Impact of DNA ligase IV on nonhomologous end joining pathways during class switch recombination in human cells

Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are subsequently processed and resolved, leading to recombination of the two targeted S regions. The mechanisms by which repair and ligation of the broken DNA ends occurs is still elusive. Recently, a small number of patients lacking DNA ligase IV, a critical component of the nonhomologous end joining (NHEJ) machinery, have been identified. We show that these patients display a considerably increased donor/acceptor homology at Sμ–Sα junctions compared with healthy controls. In contrast, Sμ–Sγ junctions show an increased frequency of insertions but no increase in junctional homology. These altered patterns of junctional resolution may be related to differences in the homology between the Sμ and the downstream isotype S regions, and could reflect different modes of switch junction resolution when NHEJ is impaired. These findings link DNA ligase IV, and thus NHEJ, to CSR.

Alternative end joining during switch recombination in patients with ataxia-telangiectasia

Ataxia-Telangiectasia (A-T) and Nijmegen breakage syndrome (NBS) are recessive genetic diseases with similar cellular phenotypes that are caused by mutations in the recently described ATM (encoding ATM) and NBS1 (encoding p95) genes, respectively. Both disorders are accompanied by immunodeficiency in a majority of patients, but the mechanism involved has as yet not been established. We demonstrate that in cells from A-T patients, the switch (S) recombination junctions are aberrant and characterized by a strong dependence on short sequence homologies and devoid of normally occurring mutations around the breakpoint. A low number of S fragments were generated in cells from NBS patients and showed only limited dependence on sequence identity and mutation frequencies were similar to those observed in normal controls. We propose that ATM and p95 are both involved in the final step(s) in class switch recombination with related, but disparate, functional roles. Thus, the general pathway involved in DNA repair also has a major influence on the immunoglobulin isotype switching process.

Delineation of the role of the Mre11 complex in class switch recombination

Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are processed and resolved, leading to a recombination of the two S regions involved. The mechanism involved in the repair and ligation of the broken DNA ends is however still unclear. Here, we describe that switching is less efficient in cells from patients with Mre11 deficiency (Ataxia-Telangiectasia-like disorder, ATLD) and, more importantly, that the switch recombination junctions resulting from the in vivo switching events are aberrant. There was a trend toward an increased usage of microhomology (> or =4 bp) at the switch junctions in both ATLD and Nijmegen breakage syndrome (NBS) patients. However, the DNA ends were not joined as "perfectly" as those from Ataxia-Telangiectasia (A-T) patients and 1-2 bp mutations or insertions were often observed. In switch junctions from ATLD patients, there were fewer base substitutions due to transitions and, most strikingly, the substitutions that occurred most often in controls, C --> T transitions, never occurred at, or close to, the junctions derived from the ATLD patients. In switch junctions from NBS patients, all base substitutions were observed at the G/C nucleotides, and transitions were preferred. These data suggest that the Mre11-Rad50-Nbs1 complex (Mre11 complex) is involved in the nonhomologous end joining pathway in CSR and that Mre11, Nbs1, and protein mutated in ataxia-telangiectasia (ATM) might have both common and independent roles in this process.

Comparing Laparoscopic Elective Sigmoid Resection With Conservative Treatment in Improving Quality of Life of Patients With Diverticulitis: The Laparoscopic Elective Sigmoid Resection Following Diverticulitis (LASER) Randomized Clinical Trial

Question

Does elective sigmoid resection improve the quality of life in patients with recurrent diverticulitis, complicated diverticulitis, and/or chronic pain after an episode of diverticulitis?

Findings

In this randomized clinical trial that included 85 adults, the Gastrointestinal Quality of Life Index (GIQLI) score improved 11.8 points in patients randomized to sigmoid resection and 0.2 points in patients randomized to conservative treatment between baseline and 6 months, a statistically and clinically significant difference. Among 41 patients randomized to sigmoid resection, 4 (10%) experienced major complications.

Meaning

Sigmoid resection improved quality of life in patients with recurrent, complicated, or persistent painful diverticulitis but was associated with a small but significant risk of major complications.

Importance

Diverticulitis has a tendency to recur and affect quality of life.

Objective

To assess whether sigmoid resection is superior to conservative treatment in improving quality of life of patients with recurrent, complicated, or persistent painful diverticulitis.

Design, Setting, and Participants

This open-label randomized clinical trial assessed for eligibility 128 patients with recurrent, complicated, or persistent painful diverticulitis in 6 Finnish hospitals from September 29, 2014, to October 10, 2018. Exclusion criteria included age younger than 18 years or older than 75 years; lack of (virtual) colonoscopy or sigmoidoscopy data within 2 years, or presence of cancer, contraindication to laparoscopy, or fistula. Outcomes were assessed using intention-to-treat analysis. A prespecified interim analysis was undertaken when 66 patients had been randomized and their 6-month follow-up was assessable. Data were analyzed from June 2018 to May 2020.

Interventions

Laparoscopic sigmoid resection or conservative treatment.

Main Outcomes and Measures

The primary outcome was difference in Gastrointestinal Quality of Life Index (GIQLI) score between randomization and 6 months.

Results

Of 128 patients assessed for eligibility, 90 were randomized (28 male [31%]; mean [SD] age, 54.11 [11.9] years; 62 female [69%]; mean [SD] age, 57.13 [7.6] years). A total of 72 patients were included in analyses for the primary outcome (37 in the surgery group and 35 in the conservative treatment group), and 85 were included in analyses for clinical outcomes (41 in the surgery group and 44 in the conservative treatment group). The difference between GIQLI score at randomization and 6 months was a mean of 11.96 points higher in the surgery group than in the conservative treatment group (mean [SD] of 11.76 [15.89] points vs −0.2 [19.07] points; difference, 11.96; 95% CI, 3.72-20.19; P = .005). Four patients (10%) in the surgery group and no patients in the conservative treatment group experienced major complications (Clavien-Dindo grade III or higher). There were 2 patients (5%) in the surgery group and 12 patients (31%) in the conservative treatment group who had new episodes of diverticulitis within 6 months.

Conclusions and Relevance

In this randomized clinical trial, elective laparoscopic sigmoid resection improved quality of life in patients with recurrent, complicated, or persistent painful diverticulitis but carried a 10% risk of major complications.

Trial Registration

ClinicalTrials.gov Identifier: NCT02174926.

Primary immunodeficiency mutation databases

Primary immunodeficiencies are intrinsic defects of immune systems. Mutations in a large number of cellular functions can lead to impaired immune responses. More than 80 primary immunodeficiencies are known to date. During the last years genes for several of these disorders have been identified. Here, mutation information for 23 genes affected in 14 immunodefects is presented. The proteins produced are employed in widely diverse functions, such as signal transduction, cell surface receptors, nucleotide metabolism, gene diversification, transcription factors, and phagocytosis. Altogether, the genetic defect of 2,140 families has been determined. Diseases with X-chromosomal origin constitute about 70% of all the cases, presumably due to full penetrance and because the single affected allele causes the phenotype. All types of mutations have been identified; missense mutations are the most common mutation type, and truncation is the most common effect on the protein level. Mutational hotspots in many disorders appear in CPG dinucleotides. The mutation data for the majority of diseases are distributed on the Internet with a special database management system, MUTbase. Despite large numbers of mutations, it has not been possible to make genotype-phenotype correlations for many of the diseases.

Disparate roles of ATR and ATM in immunoglobulin class switch recombination and somatic hypermutation

Class switch recombination (CSR) and somatic hypermutation (SHM) are mechanistically related processes initiated by activation-induced cytidine deaminase. Here, we have studied the role of ataxia telangiectasia and Rad3-related protein (ATR) in CSR by analyzing the recombinational junctions, resulting from in vivo switching, in cells from patients with mutations in the ATR gene. The proportion of cells that have switched to immunoglobulin (Ig)A and IgG in the peripheral blood seems to be normal in ATR-deficient (ATRD) patients and the recombined S regions show a normal "blunt end-joining," but impaired end joining with partially complementary (1-3 bp) DNA ends. There was also an increased usage of microhomology at the mu-alpha switch junctions, but only up to 9 bp, suggesting that the end-joining pathway requiring longer microhomologies (> or =10 bp) may be ATR dependent. The SHM pattern in the Ig variable heavy chain genes is altered, with fewer mutations occurring at A and more mutations at T residues and thus a loss of strand bias in targeting A/T pairs within certain hotspots. These data suggest that the role of ATR is partially overlapping with that of ataxia telangiectasia-mutated protein, but that the former is also endowed with unique functional properties in the repair processes during CSR and SHM.

Characterization of ATM mutations in 41 Nordic families with ataxia telangiectasia

The Ataxia Telangiectasia Mutation (ATM) gene is mutated in the rare recessive syndrome Ataxia Telangiectasia (AT), which is characterized by cerebellar degeneration, immunodeficiency, and cancer predisposition. In this study, 41 AT families from Denmark, Finland, Norway, and Sweden were screened for ATM mutations. The protein truncation test (PTT), fragment length and heteroduplex analyses of large (0.8-1.2 kb) cDNA fragments were used. In total, 67 of 82 (82%) of the disease-causing alleles were characterized. Thirty-seven unique mutations were detected of which 25 have not previously been reported. The mutations had five different consequences for the ATM transcript: mutations affecting splicing (43%); frameshift mutations (32%); nonsense mutations (16%); small in-frame deletions (5%); and one double substitution (3%). In 28 of the probands mutations were found in both alleles, in 11 of the probands only one mutated allele was detected, and no mutations were detected in two Finnish probands. One-third of the probands (13) were homozygous, whereas the majority of the probands (26) were compound heterozygote with at least one identified allele. Ten alleles were found more than once; one Norwegian founder mutation constituted 57% of the Norwegian alleles. Several sequence variants were identified, none of them likely to be disease-causing. Some of them even involved partial skipping of exons, leading to subsequent truncation of the ATM protein.

Both normal and leukemic B lymphocytes express multiple isoforms of the human Aiolos gene

Aiolos is a chromatin remodeling transcription regulator that plays an antiproliferative role in B lymphocyte function. In contrast to the related Ikaros factors, mammalian Aiolos has not been reported to generate splice variants. In addition, although human leukemic lymphoblasts express non-DNA-binding Ikaros isoforms with potential dominant negative effect on other interacting factors,the role of Aiolos in human lymphoid disorders has remained obscure. To address the question, why Aiolos should delineate from Ikaros in such a marked way, we have here analyzed whether also human Aiolos could generate alternate isoforms. According to the results obtained, both normal and neoplastic B lineage cells were found to express at least five novel Aiolos variants. Also structurally dominant negative variants with less than three DNA-binding domains were identified. In conclusion, given the multiplicity of also human Aiolos isoforms and thereby the evidently more intricate contribution of Aiolos to the chromatin remodeling machinery, it is suggested, that not only Ikaros, but also Aiolos could participate in a more versatile manner in the regulation of B lymphocyte function.

Quality-of-Life and Recurrence Outcomes Following Laparoscopic Elective Sigmoid Resection vs Conservative Treatment Following Diverticulitis: Prespecified 2-Year Analysis of the LASER Randomized Clinical Trial

Importance

Both elective sigmoid resection and conservative treatment are options for patients with recurrent, complicated, or persistent painful diverticulitis; understanding outcomes following each can help inform decision-making.

Objective

To compare outcomes of elective sigmoid resection and conservative treatment for patients with recurrent, complicated, or persistent painful diverticulitis at 2-year follow-up.

Design, Setting, and Participants

This multicenter parallel open-label individually randomized clinical trial comparing elective sigmoid resection to conservative treatment in patients with recurrent, complicated, or persistent painful diverticulitis was carried out in 5 Finnish hospitals between September 2014 and October 2018. Follow-up up to 2 years is reported. Of 85 patients randomized and included, 75 and 70 were available for QOL outcomes at 1 year and 2 years, respectively, and 79 and 78 were available for the recurrence outcome at 1 year and 2 years, respectively. The present analysis was conducted from September 2015 to June 2022.

Interventions

Laparoscopic elective sigmoid resection vs conservative treatment (patient education and fiber supplementation).

Main Outcomes and Measures

Prespecified secondary outcomes included Gastrointestinal Quality of Life Index (GIQLI) score, complications, and recurrences within 2 years.

Results

Ninety patients (28 male [31%]; mean [SD] age, 54.11 [11.9] years and 62 female [69%]; mean [SD] age, 57.13 [7.6] years) were randomized either to elective sigmoid resection or conservative treatment. After exclusions, 41 patients in the surgery group and 44 in the conservative group were included in the intention-to-treat analyses. Eight patients (18%) in the conservative treatment group underwent sigmoid resection within 2 years. The mean GIQLI score at 1 year was 9.51 points higher in the surgery group compared to the conservative group (mean [SD], 118.54 [17.95] vs 109.03 [19.32]; 95% CI, 0.83-18.18; P = .03), while the mean GIQLI score at 2 years was similar between the groups. Within 2 years, 25 of 41 patients in the conservative group (61%) had recurrent diverticulitis compared to 4 of 37 patients in the surgery group (11%). Four of 41 patients in the surgery group (10%) and 2 of 44 in the conservative group (5%) had major postoperative complications within 2 years. In per-protocol analyses, the mean (SD) GIQLI score was higher in the surgery group compared to the conservative treatment group by 11.27 points at 12 months (119.42 [17.98] vs 108.15 [19.28]; 95% CI, 2.24-20.29; P = .02) and 10.43 points at 24 months (117.24 [15.51] vs 106.82 [18.94]; 95% CI, 1.52-19.33; P = .02).

Conclusions and Relevance

In this randomized clinical trial, elective sigmoid resection was effective in preventing recurrent diverticulitis and improved quality of life over conservative treatment within 2 years.

Trial Registration

ClinicalTrials.gov Identifier: NCT02174926.

Sigmoid Resection vs Conservative Treatment After Diverticulitis: Prespecified 4-Year Analysis of the LASER Randomized Clinical Trial

Importance

Laparoscopic elective sigmoid resection is a treatment option for patients with recurring, persistent painful, or complicated diverticulitis, but outcomes of surgery compared with conservative treatment are unclear in long-term follow-up.

Objective

To compare quality-of-life (QOL), complication, and recurrence outcomes of surgery vs conservative treatment in patients with recurring, persistent painful, or complicated diverticulitis.

Design, Setting, and Participants

The open-label Laparoscopic Elective Sigmoid Resection Following Diverticulitis (LASER) randomized clinical trial was conducted in 6 Finnish hospitals. Ninety patients with recurring, persistent painful, or complicated diverticulitis were randomized (1:1) to elective sigmoid resection or conservative treatment from September 2014 to October 2018. Herein, outcomes are reported at 4-year follow-up using the intention-to-treat principle. Data analysis for this 4-year follow-up was performed from October 2023 to November 2024.

Interventions

Laparoscopic elective sigmoid resection vs conservative treatment.

Main Outcomes and Measures

Secondary outcomes, such as Gastrointestinal Quality of Life Index (GIQLI) scores, complications, and recurrences, within 4 years are reported using intention-to-treat and post hoc per-protocol analyses.

Results

Of 90 enrolled patients (28 male [31%] with mean [SD] age of 54.11 [11.9] years; 62 female [69%] with mean [SD] age of 57.13 [7.6] years), 45 were randomized to elective sigmoid resection and 45 to conservative treatment. Among those randomized to conservative treatment, 14 of 44 (32%) underwent sigmoid resection within 4 years (patients with lower QOL on average). The mean (SD) GIQLI score was 115.3 (17.8) in the surgery group vs 109.8 (19.8) in the conservative treatment group (mean difference, 5.54 [95% CI, -2.98 to 14.06]) at 4 years. Recurrence of diverticulitis occurred in 6 of 38 patients (16%) (4 [10%] after surgery) in the surgery group vs 34 of 37 patients (92%) in the conservative treatment group. Severe postoperative complications occurred in 4 patients (10%) in the surgery group vs 5 patients (11%) in the conservative treatment group.

Conclusions and Relevance

High crossover rates from conservative treatment to surgery indicate that patients with low QOL in the conservative treatment group often require surgical intervention; elective sigmoid resection did not improve QOL compared with conservative treatment in 4-year follow-up, even though it was effective in preventing recurrences of diverticulitis and did not lead to increased rates of postoperative complications. Upfront surgery may be preferable in patients with low QOL, but initial conservative treatment is an option for patients with near-normal QOL.

Trial Registration

ClinicalTrials.gov Identifier: NCT02174926.

[Ataxia-telangiectasia surveyed in Sweden]

Ataxia-telangiectasia (AT) is a rare autosomal recessive disease with a complex phenotype involving cerebellar degeneration, immunodeficiency, cancer risk and radiosensitivity. Our aim has been to identify Swedish AT patients in order to study the possible "Swedish phenotype" of the disease. In the 19 patients identified in Sweden we found a phenotype fairly similar to what has been described internationally, with the exception of some differences including lower cancer incidence in patients and their relatives and somewhat more pronounced immunodeficiency and concomitant susceptibility to infections.