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1.
Annu Rev Biochem ; 84: 199-226, 2015.
Article in English | MEDLINE | ID: mdl-25580529

ABSTRACT

DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSß and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway.


Subject(s)
DNA Mismatch Repair , Trinucleotide Repeat Expansion , Animals , Chromatin/metabolism , Escherichia coli , Genomic Instability , Histones/metabolism , Humans , Nervous System Diseases/genetics , Nervous System Diseases/metabolism , Nucleic Acid Conformation
2.
Mol Cell ; 82(19): 3538-3552.e5, 2022 10 06.
Article in English | MEDLINE | ID: mdl-36075220

ABSTRACT

DNA becomes single stranded (ssDNA) during replication, transcription, and repair. Transiently formed ssDNA segments can adopt alternative conformations, including cruciforms, triplexes, and quadruplexes. To determine whether there are stable regions of ssDNA in the human genome, we utilized S1-END-seq to convert ssDNA regions to DNA double-strand breaks, which were then processed for high-throughput sequencing. This approach revealed two predominant non-B DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulate in microsatellite unstable human cancer cell lines and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine mirror repeats common across a variety of cell lines. We show that H-DNA is enriched during replication, that its genomic location is highly conserved, and that H-DNA formed by (GAA)n repeats can be disrupted by treatment with a (GAA)n-binding polyamide. Finally, we show that triplex-forming repeats are hotspots for mutagenesis. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability.


Subject(s)
DNA, Cruciform , Nylons , DNA/metabolism , DNA Breaks, Double-Stranded , DNA Replication , Humans , Nucleic Acid Conformation
3.
Proc Natl Acad Sci U S A ; 120(1): e2211683120, 2023 01 03.
Article in English | MEDLINE | ID: mdl-36574697

ABSTRACT

Centromeres are the specialized regions of the chromosomes that direct faithful chromosome segregation during cell division. Despite their functional conservation, centromeres display features of rapidly evolving DNA and wide evolutionary diversity in size and organization. Previous work found that the noncanonical B-form DNA structures are abundant in the centromeres of several eukaryotic species with a possible implication for centromere specification. Thus far, systematic studies into the organization and function of non-B-form DNA in plants remain scarce. Here, we applied the oat system to investigate the role of non-B-form DNA in centromeres. We conducted chromatin immunoprecipitation sequencing using an antibody to the centromere-specific histone H3 variant (CENH3); this accurately positioned oat centromeres with different ploidy levels and identified a series of centromere-specific sequences including minisatellites and retrotransposons. To define genetic characteristics of oat centromeres, we surveyed the repeat sequences and found that dyad symmetries were abundant in oat centromeres and were predicted to form non-B-DNA structures in vivo. These structures including bent DNA, slipped DNA, Z-DNA, G-quadruplexes, and R-loops were prone to form within CENH3-binding regions. Dynamic conformational changes of predicted non-B-DNA occurred during the evolution from diploid to tetraploid to hexaploid oat. Furthermore, we applied the single-molecule technique of AFM and DNA:RNA immunoprecipitation with deep sequencing to validate R-loop enrichment in oat centromeres. Centromeric retrotransposons exhibited strong associations with R-loop formation. Taken together, our study elucidates the fundamental character of non-B-form DNA in the oat genome and reveals its potential role in centromeres.


Subject(s)
Avena , Retroelements , Avena/genetics , Avena/metabolism , Centromere/genetics , Centromere/metabolism , Histones/genetics , Histones/metabolism , Polyploidy
4.
Mol Cell ; 68(5): 901-912.e3, 2017 Dec 07.
Article in English | MEDLINE | ID: mdl-29220655

ABSTRACT

DNA double-strand breaks (DSBs) occurring within fragile zones of less than 200 base pairs account for the formation of the most common human chromosomal translocations in lymphoid malignancies, yet the mechanism of how breaks occur remains unknown. Here, we have transferred human fragile zones into S. cerevisiae in the context of a genetic assay to understand the mechanism leading to DSBs at these sites. Our findings indicate that a combination of factors is required to sensitize these regions. Foremost, DNA strand separation by transcription or increased torsional stress can expose these DNA regions to damage from either the expression of human AID or increased oxidative stress. This damage causes DNA lesions that, if not repaired quickly, are prone to nuclease cleavage, resulting in DSBs. Our results provide mechanistic insight into why human neoplastic translocation fragile DNA sequences are more prone to enzymes or agents that cause longer-lived DNA lesions.


Subject(s)
Chromosomes, Human/genetics , Cytidine Deaminase/genetics , DNA Breaks, Double-Stranded , DNA, Fungal/genetics , Oxidative Stress , Reactive Oxygen Species/metabolism , Saccharomyces cerevisiae/genetics , Translocation, Genetic , Chromosomes, Human/chemistry , Chromosomes, Human/metabolism , Cytidine Deaminase/metabolism , DNA, Fungal/chemistry , DNA, Fungal/metabolism , DNA-Binding Proteins , Endonucleases/genetics , Endonucleases/metabolism , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Fungal , Humans , Nucleic Acid Conformation , Peroxidases/genetics , Peroxidases/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Structure-Activity Relationship , Transcription, Genetic , Uracil-DNA Glycosidase/genetics , Uracil-DNA Glycosidase/metabolism
5.
Cell Mol Life Sci ; 81(1): 21, 2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38196006

ABSTRACT

BCL6 translocation is one of the most common chromosomal translocations in cancer and results in its enhanced expression in germinal center B cells. It involves the fusion of BCL6 with any of its twenty-six Ig and non-Ig translocation partners associated with diffuse large B cell lymphoma (DLBCL). Despite being discovered long back, the mechanism of BCL6 fragility is largely unknown. Analysis of the translocation breakpoints in 5' UTR of BCL6 reveals the clustering of most of the breakpoints around a region termed Cluster II. In silico analysis of the breakpoint cluster sequence identified sequence motifs that could potentially fold into non-B DNA. Results revealed that the Cluster II sequence folded into overlapping hairpin structures and identified sequences that undergo base pairing at the stem region. Further, the formation of cruciform DNA blocked DNA replication. The sodium bisulfite modification assay revealed the single-strandedness of the region corresponding to hairpin DNA in both strands of the genome. Further, we report the formation of intramolecular parallel G4 and triplex DNA, at Cluster II. Taken together, our studies reveal that multiple non-canonical DNA structures exist at the BCL6 cluster II breakpoint region and contribute to the fragility leading to BCL6 translocation in DLBCL patients.


Subject(s)
Lymphoma, Large B-Cell, Diffuse , Translocation, Genetic , Humans , Translocation, Genetic/genetics , Gene Rearrangement , Lymphoma, Large B-Cell, Diffuse/genetics , B-Lymphocytes , 5' Untranslated Regions , DNA , Proto-Oncogene Proteins c-bcl-6/genetics
6.
Proc Natl Acad Sci U S A ; 119(19): e2203967119, 2022 05 10.
Article in English | MEDLINE | ID: mdl-35503911

ABSTRACT

Certain DNA sequences, including mirror-symmetric polypyrimidine•polypurine runs, are capable of folding into a triple-helix­containing non­B-form DNA structure called H-DNA. Such H-DNA­forming sequences occur frequently in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)­specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides an approach for studying DNA secondary structure genome-wide at high spatial resolution.


Subject(s)
Genome , Nucleotide Motifs , Animals , Base Sequence , Genome/genetics , Mice , Nucleic Acid Conformation
7.
Crit Rev Biochem Mol Biol ; 57(3): 227-243, 2022 06.
Article in English | MEDLINE | ID: mdl-34875186

ABSTRACT

The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.


Subject(s)
Immunoglobulin Class Switching , Translocation, Genetic , Base Sequence , DNA , Humans
8.
J Virol ; 97(10): e0082323, 2023 10 31.
Article in English | MEDLINE | ID: mdl-37768085

ABSTRACT

IMPORTANCE: Pathogenesis of HIV-1 is enhanced through several viral-encoded proteins that counteract a range of host restriction molecules. HIV-1 Nef counteracts the cell membrane protein SERINC5 by downregulating it from the cell surface, thereby enhancing virion infectivity. Some subtype B reference Envelope sequences have shown the ability to bypass SERINC5 infectivity restriction independent of Nef. However, it is not clear if and to what extent circulating HIV-1 strains can exhibit resistance to SERINC5 restriction. Using a panel of Envelope sequences isolated from 50 Tanzanians infected with non-B HIV-1 subtypes, we show that the lentiviral reporters pseudotyped with patient-derived Envelopes have reduced sensitivity to SERINC5 and that this sensitivity differed among viral subtypes. Moreover, we found that SERINC5 sensitivity within patient-derived Envelopes can be modulated by separate regions, highlighting the complexity of viral/host interactions.


Subject(s)
HIV Infections , HIV-1 , Host Microbial Interactions , Membrane Proteins , env Gene Products, Human Immunodeficiency Virus , Humans , Cell Membrane/metabolism , env Gene Products, Human Immunodeficiency Virus/genetics , HIV Infections/metabolism , HIV Infections/virology , HIV-1/classification , HIV-1/pathogenicity , HIV-1/physiology , Membrane Proteins/metabolism , nef Gene Products, Human Immunodeficiency Virus/metabolism , Tanzania
9.
J Virol ; 97(1): e0163822, 2023 01 31.
Article in English | MEDLINE | ID: mdl-36511698

ABSTRACT

Small CD4-mimetic compound (CD4mc), which inhibits the interaction between gp120 with CD4, acts as an entry inhibitor and induces structural changes in the HIV-1 envelope glycoprotein trimer (Env) through its insertion within the Phe43 cavity of gp120. We recently developed YIR-821, a novel CD4mc, that has potent antiviral activity and lower toxicity than the prototype NBD-556. To assess the possibility of clinical application of YIR-821, we tested its antiviral activity using a panel of HIV-1 pseudoviruses from different subtypes. YIR-821 displayed entry inhibitor activity against 53.5% (21/40) of the pseudoviruses tested and enhanced neutralization mediated by coreceptor binding site (CoRBS) antibodies in 50% (16/32) of these. Furthermore, when we assessed the antiviral effects using a panel of pseudoviruses and autologous plasma IgG, enhancement of antibody-mediated neutralization activity was observed for 48% (15/31) of subtype B strains and 51% (28/55) of non-B strains. The direct antiviral activity of YIR-821 as an entry inhibitor was observed in 53% of both subtype B (27/51) and non-B subtype (40/75) pseudoviruses. Enhancement of antibody-dependent cellular cytotoxicity was also observed with YIR-821 for all six selected clinical isolates, as well as for the transmitted/founder (T/F) CH58 virus-infected cells. The sequence diversity in the CD4 binding site as well as other regions, such as the gp120 inner domain layers or gp41, may be involved in the multiple mechanisms related to the sensitive/resistant phenotype of the virus to YIR-821. Our findings may facilitate the clinical application of YIR-821. IMPORTANCE Small CD4-mimetic compound (CD4mc) interacts with the Phe43 cavity and triggers conformational changes, enhancing antibody-mediated neutralization and antibody-dependent cellular cytotoxicity (ADCC). Here, we evaluated the effect of YIR-821, a novel CD4mc, against clinical isolates, including both subtype B and non-B subtype viruses. Our results confirm the desirable properties of YIR-821, which include entry inhibition, enhancement of IgG-neutralization, binding, and ADCC, in addition to low toxicity and long half-life in a rhesus macaque model, that might facilitate the clinical application of this novel CD4mc. Our observation of primary viruses that are resistant to YIR-821 suggests that further development of CD4mcs with different structural properties is required.


Subject(s)
HIV Fusion Inhibitors , HIV Infections , HIV-1 , Animals , CD4 Antigens/metabolism , HIV Antibodies/blood , HIV Envelope Protein gp120 , HIV Fusion Inhibitors/pharmacology , HIV Infections/drug therapy , HIV-1/drug effects , Immunoglobulin G/blood , Macaca mulatta
10.
New Phytol ; 241(2): 607-622, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37897058

ABSTRACT

The fine centromere structure in Robertsonian wheat-rye translocation chromosomes exhibits variation among different translocation genotypes. Within extensively employed wheat-rye 1RS.1BL translocation lines in wheat breeding, their translocated chromosomes frequently display fused centromere. Nevertheless, the mechanism governing the functionality of the fused centromere in 1RS.1BL translocated chromosomes remains to be clarified. In this study, we investigated the fine centromere structure of the 1RS.1BL translocated chromosome through a combination of cytological and genomics methods. We found that only the rye-derived centromere exhibits functional activity, whether in breeding applications or artificially synthesized translocation chromosomes. The active rye-derived centromere had higher proportion of young full-length long terminal repeat retrotransposons (flLTR-RTs) and more stable non-B DNA structures, which may be beneficial toward transcription of centromeric repeats and CENH3 loading to maintain the activity of rye centromeres. High levels of DNA methylation and H3K9me2 were found in the inactive wheat-derived centromeres, suggesting that it may play a crucial role in maintaining the inactive status of the wheat centromere. Our works elucidate the fine structure of 1RS.1BL translocations and the potential mechanism of centromere inactivation in the fused centromere, contributing knowledge to the application of fused centromere in wheat breeding formation of new wheat-rye translocation lines.


Subject(s)
Retroelements , Secale , Retroelements/genetics , Secale/genetics , Plant Breeding , Chromosomes, Plant/genetics , Triticum/genetics , Centromere/genetics , Translocation, Genetic
11.
Ann Vasc Surg ; 2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39127369

ABSTRACT

OBJECTIVE: To evaluate outcomes achieved after implementing a treatment strategy for non-A non-B (NANB) (B 1-2 D according to the latest consensus document of the Society of Vascular Surgery (SVS) and Society of Thoracic Surgeons (STS) acute aortic dissection (AAD). METHODS: This retrospective observational study adhered to the STROBE checklist. All cases of NANB AAD (B 1-2 D) treated at our Institution between January 2016 and December 2022 were reviewed. Morbidity, mortality, aortic-related reintervention, and remodelling were analysed. RESULTS: Among 519 cases of acute aortic syndrome, n=22 (4.2%) patients presented with NANB AAD (B 1-2 D) (n=16,72.7% men, mean age 61.5 years+/14.7). Eleven cases were managed with best medical treatment (BMT) alone. Among them, one patient (9.1%) died suddenly two days after diagnosis for aortic rupture. Frozen elephant trunk procedure (FET) was required in the remaining 11 patients: 7(31.8%) needed emergent operation for risks of impending aortic rupture/retrograde AD extension and 4(26.7%) underwent delayed surgery within a month from initial presentation. Overall, in-hospital mortality was 9.1% with both FET and BMT. At a median follow-up of 40 months (range 2 days-200 months) no other deaths occurred. A statistically significant differences in the rate of FL thrombosis (100% vs 55.5%, p=.033) and a significant positive aortic remodelling in zone 3 (p<.001) and 4 (p=0.038) were reported in operated versus medically managed patients. CONCLUSION: The best treatment for NANB is not established. We advocate for medical stabilisation with an operative approach that favours open surgery in the acute post dissection period, promotes aortic remodelling and carries acceptable risk in centres where FET is performed routinely.

12.
Adv Exp Med Biol ; 1445: 3-10, 2024.
Article in English | MEDLINE | ID: mdl-38967746

ABSTRACT

The canonical theory of immunology stating that "Immunoglobulin (Ig) is produced by B lymphocytes and exerts antibody activity" has been established since the 1970s. However, the discovery of non B cell-derived Igs (non B-Igs), which can exert multiple biological activities in addition to their antibody activities, necessitates a reevaluation of the classic concept of Ig. This has been documented with a number of characteristics related to their structure, modification, genetic regulation as well as the functions associated with clinical conditions, particularly multiple cancers. The discovery of non B-Ig provides us with a new perspective to better understand not only basic immunology, but also various Ig-related clinical manifestations including autoimmune diseases, chronic inflammation, and anaphylaxis. Notably, non B-Ig can directly promote the occurrence of malignant tumours.


Subject(s)
Immunoglobulins , Humans , Immunoglobulins/immunology , Immunoglobulins/genetics , Animals , B-Lymphocytes/immunology , Neoplasms/immunology , Neoplasms/therapy , Autoimmune Diseases/immunology , Inflammation/immunology
13.
Adv Exp Med Biol ; 1445: 73-88, 2024.
Article in English | MEDLINE | ID: mdl-38967751

ABSTRACT

Immunoglobulin (Ig) has been widely acknowledged to be produced solely by B-lineage cells. However, growing evidence has demonstrated the expression of Ig in an array of cancer cells, as well as normal cells including epithelial cells, epidermal cells, mesangial cells, monocytes, and neutrophils. Ig has even been found to be expressed in non-B cells at immune-privileged sites such as neurons and spermatogenic cells. Despite these non-B cell-derived Igs (non-B-Igs) sharing the same symmetric structures with conventional Igs (B-Igs), further studies have revealed unique characteristics of non-B-Ig, such as restricted variable region and aberrant glycosylation. Moreover, non-B-Ig exhibits properties of promoting malignant behaviours of cancer cells, therefore it could be utilised in the clinic as a potential therapeutic biomarker or target. The elucidation of the generation and regulation of non-B-Ig will certainly broaden our understanding of immunology.


Subject(s)
Immunoglobulins , Humans , Animals , Immunoglobulins/genetics , Immunoglobulins/metabolism , Immunoglobulins/immunology , Glycosylation , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Neoplasms/immunology , Neoplasms/genetics , Neoplasms/pathology , Neoplasms/metabolism
14.
Adv Exp Med Biol ; 1445: 11-36, 2024.
Article in English | MEDLINE | ID: mdl-38967747

ABSTRACT

Although V(D)J recombination and immunoglobulin (Ig) production are traditionally recognised to occur only in B lymphocytes and plasma cells, the expression of Igs in non-lymphoid cells, which we call non B cell-derived Igs (non B Igs), has been documented by growing studies. It has been demonstrated that non B-Igs can be widely expressed in most cell types, including, but not limited to, epithelial cells, cardiomyocytes, hematopoietic stem/progenitor cells, myeloid cells, and cells from immune-privileged sites, such as neurons and spermatogenic cells. In particular, malignant tumour cells express high level of IgG. Moreover, different from B-Igs that mainly localised on the B cell membrane and in the serum and perform immune defence function mainly, non B-Igs have been found to distribute more widely and play critical roles in immune defence, maintaining cell proliferation and survival, and promoting progression. The findings of non B-Igs may provide a wealthier breakthrough point for more therapeutic strategies for a wide range of immune-related diseases.


Subject(s)
Immunoglobulins , Humans , Animals , Immunoglobulins/genetics , Immunoglobulins/metabolism , Immunoglobulins/immunology , Hematopoietic Stem Cells/metabolism , Hematopoietic Stem Cells/immunology , Hematopoietic Stem Cells/cytology , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Epithelial Cells/metabolism , Epithelial Cells/immunology , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/immunology , Myeloid Cells/immunology , Myeloid Cells/metabolism
15.
Adv Exp Med Biol ; 1445: 37-46, 2024.
Article in English | MEDLINE | ID: mdl-38967748

ABSTRACT

It is widely acknowledged that immunoglobulins (Igs) are produced solely by B-lineage cells. The Ig gene is created by the rearrangement of a group of gene segments [variable (V), diversity (D), and joining (J) segments rearrangement, or V(D)J recombination], which results in the vast diversity of B cell-derived Ig responsible for recognising various antigens. Ig subsequently undergoes somatic hypermutation (SHM) and class switch recombination (CSR) after exposure to antigens, thus converting the low-affinity IgM to IgG, IgA, or IgE antibodies. IgM and IgD are primarily expressed in naïve B cells that have not been exposed to antigens, they do not undergo somatic hypermutation; hence, their variable region sequences remain the same as those in the germline. In contrast, IgG, IgA, and IgE are expressed in antigen-stimulated memory B cells or plasma cells, and thus, they often possess high-frequency mutations in their variable region sequences. Since the discovery that Ig can be produced by non-B cells, Qiu's group has investigated and compared the genetic characteristics of B cell-derived Ig and non-B cell-derived Ig. These findings demonstrated that non-B cell-derived Ig shares certain similarities with B cell-derived Ig in that the sequence of its constant region is identical to that of B cell-derived Ig, and its variable region is also strictly dependent on the rearrangement of V, D, and J gene segments. Moreover, akin to B cell-derived Ig, the V regions of IgM and IgD are rarely mutated, while IgG, IgA, and IgE produced by cancer cells are frequently mutated. However, the non-B cell-derived Ig V region sequence displays unique characteristics. (1) Unlike the vast diversity of B cell-derived Igs, non-B cell-derived Igs exhibit restricted diversity; cells from the same lineage always select the same V(D)J recombination patterns; (2) Both mRNA and proteins of RAG1/RAG2 recombinase have been detected in Ig positive cancer cell lines and normal tissues. But Ig recombination could also be found in RAG1-/- and RAG2-/- mice, suggesting that they are not necessary for the rearrangement of non-B cell-derived Igs. These features of non-B cell-derived Igs suggest a potentially undiscovered mechanism of V(D)J recombination, ligation, and SHM in non-B cells, which necessitates further investigation with advanced technology in molecular biology.


Subject(s)
B-Lymphocytes , Genes, Immunoglobulin , Animals , Humans , Mice , B-Lymphocytes/immunology , Genes, Immunoglobulin/genetics , Immunoglobulin Class Switching/genetics , Immunoglobulin Class Switching/immunology , Immunoglobulins/genetics , Immunoglobulins/immunology , Somatic Hypermutation, Immunoglobulin/genetics
16.
Adv Exp Med Biol ; 1445: 59-71, 2024.
Article in English | MEDLINE | ID: mdl-38967750

ABSTRACT

According to classical immunology theory, immunoglobulin (Ig) is exclusively produced by differentiated B lymphocytes, which exhibit a typical tetrapeptide chain structure and are predominantly present on the surface of B cells and in bodily fluids. B-Ig is one of the critical effector molecules for humoral immune responses specifically recognising antigens and eliminating them. However, mounting evidence has demonstrated that Ig is widely expressed in non B lineage cells, especially malignant ones (referred to as non B-Ig). Interestingly, non B-Ig mainly resides in the cytoplasm and secretion, but to some extent on the cell surface. Furthermore non B-Ig not only displays a tetrapeptide chain structure but also shows free heavy chains and free light chains (FLCs). Additionally, Ig derived from non B cancer cell typically displays unique glycosylation modifications. Functionally, non B-Ig demonstrated diversity and versatility, showing antibody activity and cellular biological activity, such as promoting cell proliferation and survival, and it is implicated in cancer progression and some immune-related diseases, such as renal diseases.


Subject(s)
B-Lymphocytes , Humans , Animals , Glycosylation , B-Lymphocytes/immunology , Immunoglobulins/immunology , Immunoglobulins/metabolism , Immunoglobulins/chemistry , Neoplasms/immunology , Neoplasms/pathology , Immunoglobulin Light Chains/chemistry , Immunoglobulin Light Chains/immunology , Immunoglobulin Light Chains/metabolism
17.
Adv Exp Med Biol ; 1445: 137-149, 2024.
Article in English | MEDLINE | ID: mdl-38967756

ABSTRACT

Intestinal epithelium constitutes a barrier to the unrestricted movement of pathogens, and other detrimental substances from the external world (gut lumen) into the interstitial environment. Intestinal epithelial cells obstruct harmful substances passing through the epithelium as a physical and chemical barrier; Moreover, the epithelial cells can express Toll-like receptors (TLRs) and cytokines to exert innate immune function. In addition, high levels of immunoglobulin A (IgA) and other antibodies exist in the intestinal mucosa, maintaining intestinal immune homeostasis in conjunction with intestinal probiotics. Traditionally, these antibodies have been deemed to be secreted by submucosal plasma cells. Nonetheless, in recent years, it has been demonstrated that intestinal epithelial cells produce a substantial amount of Igs, especially IgA or free Ig light chains, which are involved in intestinal immune homeostasis and the survival of normal epithelial cells. Furthermore, mounting evidence affirms that many human carcinoma cells, including colorectal cancer (CRC), can overexpress Igs, particularly IgG. Cancer-derived Igs exhibit a unique V(D)J rearrangement pattern distinct from B cell-derived Ig; moreover, this cancer cell-derived IgG also has a unique sialic acid modification on the 162 site of CH1 domain (SIA-IgG). The SIA-IgG plays a crucial role in promoting cancer initiation, progression, metastasis, and tumour immune escape. Simultaneously, CRC cells can also express free Ig light chains, which promote colitis, colitis-associated colon carcinogenesis, and CRC progression. Therefore, Igs expressed by CRC cells could be a potential target for diagnosing and preventing the transformation of inflammation into cancer, as well as treating CRC.


Subject(s)
Intestinal Mucosa , Humans , Intestinal Mucosa/immunology , Intestinal Mucosa/metabolism , Animals , Immunoglobulins/immunology , Immunoglobulins/metabolism , Colorectal Neoplasms/immunology , Colorectal Neoplasms/pathology
18.
Proc Natl Acad Sci U S A ; 118(48)2021 11 30.
Article in English | MEDLINE | ID: mdl-34815340

ABSTRACT

Common fragile sites (CFSs) are difficult-to-replicate genomic regions that form gaps and breaks on metaphase chromosomes under replication stress. They are hotspots for chromosomal instability in cancer. Repetitive sequences located at CFS loci are inefficiently copied by replicative DNA polymerase (Pol) delta. However, translesion synthesis Pol eta has been shown to efficiently polymerize CFS-associated repetitive sequences in vitro and facilitate CFS stability by a mechanism that is not fully understood. Here, by locus-specific, single-molecule replication analysis, we identified a crucial role for Pol eta (encoded by the gene POLH) in the in vivo replication of CFSs, even without exogenous stress. We find that Pol eta deficiency induces replication pausing, increases initiation events, and alters the direction of replication-fork progression at CFS-FRA16D in both lymphoblasts and fibroblasts. Furthermore, certain replication pause sites at CFS-FRA16D were associated with the presence of non-B DNA-forming motifs, implying that non-B DNA structures could increase replication hindrance in the absence of Pol eta. Further, in Pol eta-deficient fibroblasts, there was an increase in fork pausing at fibroblast-specific CFSs. Importantly, while not all pause sites were associated with non-B DNA structures, they were embedded within regions of increased genetic variation in the healthy human population, with mutational spectra consistent with Pol eta activity. From these findings, we propose that Pol eta replicating through CFSs may result in genetic variations found in the human population at these sites.


Subject(s)
Chromosome Fragile Sites/genetics , DNA-Directed DNA Polymerase/metabolism , DNA-Directed DNA Polymerase/physiology , Cell Line , Chromosome Fragility/genetics , Chromosome Fragility/physiology , DNA/genetics , DNA Damage/genetics , DNA Polymerase III/metabolism , DNA Repair/genetics , DNA Repair/physiology , DNA Replication/physiology , Genetic Variation/genetics , Genomic Instability/genetics , Humans , Proliferating Cell Nuclear Antigen/metabolism
19.
J Vasc Surg ; 77(4): 1016-1027.e9, 2023 04.
Article in English | MEDLINE | ID: mdl-36410607

ABSTRACT

OBJECTIVE: In the present report, we have described the outcomes of endovascular repair, hybrid arch repair, and open surgical repair for type B dissection involving the aortic arch (B1-2, D). METHODS: Cases of endovascular repair, hybrid arch repair, and open surgical repair performed between January 2015 and December 2019 for aortic dissection designated as B1-2, D by the Society for Vascular Surgery/Society of Thoracic Surgeons classification were retrospectively analyzed. The primary end point was all-cause mortality at follow-up. The secondary end points included early mortality, early morbidities, and aortic-related late events. Kaplan-Meier curves were created to analyze survival from all-cause mortality and freedom from aortic-related late events in the endovascular, hybrid, and open groups. Propensity score matching and stratification (stratified by proximal dissection extension: B1, D and B2, D) were performed as sensitivity analyses to compare the outcomes among the three treatment patterns after controlling for major confounders. RESULTS: The present study included 151 patients (men, 79.5%; mean age, 47.3 ± 10.5 years), with 72 (47.7%) in the endovascular group, 46 (30.5%) in the hybrid group, and 33 (21.8%) in the open group. No significant difference was noted in early mortality between the endovascular, hybrid, and open groups (1.4% vs 2.2% vs 3.0%; P = .791). The incidence of early endoleak was significantly greater (33.3% vs 13.0% vs 6.1%; P = .002) and the incidence of renal function deterioration was less (4.2% vs 26.1% vs 24.2%; P = .001) after endovascular repair vs hybrid arch repair and open surgery. After a median follow-up of 40.0 months (range, 0-84.0 months), no significant differences were found in all-cause mortality (5.6% vs 4.3% vs 3.0%; P = 1.0), aortic-related late events (16.7% vs 15.2% vs 12.1%; P = .834), or late endoleak (9.7% vs 4.3% vs 6.1%; P = .630) after endovascular, hybrid, and open surgery. The propensity score matching and stratification analyses displayed consistent outcomes for early mortality, all-cause mortality, and aortic-related late events among the three groups. CONCLUSIONS: The mid- to long-term outcomes after endovascular repair, hybrid arch repair, and open surgical repair for type B dissection involving the aortic arch (B1-2, D) were favorable and comparable in selected patients. Extensive experience and multidisciplinary teamwork are prerequisites for individualized strategies for repair of B1-2, D.


Subject(s)
Aortic Aneurysm, Thoracic , Aortic Dissection , Blood Vessel Prosthesis Implantation , Endovascular Procedures , Male , Humans , Adult , Middle Aged , Aorta, Thoracic/diagnostic imaging , Aorta, Thoracic/surgery , Endoleak/surgery , Retrospective Studies , Blood Vessel Prosthesis Implantation/adverse effects , Endovascular Procedures/adverse effects , Aortic Dissection/diagnostic imaging , Aortic Dissection/surgery , Aortic Aneurysm, Thoracic/diagnostic imaging , Aortic Aneurysm, Thoracic/surgery , Treatment Outcome , Blood Vessel Prosthesis
20.
BMC Gastroenterol ; 23(1): 289, 2023 Aug 23.
Article in English | MEDLINE | ID: mdl-37612653

ABSTRACT

BACKGROUND: The incidence of HBV-negative and HCV-negative hepatocellular carcinoma (NBNC-HCC) is significantly increasing. However, their clinicopathologic features and prognosis remain elucidated. Our study aimed to compare the clinicopathologic characteristics and survival outcomes of NBNC-HCC with hepatitis virus-related HCC. METHOD: A literature review was performed in several databases, including PubMed, Embase, Cochrane Library and Web of Science, to identify the studies comparing NBNC-HCC with HBV-positive HCV-negative HCC (B-HCC), HBV-negative HCV-positive (C-HCC) and/or HBV-positive HCV-positive HCC (BC-HCC). The clinicopathologic characteristics and survival outcomes were extracted and pooled to access the difference. RESULTS: Thirty-two studies with 26,297 patients were included: 5390 patients in NBNC-HCC group, 9873 patients in B-HCC group, 10,848 patients in C-HCC group and 186 patients in BC-HCC group. Patients in NBNC-HCC group were more liable to be diagnosed at higher ages, but with better liver functions and lighter liver cirrhosis. Comparing to B-HCC and C-HCC groups, although NBNC-HCC group was prone to have larger tumor sizes, it did not have more advanced tumors. Meanwhile, there were no significant differences in both 5-year and 10-year disease-free survival and overall survival between NBNC-HCC group and B-HCC or C-HCC group. CONCLUSIONS: Our meta-analysis revealed patients with NBNC-HCC had as worse prognosis as those with hepatitis virus-related HCC. More attention should be paid on patients with non-alcoholic steatohepatitis or metabolic syndromes to prevent the incidence of NBNC-HCC.


Subject(s)
Carcinoma, Hepatocellular , Hepatitis C , Liver Neoplasms , Humans , Hepatectomy , Carcinoma, Hepatocellular/surgery , Hepatitis B virus , Liver Neoplasms/surgery , Hepatitis C/complications
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