A novel splice donor mutation in DCLRE1C caused atypical severe combined immunodeficiency in a patient with colon lymphoma: case report and literature review

Introduction

Hypomorphic mutations of DCLRE1C cause an atypical severe combined immunodeficiency (SCID), and Epstein-Barr virus (EBV)-related colon lymphoma is a rare complication.

Case presentation

A teenage boy presented with colon EBV-related colon lymphoma, plantar warts, and a history of recurrent pneumonia. His peripheral blood lymphocyte count and serum level of immunoglobulin (Ig) G were normal, but he exhibited a T+B-NK+ immunophenotype. Genetic analysis by whole exome sequencing revealed compound heterozygous mutations of DCLRE1C (NM_001033855.3), including a novel paternal splicing donor mutation (c.109 + 2T>C) in intron 1, and a maternal c.1147C>T (p.R383X) nonsense mutation in exon 13. Based on his clinical features and genetic results, the diagnosis of atypical SCID with colon lymphoma was established. Our review shows that seven patients, including our patient, have been reported to develop lymphoma, all with hypomorphic DCLRE1C mutations. Among these cases, six had EBV-related B-cell lineage lymphoma, and one had Hodgkin lymphoma with EBV reactivation. Unfortunately, all of the patients died.

Conclusion

Recognizing the radiosensitivity of the disease is critical for the prognosis. Hematopoietic stem cell transplantation before being infected with EBV is an optimal treatment.

PTEN in triple-negative breast carcinoma: protein expression and genomic alteration in pretreatment and posttreatment specimens

Background

Recent advances have been made in targeting the phosphoinositide 3-kinase pathway in breast cancer. Phosphatase and tensin homolog (PTEN) is a key component of that pathway.

Objective

To understand the changes in PTEN expression over the course of the disease in patients with triple-negative breast cancer (TNBC) and whether PTEN copy number variation (CNV) by next-generation sequencing (NGS) can serve as an alternative to immunohistochemistry (IHC) to identify PTEN loss.

Methods

We compared PTEN expression by IHC between pretreatment tumors and residual tumors in the breast and lymph nodes after neoadjuvant chemotherapy in 96 patients enrolled in a TNBC clinical trial. A correlative analysis between PTEN protein expression and PTEN CNV by NGS was also performed.

Results

With a stringent cutoff for PTEN IHC scoring, PTEN expression was discordant between pretreatment and posttreatment primary tumors in 5% of patients (n = 96) and between posttreatment primary tumors and lymph node metastases in 9% (n = 33). A less stringent cutoff yielded similar discordance rates. Intratumoral heterogeneity for PTEN loss was observed in 7% of the patients. Among pretreatment tumors, PTEN copy numbers by whole exome sequencing (n = 72) were significantly higher in the PTEN-positive tumors by IHC compared with the IHC PTEN-loss tumors (p < 0.0001). However, PTEN-positive and PTEN-loss tumors by IHC overlapped in copy numbers: 14 of 60 PTEN-positive samples showed decreased copy numbers in the range of those of the PTEN-loss tumors.

Conclusion

Testing various specimens by IHC may generate different PTEN results in a small proportion of patients with TNBC; therefore, the decision of testing one versus multiple specimens in a clinical trial should be defined in the patient inclusion criteria. Although a distinct cutoff by which CNV differentiated PTEN-positive tumors from those with PTEN loss was not identified, higher copy number of PTEN may confer positive PTEN, whereas lower copy number of PTEN would necessitate additional testing by IHC to assess PTEN loss.

Trial registration

NCT02276443.

Artemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia

As effective therapies for relapse and refractory B-cell acute lymphoblastic leukemia (B-ALL) remain problematic, novel therapeutic strategies are needed. Artemis is a key endonuclease in V(D)J recombination and nonhomologous end joining (NHEJ) of DNA double-strand break (DSB) repair. Inhibition of Artemis would cause chromosome breaks during maturation of RAG-expressing T- and B-cells. Though this would block generation of new B- and T-cells temporarily, it could be oncologically beneficial for reducing the proliferation of B-ALL and T-ALL cells by causing chromosome breaks in these RAG-expressing tumor cells. Currently, pharmacological inhibition is not available for Artemis. According to gene expression analyses from 207 children with high-risk pre-B acute lymphoblastic leukemias high Artemis expression is correlated with poor outcome. Therefore, we evaluated four compounds (827171, 827032, 826941, and 825226), previously generated from a large Artemis targeted drug screen. A biochemical assay using a purified Artemis:DNA-PKcs complex shows that the Artemis inhibitors 827171, 827032, 826941, 825226 have nanomolar IC50 values for Artemis inhibition. We compared these 4 compounds to a DNA-PK inhibitor (AZD7648) in three patient-derived B-ALL cell lines (LAX56, BLQ5 and LAX7R) and in two mature B-cell lines (3301015 and 5680001) as controls. We found that pharmacological Artemis inhibition substantially decreases proliferation of B-ALL cell lines while normal mature B-cell lines are not markedly affected. Inhibition of DNA-PKcs (which regulates Artemis) using the DNA-PK inhibitor AZD7648 had minor effects on these same primary patient-derived ALL lines, indicating that inhibition of V(D)J hairpin opening requires direct inhibition of Artemis, rather than indirect suppression of the kinase that regulates Artemis. Our data provides a basis for further evaluation of pharmacological Artemis inhibition of proliferation of B- and T-ALL.

Could β-Lactam Antibiotics Block Humoral Immunity?

It has been reported that treatment with β-lactam antibiotics induces leukopenia and candidemia, worsens the clinical response to anticancer immunotherapy and decreases immune response to vaccination. β-lactamases can cleave β-lactam antibiotics by blocking their activity. Two distincts superfamilies of β-lactamases are described, the serine β-lactamases and the zinc ion dependent metallo-β-lactamases. In human, 18 metallo-β-lactamases encoding genes (hMBLs) have been identified. While the physiological role of most of them remains unknown, it is well established that the SNM1A, B and C proteins are involved in DNA repair. The SNM1C/Artemis protein is precisely associated in the V(D)J segments rearrangement, that leads to immunoglobulin (Ig) and T-cell receptor variable regions, which have a crucial role in the immune response. Thus in humans, SNM1C/Artemis mutation is associated with severe combined immunodeficiency characterized by hypogammaglobulinemia deficient cellular immunity and opportunistic infections. While catalytic site of hMBLs and especially that of the SNM1 family is highly conserved, in vitro studies showed that some β-lactam antibiotics, and precisely third generation of cephalosporin and ampicillin, inhibit the metallo-β-lactamase proteins SNM1A & B and the SNM1C/Artemis protein complex. By analogy, the question arises as to whether β-lactam antibiotics can block the SNM1C/Artemis protein in humans inducing transient immunodeficiency. We reviewed here the literature data supporting this hypothesis based on in silico, in vitro and in vivo evidences. Understanding the impact of β-lactam antibiotics on the immune cell will offer new therapeutic clues and new clinical approaches in oncology, immunology, and infectious diseases.

A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair

Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the DCLRE1C gene in a T^-B^-NK⁺ SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the DCLRE1C transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all DCLRE1C splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the DCLRE1C gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.

Advancing research to eliminate mental illness stigma: an interventional study to improve community attitudes towards depression among University students in Singapore

BACKGROUND

After decades of anti-stigma initiatives, the Advancing Research To Eliminate Mental Illness Stigma (ARTEMIS) intervention study is one of the first in Singapore to evaluate the effects of an anti-stigma intervention on attitudes towards depression in university students.

METHODS

390 university students from a local university in Singapore were voluntarily recruited for the study. The ARTEMIS intervention comprises an educational and social contact component, as well as a question and answer (Q&A) session with experts in the area of mental health. The Community Attitudes towards Mental Illness (CAMI) scale was administered at baseline, post-intervention and at 3-months follow-up. A confirmatory factor analysis (CFA) was conducted.

RESULTS

The CFA identified a 3-factor model for the CAMI with a decent fit (RMSEA = 0.06, CFI = 0.93, TLI = 0.93, SRMR = 0.06). Favourable shifts in attitudes across the factors were observed immediately after the intervention (p <  0.001). Gender (β = - 1.19, 95% CI: - 2.10, - 0.27, p = 0.01) and nationality (β = - 1.23, 95% CI: - 2.35, - 0.11, p = 0.03) were identified as significant correlates for the community mental health ideology (CMHI) factor. Linear effects indicated that having a close social contact with mental illness observed a smaller decrease in authoritarianism scores from pre- to post-intervention (β = 0.85, 95% CI: 0.18, 1.53, p = 0.01); whereas quadratic effects found a greater decrease in scores from post-intervention to after 3-months for benevolence (β = - 0.34, 95% CI: - 0.52, - 0.16, p <  0.001) and CMHI (β = - 0.22, 95% CI: - 0.45, - 0.002, p = 0.048).

CONCLUSION

The anti-stigma intervention shows promising short-term results across the CAMI dimensions even after adjusting for sociodemographic correlates. However, the intervention did not observe the sustained attitude shifts after 3-months. Recommendations for future anti-stigma interventions were also considered.

New evidence in diagnosis of pulmonary embolism during pregnancy

Diagnosis of pulmonary embolism (PE) in pregnancy is notoriously difficult and lacking high quality evidence. Three studies (DiPEP, ARTEMIS and CT-PE-Pregnancy) evaluating a systematic approach to PE diagnosis have recently been published. DiPEP is a retrospective case-control study that found a poor utility of clinical decision rules or D-dimer testing for PE diagnosis in pregnancy. ARTEMIS and CT-PE-Pregnancy are well conducted prospective management studies that proposed two algorithms with different clinical decision rules and D-dimer criteria for the diagnosis of PE in pregnancy. They included few events in high risk patients, which makes difficult the assessment of both algorithm's safety in women with a high probability of PE. Considering this new evidence, D-dimer testing might be useful to avoid radiation imaging in pregnant women considered at low risk for PE. In contrast, a negative D-dimer cannot be considered sufficiently safe to rule out PE when clinicians estimate that PE is the most likely diagnosis.

Magnetotail Fast Flow Occurrence Rate and Dawn-Dusk Asymmetry at XGSM ∼ -60 RE

As a direct result of magnetic reconnection, plasma sheet fast flows act as primary transporter of mass, flux, and energy in the Earth's magnetotail. During the last decades, these flows were mainly studied within X_GSM>-60R_E , as observations near or beyond lunar orbit were limited. By using 5 years (2011-2015) of ARTEMIS (Acceleration, Reconnection, Turbulence, and Electrodynamics of the Moons Interaction with the Sun) data, we statistically investigate earthward and tailward flows at around 60 R_E downtail. A significant fraction of fast flows is directed earthward, comprising 43% (v_x >400 km/s) to 56% (v_x >100 km/s) of all observed flows. This suggests that near-Earth and midtail reconnection are equally probable of occurring on either side of the ARTEMIS downtail distance. For fast convective flows (v_⊥x >400 km/s), this fraction of earthward flows is reduced to about 29%, which is in line with reconnection as source of these flows and a downtail decreasing Alfvén velocity. More than 60% of tailward convective flows occur in the dusk sector (as opposed to the dawn sector), while earthward convective flows are nearly symmetrically distributed between the two sectors for low AL (>-400 nT) and asymmetrically distributed toward the dusk sector for high AL (<-400 nT). This indicates that the dawn-dusk asymmetry is more pronounced closer to Earth and moves farther downtail during high geomagnetic activity. This is consistent with similar observations pointing to the asymmetric nature of tail reconnection as the origin of the dawn-dusk asymmetry of flows and other related observables. We infer that near-Earth reconnection is preferentially located at dusk, whereas midtail reconnection (X >- 60R_E ) is likely symmetric across the tail during weak substorms and asymmetric toward the dusk sector for strong substorms, as the dawn-dusk asymmetric nature of reconnection onset in the near-Earth region progresses downtail.

Technical Note: Detective quantum efficiency simulation of a-Se imaging detectors using ARTEMIS

PURPOSE

This work studies the detective quantum efficiency (DQE) of a-Se-based solid state x-ray detectors for medical imaging applications using ARTEMIS, a Monte Carlo simulation tool for modeling x-ray photon, electron and charged carrier transport in semiconductors with the presence of applied electric field.

METHODS

ARTEMIS is used to model the signal formation process in a-Se. The simulation model includes x-ray photon and high-energy electron interactions, and detailed electron-hole pair transport with applied detector bias taking into account drift, diffusion, Coulomb interactions, recombination and trapping. For experimental validation, the DQE performance of prototype a-Se detectors is measured following IEC Testing Standard 62220-1-3.

RESULTS

Comparison of simulated and experimental DQE results show reasonable agreement for RQA beam qualities. Experimental validation demonstrated within 5% percentage difference between simulation and experimental DQE results for spatial frequency above 0.25 cycles/mm using uniform applied electric field for RQA beam qualities (RQA5, RQA7 and RQA9). Results include two different prototype detectors with thicknesses of 240 μm and 1 mm.

CONCLUSIONS

ARTEMIS can be used to model the DQE of a-Se detectors as a function of x-ray energy, detector thickness, and spatial frequency. The ARTEMIS model can be used to improve understanding of the physics of x-ray interactions in a-Se and in optimization studies for the development of novel medical imaging applications.

Autoinhibition of the Nuclease ARTEMIS Is Mediated by a Physical Interaction between Its Catalytic and C-terminal Domains

The nuclease ARTEMIS is essential for the development of B and T lymphocytes. It is required for opening DNA hairpins generated during antigen receptor gene assembly from variable (V), diversity (D), and joining (J) subgenic elements (V(D)J recombination). As a member of the non-homologous end-joining pathway, it is also involved in repairing a subset of pathological DNA double strand breaks. Loss of ARTEMIS function therefore results in radiosensitive severe combined immunodeficiency (RS-SCID). The hairpin opening activity is dependent on the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which can bind to and phosphorylate ARTEMIS. The ARTEMIS C terminus is dispensable for cellular V(D)J recombination and in vitro nuclease assays with C-terminally truncated ARTEMIS showing DNA-PKcs-independent hairpin opening activity. Therefore, it has been postulated that ARTEMIS is regulated via autoinhibition by its C terminus. To obtain evidence for the autoinhibition model, we performed co-immunoprecipitation experiments with combinations of ARTEMIS mutants. We show that an N-terminal fragment comprising the catalytic domain can interact both with itself and with a C-terminal fragment. Amino acid exchanges N456A+S457A+E458Q in the C terminus of full-length ARTEMIS resulted in unmasking of the N terminus and in increased ARTEMIS activity in cellular V(D)J recombination assays. Mutations in ARTEMIS-deficient patients impaired the interaction with the C terminus and also affected protein stability. The interaction between the N- and C-terminal domains was not DNA-PKcs-dependent, and phosphomimetic mutations in the C-terminal domain did not result in unmasking of the catalytic domain. Our experiments provide strong evidence that a physical interaction between the C-terminal and catalytic domains mediates ARTEMIS autoinhibition.

Effects of once-daily darunavir/ritonavir versus lopinavir/ritonavir on metabolic parameters in treatment-naive HIV-1-infected patients at week 96: ARTEMIS

In the ARTEMIS trial, 689 treatment-naïve, HIV-1-infected adults received darunavir/ritonavir (DRV/r) 800/100 mg every day or lopinavir/ritonavir (LPV/r) 800/200 mg total daily dose plus fixed-dose tenofovir/emtricitabine. Week 96 metabolic parameters are reported. Adverse events (AEs) classed as metabolism/nutrition disorders were observed in 14% of DRV/r and 22% of LPV/r patients. Lipid-related AEs were reported in fewer DRV/r (8%) than LPV/r (16%) patients. A small increase in glucose and insulin levels was observed at week 96 in both groups. Lipoma was the only lipodystrophy-related AE reported in >1% of patients (DRV/r, n = 1; LPV/r, n = 4) and no grade 3 or 4 lipodystrophy-related AEs were reported. No clinically relevant changes from baseline were seen in anthropometric measurements in either group. Median mid-waist/hip ratio at week 96 was comparable to baseline in both arms. Over 96 weeks, DRV/r had a similar effect on glucose and insulin levels but a more favourable lipid profile than LPV/r in treatment-naïve, HIV-infected patients.