Deoxyuridine-rich cytoplasmic DNA antagonizes STING-dependent innate immune responses and sensitizes resistant tumors to anti-PD-L1 therapy.

DNA damage and cytoplasmic DNA induce type-1 interferon (IFN-1) and potentiate responses to immune checkpoint inhibitors. Our prior work found that inhibitors of the DNA damage response kinase ATR (ATRi) induce IFN-1 and deoxyuridine (dU) incorporation by DNA polymerases, akin to antimetabolites. Whether and how dU incorporation is required for ATRi-induced IFN-1 signaling is not known. Here, we show that ATRi-dependent IFN-1 responses require uracil DNA glycosylase (UNG)-initiated base excision repair and STING. Quantitative analyses of nine distinct nucleosides reveals that ATRi induce dU incorporation more rapidly in UNG wild-type than knockout cells, and that induction of IFN-1 is associated with futile cycles of repair. While ATRi induce similar numbers of micronuclei in UNG wild-type and knockout cells, dU containing micronuclei and cytoplasmic DNA are increased in knockout cells. Surprisingly, DNA fragments containing dU block STING-dependent induction of IFN-1, MHC-1, and PD-L1. Furthermore, UNG knockout sensitizes cells to IFN-γ in vitro , and potentiates responses to anti-PD-L1 in resistant tumors in vivo . These data demonstrate an unexpected and specific role for dU-rich DNA in suppressing STING-dependent IFN-1 responses, and show that UNG-deficient tumors have a heightened response to immune checkpoint inhibitors. STATEMENT OF SIGNIFICANCE: Antimetabolites disrupt nucleotide pools and increase dU incorporation by DNA polymerases. We show that unrepaired dU potentiates responses to checkpoint inhibitors in mouse models of cancer. Patients with low tumor UNG may respond to antimetabolites combined with checkpoint inhibitors, and patients with high tumor UNG may respond to UNG inhibitors combined with checkpoint inhibitors.

Meet the authors: Kate M. MacDonald and Shane M. Harding.

We talk to authors Kate M. MacDonald and Shane M. Harding about their paper "The proteomic landscape of genotoxic stress-induced micronuclei" (this issue of Molecular Cell), being driven by curiosity, and the excitement of learning something new about the world.

The proteomic landscape of genotoxic stress-induced micronuclei.

Micronuclei (MN) are induced by various genotoxic stressors and amass nuclear- and cytoplasmic-resident proteins, priming the cell for MN-driven signaling cascades. Here, we measured the proteome of micronuclear, cytoplasmic, and nuclear fractions from human cells exposed to a panel of six genotoxins, comprehensively profiling their MN protein landscape. We find that MN assemble a proteome distinct from both surrounding cytoplasm and parental nuclei, depleted of spliceosome and DNA damage repair components while enriched for a subset of the replisome. We show that the depletion of splicing machinery within transcriptionally active MN contributes to intra-MN DNA damage, a known precursor to chromothripsis. The presence of transcription machinery in MN is stress-dependent, causing a contextual induction of MN DNA damage through spliceosome deficiency. This dataset represents a unique resource detailing the global proteome of MN, guiding mechanistic studies of MN generation and MN-associated outcomes of genotoxic stress.

Antecedent chromatin organization determines cGAS recruitment to ruptured micronuclei.

Micronuclei (MN) are cytosolic bodies that sequester acentric fragments or mis-segregated chromosomes from the primary nucleus. Spontaneous rupture of the MN envelope allows recognition by the viral receptor cyclic GMP-AMP synthase (cGAS), initiating interferon signaling downstream of DNA damage. Here, we demonstrate that MN rupture is permissive but not sufficient for cGAS localization. Chromatin characteristics such as histone 3, lysine 79 dimethylation (H3K79me2) are present in the nucleus before DNA damage, retained in ruptured MN, and regulate cGAS recruitment. cGAS is further responsive to dynamic intra-MN processes occurring prior to rupture, including transcription. MN chromatin tethering via the nucleosome acidic patch is necessary for cGAS-dependent interferon signaling. Our data suggest that both damage-antecedent nuclear chromatin status and MN-contained chromatin organizational changes dictate cGAS recruitment and the magnitude of the cGAS-driven interferon cascade. Our work defines MN as integrative signaling hubs for the cellular response to genotoxic stress.

Alerting the immune system to DNA damage: micronuclei as mediators.

Healthy cells experience thousands of DNA lesions per day during normal cellular metabolism, and ionizing radiation and chemotherapeutic drugs rely on DNA damage to kill cancer cells. In response to such lesions, the DNA damage response (DDR) activates cell-cycle checkpoints, initiates DNA repair mechanisms, or promotes the clearance of irreparable cells. Work over the past decade has revealed broader influences of the DDR, involving inflammatory gene expression following unresolved DNA damage, and immune surveillance of damaged or mutated cells. Subcellular structures called micronuclei, containing broken fragments of DNA or whole chromosomes that have been isolated away from the rest of the genome, are now recognized as one mediator of DDR-associated immune recognition. Micronuclei can initiate pro-inflammatory signaling cascades, or massively degrade to invoke distinct forms of genomic instability. In this mini-review, we aim to provide an overview of the current evidence linking the DDR to activation of the immune response through micronuclei formation, identifying key areas of interest, open questions, and emerging implications.

Transplantation of donor grafts with defined ratio of conventional and regulatory T cells in HLA-matched recipients.

BACKGROUNDIn preclinical murine and early clinical studies of hematopoietic cell transplantation, engineering of donor grafts with defined ratios of CD4+CD25+FoxP3+ Tregs to conventional T cells (Tcons) results in the prevention of graft-versus-host disease and improved immune reconstitution. The use of highly purified primary graft Tregs for direct cell infusion has potential advantages over impure immunomagnetic selection or culture expansion, but has not been tested clinically. We performed a phase I study of the timed addition of CD34-selected hematopoietic stem cells and Tregs, followed by Tcons for the treatment of patients with high-risk hematological malignancies.METHODSWe present interim evaluation of a single-center open phase I/II study of administration of human leukocyte-matched Tregs and CD34-selected hematopoietic cells, followed by infusion of an equal ratio of Tcons in adult patients undergoing myeloablative hematopoietic stem cell transplantation (HCT) for high-risk or active hematological malignancies. Tregs were purified by immunomagnetic selection and high-speed cell sorting.RESULTSHere we report results for the first 12 patients who received Tregs of between 91% and 96% purity. Greater than grade II GVHD was noted in 2 patients in the first cohort of 5 patients, who received cryopreserved Tregs, but neither acute nor chronic GVHD was noted in the second cohort of 7 patients, who received fresh Tregs and single-agent GVHD prophylaxis. Patients in the second cohort appeared to have normal immune reconstitution compared with patients who underwent transplantation and did not develop GVHD.CONCLUSIONOur study shows that the use of highly purified fresh Tregs is clinically feasible and supports continued investigation of the strategy.TRIAL REGISTRATIONClinicalTrials.gov NCT01660607.FUNDINGNIH NHBLI R01 HL114591 and K08HL119590.

Luciferase-tagged wild-type and tropism-deficient mouse cytomegaloviruses reveal early dynamics of host colonization following peripheral challenge.

Cytomegaloviruses (CMVs) establish persistent, systemic infections and cause disease by maternal-foetal transfer, suggesting that their dissemination is a key target for antiviral intervention. Late clinical presentation has meant that human CMV (HCMV) dissemination is not well understood. Murine CMV (MCMV) provides a tractable model. Whole mouse imaging of virus-expressed luciferase has proved a useful way to track systemic infections. MCMV, in which the abundant lytic gene M78 was luciferase-tagged via a self-cleaving peptide (M78-LUC), allowed serial, unbiased imaging of systemic and peripheral infection without significant virus attenuation. Ex vivo luciferase imaging showed greater sensitivity than plaque assay, and revealed both well-known infection sites (the lungs, lymph nodes, salivary glands, liver, spleen and pancreas) and less explored sites (the bone marrow and upper respiratory tract). We applied luciferase imaging to tracking MCMV lacking M33, a chemokine receptor conserved in HCMV and a proposed anti-viral drug target. M33-deficient M78-LUC colonized normally in peripheral sites and local draining lymph nodes but spread poorly to the salivary gland, suggesting a defect in vascular transport consistent with properties of a chemokine receptor.

Murine Cytomegalovirus Exploits Olfaction To Enter New Hosts.

UNLABELLED: Viruses transmit via the environmental and social interactions of their hosts. Herpesviruses have colonized mammals since their earliest origins, suggesting that they exploit ancient, common pathways. Cytomegaloviruses (CMVs) are assumed to enter new hosts orally, but no site has been identified. We show by live imaging that murine CMV (MCMV) infects nasally rather than orally, both after experimental virus uptake and during natural transmission. Replication-deficient virions revealed the primary target as olfactory neurons. Local, nasal replication by wild-type MCMV was not extensive, but there was rapid systemic spread, associated with macrophage infection. A long-term, transmissible infection was then maintained in the salivary glands. The viral m131/m129 chemokine homolog, which influences tropism, promoted salivary gland colonization after nasal entry but was not required for entry per se The capacity of MCMV to transmit via olfaction, together with previous demonstrations of experimental olfactory infection by murid herpesvirus 4 (MuHV-4) and herpes simplex virus 1 (HSV-1), suggest that this is a common, conserved route of mammalian herpesvirus entry. IMPORTANCE: Cytomegaloviruses (CMVs) infect most mammals. Human CMV (HCMV) harms people with poor immune function and can damage the unborn fetus. It infects approximately 1% of live births. We lack a good vaccine. One problem is that how CMVs first enter new hosts remains unclear. Oral entry is often assumed, but the evidence is indirect, and no infection site is known. The difficulty of analyzing HCMV makes related animal viruses an important source of insights. Murine CMV (MCMV) infected not orally but nasally. Specifically, it targeted olfactory neurons. Viral transmission was also a nasal infection. Like HCMV, MCMV infected cells by binding to heparan, and olfactory surfaces display heparan to incoming viruses, whereas most other mucosal surfaces do not. These data establish a new understanding of CMV infections and a basis for infection control.

Differential hippocampal shapes in posterior cortical atrophy patients: A comparison with control and typical AD subjects.

Posterior cortical atrophy (PCA) is a neurodegenerative syndrome characterized by predominant visual deficits and parieto-occipital atrophy, and is typically associated with Alzheimer's disease (AD) pathology. In AD, assessment of hippocampal atrophy is widely used in diagnosis, research, and clinical trials; its utility in PCA remains unclear. Given the posterior emphasis of PCA, we hypothesized that hippocampal shape measures may give additional group differentiation information compared with whole-hippocampal volume assessments. We investigated hippocampal volume and shape in subjects with PCA (n = 47), typical AD (n = 29), and controls (n = 48). Hippocampi were outlined on MRI scans and their 3D meshes were generated. We compared hippocampal volume and shape between disease groups. Mean adjusted hippocampal volumes were ∼ 8% smaller in PCA subjects (P < 0.001) and ∼ 22% smaller in tAD subject (P < 0.001) compared with controls. Significant inward deformations in the superior hippocampal tail were observed in PCA compared with controls even after adjustment for hippocampal volume. Inward deformations in large areas of the hippocampus were seen in tAD subjects compared with controls and PCA subjects, but only localized shape differences remained after adjusting for hippocampal volume. The shape differences observed, even allowing for volume differences, suggest that PCA and tAD are each associated with different patterns of hippocampal tissue loss that may contribute to the differential range and extent of episodic memory dysfunction in the two groups.

Automated template-based hippocampal segmentations from MRI: the effects of 1.5T or 3T field strength on accuracy.

Hippocampal volumetric measures may be useful for Alzheimer's disease (AD) diagnosis and disease tracking; however, manual segmentation of the hippocampus is labour-intensive. Therefore, automated techniques are necessary for large studies and to make hippocampal measures feasible for clinical use. As large studies and clinical centres are moving from using 1.5 Tesla (T) scanners to higher field strengths it is important to assess whether specific image processing techniques can be used at these field strengths. This study investigated whether an automated hippocampal segmentation technique (HMAPS: hippocampal multi-atlas propagation and segmentation) and volume change measures (BSI: boundary shift integral) were as accurate at 3T as at 1.5T. Eighteen Alzheimer's disease patients and 18 controls with 1.5T and 3T scans at baseline and 12-month follow-up were used from the Alzheimer's Disease Neuroimaging Initiative cohort. Baseline scans were segmented manually and using HMAPS and their similarity was measured by the Jaccard index. BSIs were calculated for serial image pairs. We calculated pair-wise differences between manual and HMAPS rates at 1.5T and 3T and compared the SD of these differences at each field strength. The difference in mean Jaccards (manual and HMAPS) between 1.5T and 3T was small with narrow confidence intervals (CIs) and did not appear to be segmentor dependent. The SDs of the difference between volumes from manual and automated segmentations were similar at 1.5T and 3T, with a relatively narrow CI for their ratios. The SDs of the difference between BSIs from manual and automated segmentations were also similar at 1.5T and 3T but with a wider CI for their ratios. This study supports the use of our automated hippocampal voluming methods, developed using 1.5T images, with 3T images.

Atrophy rates in asymptomatic amyloidosis: implications for Alzheimer prevention trials.

There is considerable interest in designing therapeutic studies of individuals at risk of Alzheimer disease (AD) to prevent the onset of symptoms. Cortical ß-amyloid plaques, the first stage of AD pathology, can be detected in vivo using positron emission tomography (PET), and several studies have shown that ~1/3 of healthy elderly have significant ß-amyloid deposition. Here we assessed whether asymptomatic amyloid-PET-positive controls have increased rates of brain atrophy, which could be harnessed as an outcome measure for AD prevention trials. We assessed 66 control subjects (age = 73.5±7.3 yrs; MMSE = 29±1.3) from the Australian Imaging Biomarkers & Lifestyle study who had a baseline Pittsburgh Compound B (PiB) PET scan and two 3T MRI scans ~18-months apart. We calculated PET standard uptake value ratios (SUVR), and classified individuals as amyloid-positive/negative. Baseline and 18-month MRI scans were registered, and brain, hippocampal, and ventricular volumes and annualized volume changes calculated. Increasing baseline PiB-PET measures of ß-amyloid load correlated with hippocampal atrophy rate independent of age (p = 0.014). Twenty-two (1/3) were PiB-positive (SUVR>1.40), the remaining 44 PiB-negative (SUVR≤1.31). Compared to PiB-negatives, PiB-positive individuals were older (76.8±7.5 vs. 71.7±7.5, p<0.05) and more were APOE4 positive (63.6% vs. 19.2%, p<0.01) but there were no differences in baseline brain, ventricle or hippocampal volumes, either with or without correction for total intracranial volume, once age and gender were accounted for. The PiB-positive group had greater total hippocampal loss (0.06±0.08 vs. 0.02±0.05 ml/yr, p = 0.02), independent of age and gender, with non-significantly higher rates of whole brain (7.1±9.4 vs. 4.7±5.5 ml/yr) and ventricular (2.0±3.0 vs. 1.1±1.0 ml/yr) change. Based on the observed effect size, recruiting 384 (95%CI 195-1080) amyloid-positive subjects/arm will provide 80% power to detect 25% absolute slowing of hippocampal atrophy rate in an 18-month treatment trial. We conclude that hippocampal atrophy may be a feasible outcome measure for secondary prevention studies in asymptomatic amyloidosis.

The value of hippocampal and temporal horn volumes and rates of change in predicting future conversion to AD.

Hippocampal pathology occurs early in Alzheimer disease (AD), and atrophy, measured by volumes and volume changes, may predict which subjects will develop AD. Measures of the temporal horn (TH), which is situated adjacent to the hippocampus, may also indicate early changes in AD. Previous studies suggest that these metrics can predict conversion from amnestic mild cognitive impairment (MCI) to AD with conversion and volume change measured concurrently. However, the ability of these metrics to predict future conversion has not been investigated. We compared the abilities of hippocampal, TH, and global measures to predict future conversion from MCI to AD. TH, hippocampi, whole brain, and ventricles were measured using baseline and 12-month scans. Boundary shift integral was used to measure the rate of change. We investigated the prediction of conversion between 12 and 24 months in subjects classified as MCI from baseline to 12 months. All measures were predictive of future conversion. Local and global rates of change were similarly predictive of conversion. There was evidence that the TH expansion rate is more predictive than the hippocampal atrophy rate (P=0.023) and that the TH expansion rate is more predictive than the TH volume (P=0.036). Prodromal atrophy rates may be useful predictors of future conversion to sporadic AD from amnestic MCI.

Human Th1 and Th17 cells exhibit epigenetic stability at signature cytokine and transcription factor loci.

The linear model of Th cell lineage commitment is being revised due to reports that mature Th cells can trans-differentiate into alternate lineages. This ability of Th cells to reprogram is thought to be regulated by epigenetic mechanisms that control expression of transcription factors characteristic of opposing lineages. It is unclear, however, to what extent this new model of Th cell plasticity holds true in human Th cell subsets that develop under physiological conditions in vivo. We isolated in vivo-differentiated human Th1 and Th17 cells, as well as intermediate Th1/17 cells, and identified distinct epigenetic signatures at cytokine (IFNG and IL17A) and transcription factor (TBX21, RORC, and RORA) loci. We also examined the phenotypic and epigenetic stability of human Th17 cells exposed to Th1-polarizing conditions and found that although they could upregulate TBX21 and IFN-γ, this occurred without loss of IL-17 or RORC expression, and resulted in cells with a Th1/17 phenotype. Similarly, Th1 cells could upregulate IL-17 upon enforced expression of RORC2, but did not lose expression of IFN-γ or TBX21. Despite alterations in expression of these signature genes, epigenetic modifications were remarkably stable aside from the acquisition of active histone methylation marks at cytokine gene promoters. The limited capacity of human Th17 and Th1 cells to undergo complete lineage conversion suggests that the bipotent Th1/17 cells may arise from Th1 and/or Th17 cells. These data also question the broad applicability of the new model of Th cell lineage plasticity to in vivo-polarized human Th cell subsets.

Automated cross-sectional and longitudinal hippocampal volume measurement in mild cognitive impairment and Alzheimer's disease.

Volume and change in volume of the hippocampus are both important markers of Alzheimer's disease (AD). Delineation of the structure on MRI is time-consuming and therefore reliable automated methods are required. We describe an improvement (multiple-atlas propagation and segmentation (MAPS)) to our template library-based segmentation technique. The improved technique uses non-linear registration of the best-matched templates from our manually segmented library to generate multiple segmentations and combines them using the simultaneous truth and performance level estimation (STAPLE) algorithm. Change in volume over 12months (MAPS-HBSI) was measured by applying the boundary shift integral using MAPS regions. Methods were developed and validated against manual measures using subsets from Alzheimer's Disease Neuroimaging Initiative (ADNI). The best method was applied to 682 ADNI subjects, at baseline and 12-month follow-up, enabling assessment of volumes and atrophy rates in control, mild cognitive impairment (MCI) and AD groups, and within MCI subgroups classified by subsequent clinical outcome. We compared our measures with those generated by Surgical Navigation Technologies (SNT) available from ADNI. The accuracy of our volumes was one of the highest reported (mean(SD) Jaccard Index 0.80(0.04) (N=30)). Both MAPS baseline volume and MAPS-HBSI atrophy rate distinguished between control, MCI and AD groups. Comparing MCI subgroups (reverters, stable and converters): volumes were lower and rates higher in converters compared with stable and reverter groups (p< or =0.03). MAPS-HBSI required the lowest sample sizes (78 subjects) for a hypothetical trial. In conclusion, the MAPS and MAPS-HBSI methods give accurate and reliable volumes and atrophy rates across the clinical spectrum from healthy aging to AD.

The relationship between pain tolerance and trait aggression: effects of sex and gender role.

The literature on pain and aggression has indicated that pain elicits aggression. However, research has generally examined pain as a situational variable and focused less on the dispositional ability of an individual to tolerate pain. The dearth of research on pain tolerance and aggression appears to contradict the existing theory on the aggression-eliciting effect of pain, in that studies have found a positive relationship between pain tolerance and aggression. The purpose of this study was to determine whether the relationship between pain tolerance and aggression is moderated by sex and whether the positive relationship could be explained by masculine gender role conformity. A sample of 195 collegiate men and women completed trait measures and a laboratory assessment of pain tolerance. Results indicated that correlations between pain tolerance and trait aggression were significant and positive for men but not women. However, when men's conformity to masculine gender role was controlled for, the relationship between pain tolerance and trait aggression was nil and nonsignificant. Results are discussed in reference to socialization and maintenance of masculine status.

Nursing handover: it's time for a change.

Nursing handover is a common part of nursing practice that is fundamental to safe patient care. Despite this, the literature provides little direction on the best way to conduct handover. This project aimed to examine nurses' perceptions of handover and to determine the strengths and imitations of the handover process. A staff survey was distributed to nurses in all inpatient wards at a metropolitan tertiary hospital. A total of 176 nurses responded to the staff survey. The findings revealed conflicting opinions about the effectiveness of the handover process; although a number of nurses were positive about current handover practice, indicating they were provided with sufficient information about patients and given opportunity to clarify patient care information, other nurses identified aspects of handover that could be improved. These included: the subjectivity of handover information, the time taken to conduct handover, repetition of information that could be found in the patients' care plans, and handing over of information by a nurse who has not cared for the patient. Some attention needs to be given to addressing the perceived weaknesses associated with the handover process.

Validation of a method for determination of the ankle-brachial index in the seated position.

OBJECTIVE: To validate a method for determination of the ankle-brachial index (ABI) in the seated position. BACKGROUND: Peripheral arterial disease (PAD) is a prevalent disorder that is associated with quality of life impairment and increased risk of a major cardiovascular event. The ABI is the initial test for screening and diagnosis of PAD. To prevent error due hydrostatic pressure, accurate measurement of the ABI requires supine patient positioning. Access to ABI measurement is limited for patients who are immobilized or unable to lie flat. METHODS: Patients presenting to a vascular laboratory for suspected arterial disease were enrolled. Arm and ankle blood pressures were measured in the supine and seated positions. Seated ankle pressures were corrected by the following physiology-based formula: Corrected ankle pressure = Measured ankle pressure - D*(.078), where D = the vertical distance between the arm and ankle cuffs (mm). This formula equates to a correction factor of 78 mm Hg per meter distance between the arm and ankle cuffs. Corrected ankle pressure measurements were used for seated ABI calculation. RESULTS: Complete data were available for 100 patients. Mean ABI was 0.97, and 31% of patients had an ABI < or =0.9. There was excellent correlation between supine and corrected seated ankle pressure measurements (r = 0.884-0.936, P < .001). The difference between measurements was negligible (<5 mm Hg). Similarly, there was excellent correlation between supine and seated ABI measures (r = 0.936, P < .001). There was no significant difference between the supine and seated ABI measures. CONCLUSION: We have developed and validated a method for determination of the ABI in the seated position which can be used to broaden availability of PAD testing. This method could also be incorporated into new technologies for ABI determination in the seated position.

Metropolis redux: the unique importance of library skills in informatics.

OBJECTIVES: The objective is to highlight the important role that librarians have in teaching within a successful medical informatics program. Librarians regularly utilize skills that, although not technology dependent, are essential to conducting computer-based research. The Metropolis analogy is used to introduce the part librarians play as informatics partners. Science fiction is a modern mythology that, beyond a technical exterior, has lasting value in its ability to reflect the human condition. The teaching of medical informatics, an intersection of technology and knowledge, is also most relevant when it transcends the operation of databases and systems. Librarians can teach students to understand, research, and utilize information beyond specific technologies. METHODS: A survey of twenty-six informatics programs was conducted during 2002, with specific emphasis on the role of the library service. RESULTS: The survey demonstrated that librarians currently do have a central role in informatics instruction, and that library-focused skills form a significant part of the curriculum in many of those programs. In addition, librarians have creative opportunities to enhance their involvement in informatics training. As a sample program in the study, the development of the informatics course at the Massachusetts College of Pharmacy and Health Sciences is included. CONCLUSIONS: Medical informatics training is a wonderful opportunity for librarians to collaborate with professionals from the sciences and other information disciplines. Librarians' unique combination of human research and technology skills provides a valuable contribution to any program.