.1084/jem.20062131. PMC   2118439 . PMID   17190840.
  25. 1 2 Zheng, Yuxuan; Lorenzo, Claire; Beal, Peter A. (27 January 2017). "DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA". Nucleic Acids Research. 45 (6): 3369–337. doi:10.1093/nar/gkx050. PMC   5389660 . PMID   28132026.
  26. ↑ Steele, E.J.; Lindley, R.A. (2017). "RNA DNA Hybrids and SHM". DNA Repair. April 15, 2017: 1–6. doi:10.1016/j.dnarep.2017.04.004. PMID   28482199.
  27. 1 2 Lindley, R.A. (2013). "The importance of codon context for understanding the Ig-like somatic hypermutation strand-biased patterns in TP53 mutations in breast cancer". Cancer Genet. 206 (6): 222–226. doi:10.1016/j.cancergen.2013.05.016. PMID   23880211.
  28. 1 2 Lindley, R.A.; Humbert, P; Larmer, C; Akmeemana, E.H.; Pendlebury, C.R.R. (2016). "Association between Targeted Somatic Mutation (TSM) signatures and HGS-OvCa progression". Cancer Med. 5 (9): 2629–2640. doi:10.1002/cam4.825. PMC   5055158 . PMID   27485054.
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