Neoantigen-specific cytotoxic Tr1 CD4 T cells suppress cancer immunotherapy.

CD4+ T cells can either enhance or inhibit tumour immunity. Although regulatory T cells have long been known to impede antitumour responses1-5, other CD4+ T cells have recently been implicated in inhibiting this response6,7. Yet, the nature and function of the latter remain unclear. Here, using vaccines containing MHC class I (MHC-I) neoantigens (neoAgs) and different doses of tumour-derived MHC-II neoAgs, we discovered that whereas the inclusion of vaccines with low doses of MHC-II-restricted peptides (LDVax) promoted tumour rejection, vaccines containing high doses of the same MHC-II neoAgs (HDVax) inhibited rejection. Characterization of the inhibitory cells induced by HDVax identified them as type 1 regulatory T (Tr1) cells expressing IL-10, granzyme B, perforin, CCL5 and LILRB4. Tumour-specific Tr1 cells suppressed tumour rejection induced by anti-PD1, LDVax or adoptively transferred tumour-specific effector T cells. Mechanistically, HDVax-induced Tr1 cells selectively killed MHC-II tumour antigen-presenting type 1 conventional dendritic cells (cDC1s), leading to low numbers of cDC1s in tumours. We then documented modalities to overcome this inhibition, specifically via anti-LILRB4 blockade, using a CD8-directed IL-2 mutein, or targeted loss of cDC2/monocytes. Collectively, these data show that cytotoxic Tr1 cells, which maintain peripheral tolerance, also inhibit antitumour responses and thereby function to impede immune control of cancer.

Publisher Correction: Cryptic connections illuminate pathogen transmission within community networks.

In Fig. 3d this Letter, the R2 value should have been '0.19' instead of '0.66'; this has been corrected online.

MHC-II neoantigens shape tumour immunity and response to immunotherapy.

The ability of the immune system to eliminate and shape the immunogenicity of tumours defines the process of cancer immunoediting1. Immunotherapies such as those that target immune checkpoint molecules can be used to augment immune-mediated elimination of tumours and have resulted in durable responses in patients with cancer that did not respond to previous treatments. However, only a subset of patients benefit from immunotherapy and more knowledge about what is required for successful treatment is needed2-4. Although the role of tumour neoantigen-specific CD8+ T cells in tumour rejection is well established5-9, the roles of other subsets of T cells have received less attention. Here we show that spontaneous and immunotherapy-induced anti-tumour responses require the activity of both tumour-antigen-specific CD8+ and CD4+ T cells, even in tumours that do not express major histocompatibility complex (MHC) class II molecules. In addition, the expression of MHC class II-restricted antigens by tumour cells is required at the site of successful rejection, indicating that activation of CD4+ T cells must also occur in the tumour microenvironment. These findings suggest that MHC class II-restricted neoantigens have a key function in the anti-tumour response that is nonoverlapping with that of MHC class I-restricted neoantigens and therefore needs to be considered when identifying patients who will most benefit from immunotherapy.

Marine reserves can buffer against environmental fluctuations for overexploited but not sustainably harvested fisheries.

Globally, decision-makers are seeking management levers that can mitigate the negative effects of climate change on ecosystems that have already been transformed from their natural state by the effects of fishing. An important question is whether marine reserves can provide buffering (i.e., population-level resilience) against climate disturbances to fished populations. Here, we examine one aspect of this question, by asking whether marine reserves can reduce the variability in either overall biomass or in fishery yield, in the face of environmental variability. This could happen because greater reproduction of longer-lived, larger fish inside reserves could supplement recruitment to the fished portion of the population. We addressed this question using age-structured population models, assuming a system where some proportion of the coastline is protected in marine reserves (0%-30%), and the remainder is fished (at a range of possible harvest rates). We modeled populations with sedentary adults and dispersal via a larval pool. Since recent extreme climate events (e.g., marine heatwaves) have reduced juvenile survival for some fish species, we assumed that environmental variability affected the survival of the first age class in our model. We viewed population variability as a question of buffering, measured as the proportion of time a simulated population spent below a target reference point, with the idea that marine reserves could prevent the population from reaching low levels in the face of fishing and environmental variability. We found that fisheries with more area in marine reserves always had less variability in biomass. However, adding marine reserves only reduced variability in fisheries yield when the fished part of the population was being harvested at a rate exceeding the maximum sustainable yield. This new result on reducing variability is in line with previous findings that the "spillover" effects of marine reserve benefits to fishery yields only accrue when the fishery outside reserve boundaries is being overharvested.

Ecological success of no-take marine protected areas: Using population dynamics theory to inform a global meta-analysis.

Adaptively managing marine protected areas (MPAs) requires accurately assessing whether established MPAs are achieving their goals of protecting and conserving biomass, especially for harvested populations. Ecological MPA assessments commonly compare inside of the MPA to a reference point outside of and/or before implementation (i.e., calculating "response ratios"). Yet, MPAs are not simple ecological experiments; by design, protected populations interact with those outside, and population dynamic responses can be nonlinear. This complicates assessment interpretations. Here, we used a two-patch population model to explore how MPA response ratios (outside-inside, before-after, and before-after-control-impact [BACI]) for fished populations behave under different conditions, like whether the population is receiving a sustainable larval supply or if it is declining despite protection from harvest. We then conducted a Bayesian evaluation of MPA effects on fish and invertebrate populations based on data collected from 82 published studies on 264 no-take MPAs worldwide, using the results of an earlier global meta-analysis as priors. We considered the effects of calculating different summary metrics on these results, drawing on the theoretical insights from our population model as a comparative framework. We demonstrate that not all response ratio comparison types provide the same information: For example, outside-inside and BACI comparisons can fail to detect population decline within MPAs, whereas before-after comparisons likely detect that pattern. Considering these limitations, we nonetheless found that MPAs globally are producing positive outcomes, with on average greater biomass, density, and organism size within their boundaries than reference sites. However, only a small portion of studies (18 of 82) provided the temporal data necessary to determine that protection, on average, has led to increased abundance of populations within MPAs over time. These findings demonstrate the importance of considering the underlying system dynamics when assessing MPA effects. Assuming that large outside-inside or BACI response ratios always reflect large and net positive conservation effects may lead to misleading conclusions, we recommend that: (1) when assessing specific MPA effects, empirical findings be considered alongside theoretical knowledge relevant to that MPA system, and (2) management should respond to the local conditions and outcomes, rather than a blanket expectation for positive MPA effects.

Southern Hemisphere climate variability forced by Northern Hemisphere ice-sheet topography.

The presence of large Northern Hemisphere ice sheets and reduced greenhouse gas concentrations during the Last Glacial Maximum fundamentally altered global ocean-atmosphere climate dynamics. Model simulations and palaeoclimate records suggest that glacial boundary conditions affected the El Niño-Southern Oscillation, a dominant source of short-term global climate variability. Yet little is known about changes in short-term climate variability at mid- to high latitudes. Here we use a high-resolution water isotope record from West Antarctica to demonstrate that interannual to decadal climate variability at high southern latitudes was almost twice as large at the Last Glacial Maximum as during the ensuing Holocene epoch (the past 11,700 years). Climate model simulations indicate that this increased variability reflects an increase in the teleconnection strength between the tropical Pacific and West Antarctica, owing to a shift in the mean location of tropical convection. This shift, in turn, can be attributed to the influence of topography and albedo of the North American ice sheets on atmospheric circulation. As the planet deglaciated, the largest and most abrupt decline in teleconnection strength occurred between approximately 16,000 years and 15,000 years ago, followed by a slower decline into the early Holocene.

Cryptic connections illuminate pathogen transmission within community networks.

Understanding host interactions that lead to pathogen transmission is fundamental to the prediction and control of epidemics1-5. Although the majority of transmissions often occurs within social groups6-9, the contribution of connections that bridge groups and species to pathogen dynamics is poorly understood10-12. These cryptic connections-which are often indirect or infrequent-provide transmission routes between otherwise disconnected individuals and may have a key role in large-scale outbreaks that span multiple populations or species. Here we quantify the importance of cryptic connections in disease dynamics by simultaneously characterizing social networks and tracing transmission dynamics of surrogate-pathogen epidemics through eight communities of bats. We then compared these data to the invasion of the fungal pathogen that causes white-nose syndrome, a recently emerged disease that is devastating North American bat populations13-15. We found that cryptic connections increased links between individuals and between species by an order of magnitude. Individuals were connected, on average, to less than two per cent of the population through direct contact and to only six per cent through shared groups. However, tracing surrogate-pathogen dynamics showed that each individual was connected to nearly fifteen per cent of the population, and revealed widespread transmission between solitarily roosting individuals as well as extensive contacts among species. Connections estimated from surrogate-pathogen epidemics, which include cryptic connections, explained three times as much variation in the transmission of the fungus that causes white-nose syndrome as did connections based on shared groups. These findings show how cryptic connections facilitate the community-wide spread of pathogens and can lead to explosive epidemics.

Magnetoelectric inversion of domain patterns.

The inversion of inhomogeneous physical states has great technological importance; for example, active noise reduction relies on the emission of an inverted sound wave that interferes destructively with the noise of the emitter1, and inverting the evolution of a spin system by using a magnetic-field pulse enables magnetic resonance tomography2. In contrast to these examples, inversion of a distribution of ferromagnetic or ferroelectric domains within a material is surprisingly difficult: field poling creates a single-domain state, and piece-by-piece inversion using a scanning tip is impractical. Here we report inversion of entire ferromagnetic and ferroelectric domain patterns in the magnetoelectric material Co3TeO6 and the multiferroic material Mn2GeO4, respectively. In these materials, an applied magnetic field reverses the magnetization or polarization, respectively, of each domain, but leaves the domain pattern intact. Landau theory indicates that this type of magnetoelectric inversion is universal across materials that exhibit complex ordering, with one order parameter holding the memory of the domain structure and another setting its overall sign. Domain-pattern inversion is only one example of a previously unnoticed effect in systems such as multiferroics, in which several order parameters are available for combination. Exploring these effects could therefore advance multiferroics towards new levels of functionality.

Publisher Correction: Magnetoelectric inversion of domain patterns.

Four incorrect figure citations in this Letter have been corrected online.

Radiation-induced neoantigens broaden the immunotherapeutic window of cancers with low mutational loads.

Immunotherapies are a promising advance in cancer treatment. However, because only a subset of cancer patients benefits from these treatments it is important to find mechanisms that will broaden the responding patient population. Generally, tumors with high mutational burdens have the potential to express greater numbers of mutant neoantigens. As neoantigens can be targets of protective adaptive immunity, highly mutated tumors are more responsive to immunotherapy. Given that external beam radiation 1) is a standard-of-care cancer therapy, 2) induces expression of mutant proteins and potentially mutant neoantigens in treated cells, and 3) has been shown to synergize clinically with immune checkpoint therapy (ICT), we hypothesized that at least one mechanism of this synergy was the generation of de novo mutant neoantigen targets in irradiated cells. Herein, we use KrasG12D x p53-/- sarcoma cell lines (KP sarcomas) that we and others have shown to be nearly devoid of mutations, are poorly antigenic, are not controlled by ICT, and do not induce a protective antitumor memory response. However, following one in vitro dose of 4- or 9-Gy irradiation, KP sarcoma cells acquire mutational neoantigens and become sensitive to ICT in vivo in a T cell-dependent manner. We further demonstrate that some of the radiation-induced mutations generate cytotoxic CD8+ T cell responses, are protective in a vaccine model, and are sufficient to make the parental KP sarcoma line susceptible to ICT. These results provide a proof of concept that induction of new antigenic targets in irradiated tumor cells represents an additional mechanism explaining the clinical findings of the synergy between radiation and immunotherapy.

Sex-biased infections scale to population impacts for an emerging wildlife disease.

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behaviour. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

Widespread Community Transmission of Hepatitis A Virus Following an Outbreak at a Local Restaurant - Virginia, September 2021-September 2022.

Hepatitis A is a vaccine-preventable liver infection caused by the hepatitis A virus (HAV); it is transmitted through ingestion of food or drink that has been contaminated by small amounts of infected stool, or through direct contact, including sexual contact, with a person who is infected (1). After years of historically low rates of hepatitis A in the United States, the incidence began increasing in 2016, with outbreaks characterized by person-to-person HAV transmission among persons who use drugs, persons experiencing homelessness, and men who have sex with men (2,3). As of September 2022, 13 states were experiencing outbreaks, including Virginia (3). In September 2021, the Roanoke City and Alleghany Health Districts (RCAHD) in southwestern Virginia investigated an outbreak of hepatitis A. The outbreak, which resulted in 51 cases, 31 hospitalizations, and three deaths, was associated with a food handler who was infected. After the outbreak, the community experienced ongoing person-to-person transmission of HAV, predominantly among persons who use injection drugs. As of September 30, 2022,* an additional 98 cases had been reported to RCAHD. The initial outbreak and community transmission have exceeded US$3 million in estimated direct costs (4,5). This report describes the initial outbreak and the ongoing community transmission of HAV. Increasing vaccination coverage among persons with risk factors for hepatitis A infection is important, including among those who use drugs. Strengthening community partnerships between public health officials and organizations that employ persons with risk factors for acquisition of HAV could help to prevent infections and outbreaks.

Shifting effects of host physiological condition following pathogen establishment.

Understanding host persistence with emerging pathogens is essential for conserving populations. Hosts may initially survive pathogen invasions through pre-adaptive mechanisms. However, whether pre-adaptive traits are directionally selected to increase in frequency depends on the heritability and environmental dependence of the trait and the costs of trait maintenance. Body condition is likely an important pre-adaptive mechanism aiding in host survival, although can be seasonally variable in wildlife hosts. We used data collected over 7 years on bat body mass, infection and survival to determine the role of host body condition during the invasion and establishment of the emerging disease, white-nose syndrome. We found that when the pathogen first invaded, bats with higher body mass were more likely to survive, but this effect dissipated following the initial epizootic. We also found that heavier bats lost more weight overwinter, but fat loss depended on infection severity. Lastly, we found mixed support that bat mass increased in the population after pathogen arrival; high annual plasticity in individual bat masses may have reduced the potential for directional selection. Overall, our results suggest that some factors that contribute to host survival during pathogen invasion may diminish over time and are potentially replaced by other host adaptations.

Environmental reservoir dynamics predict global infection patterns and population impacts for the fungal disease white-nose syndrome.

Disease outbreaks and pathogen introductions can have significant effects on host populations, and the ability of pathogens to persist in the environment can exacerbate disease impacts by fueling sustained transmission, seasonal epidemics, and repeated spillover events. While theory suggests that the presence of an environmental reservoir increases the risk of host declines and threat of extinction, the influence of reservoir dynamics on transmission and population impacts remains poorly described. Here we show that the extent of the environmental reservoir explains broad patterns of host infection and the severity of disease impacts of a virulent pathogen. We examined reservoir and host infection dynamics and the resulting impacts of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome, in 39 species of bats at 101 sites across the globe. Lower levels of pathogen in the environment consistently corresponded to delayed infection of hosts, fewer and less severe infections, and reduced population impacts. In contrast, an extensive and persistent environmental reservoir led to early and widespread infections and severe population declines. These results suggest that continental differences in the persistence or decay of P. destructans in the environment altered infection patterns in bats and influenced whether host populations were stable or experienced severe declines from this disease. Quantifying the impact of the environmental reservoir on disease dynamics can provide specific targets for reducing pathogen levels in the environment to prevent or control future epidemics.

Highly reliable creation of floxed alleles by electroporating single-cell embryos.

BACKGROUND: Floxed (flanked by loxP) alleles are a crucial portion of conditional knockout mouse models. However, an efficient and reliable strategy to flox genomic regions of any desired size is still lacking. RESULTS: Here, we demonstrate that the method combining electroporation of fertilized eggs with gRNA/Cas9 complexes and single-stranded oligodeoxynucleotides (ssODNs), assessing phasing of loxP insertions in founders using an in vitro Cre assay and an optional, highly specific and efficient second-round targeting ensures the generation of floxed F1 animals in roughly five months for a wide range of sequence lengths (448 bp to 160 kb reported here). CONCLUSIONS: Floxed alleles can be reliably obtained in a predictable timeline using the improved method of electroporation of two gRNA/Cas9 ribonucleoprotein particles (RNPs) and two ssODNs.

Field applications of zein as a precise nanoscale delivery system for methoxyfenozide.

When insecticides are applied in the environment, much of the product does not reach the target pest. Biopolymeric nanoparticles as nanocarriers have the potential to improve insecticide efficacy by improving absorption, coverage, and permeability while protecting the insecticide active ingredient from abiotic conditions and extending efficacy through controlled release. We conducted a series of experiments using a biopolymeric nanoparticle synthesized from zein, a biodegradable maize protein, to compare efficacy of a nanodelivered hydrophobic insect growth regulator (methoxyfenozide) against a commercial formulation. Positively charged zein nanoparticles (empty and loaded with methoxyfenozide) were compared to the formulated product, Intrepid 2F, as a foliar spray in-field on soybean. Chrysodeixis includens (Walker) was used as a model and was fed sprayed soybean leaves to evaluate efficacy of the tested foliar products over time. A separate set of leaves was sampled to measure residue levels of methoxyfenozide (MFZ) over time following foliar application using QuEChERS extraction and high-resolution liquid chromatography-mass spectrometry. Regression analysis found no differences in mortality slopes between positively charged zein nanoparticles loaded with methoxyfenozide [(+)ZNP(MFZ)] and Intrepid 2F, suggesting comparable efficacy of the synthesized nanoparticles to a commercial product. Higher concentrations of MFZ were present in (+)ZNP(MFZ)-treated in leaf tissue at 3 d following spray when compared to Intrepid 2F. The multiyear study results demonstrate that nanoparticles loaded with MFZ are comparable to Intrepid 2F under field conditions, with potential short-term benefits.

The impacts of adrenoleukodystrophy newborn screening on the evaluation of adrenal dysfunction in male children: An integrative literature review.

PROBLEM: Adrenoleukodystrophy (ALD) is an x-linked genetic condition with a high risk of adrenal dysfunction recommended for newborn screening. This review aims to critically appraise and synthesize existing literature identifying the impacts of ALD newborn screening in the United States on the evaluation and treatment of adrenal dysfunction in male children. ELIGIBILITYCRITERIA: An integrative literature review was conducted using the Embase, PubMed, and CINAHL databases. English-language primary source studies published in the past decade and seminal studies were included. SAMPLE: Twenty primary sources met the inclusion criteria, including five seminal studies. RESULTS: Three major themes emerged from the review: 1) prevention of adrenal crisis, 2) unexpected outcomes, and 3) ethical impacts. CONCLUSIONS: ALD screening increases disease identification. Serial adrenal evaluation prevents adrenal crisis and death; data is needed to establish predictive outcomes in ALD prognosis. Disease incidence and prognosis will become more apparent as states increasingly add ALD screening to their newborn panel. IMPLICATIONS FOR PRACTICE: Clinicians need awareness of ALD newborn screening and state screening protocols. Families first learning of ALD through newborn screening results will require education, support, and timely referrals for appropriate care.

Rupture of the gastrocnemius muscle at its distal musculotendinous junction: conservative treatment and outcomes in 11 dogs.

CASE HISTORY: Medical records from three veterinary referral centres and a university veterinary teaching hospital in Australia and the USA were reviewed to identify dogs with a diagnosis of distal gastrocnemius musculotendinous junction rupture (DGMJR) that were treated without surgery between 2007 and 2020. CLINICAL AND IMAGING FINDINGS: All dogs (n = 11) presented with unilateral, pelvic limb lameness and bruising, swelling or pain on palpation at the distal musculotendinous junction. The diagnosis was confirmed with ultrasound or MRI in six dogs; radiographs were used to excluded stifle and tarsus pathology in four dogs; and five dogs were diagnosed on physical examination findings. TREATMENT AND OUTCOME: All dogs were managed conservatively, either with complete confinement alone (n = 10; median 9 weeks), external coaptation alone (n = 1), or a combination of both (n = 4). Sporting dogs (n = 7) were completely confined (median 22 weeks) for longer periods than companion dogs (n = 3; median 5 weeks).A good to excellent outcome was achieved for all cases in this cohort. The seven sporting dogs achieved an excellent outcome; returning to their previous level of sport, with complete resolution of lameness and recovery of a normal tibiotarsal stance. The four companion dogs achieved a good outcome; returning to their previous level of activity but with persistently increased tibiotarsal standing angle compared to the contralateral limb. CLINICAL RELEVANCE: Conservative treatment represents a viable treatment option for dogs with a rupture of the gastrocnemius muscle at its distal musculotendinous junction.

No-take marine protected areas enhance the benefits of kelp-forest restoration for fish but not fisheries.

Kelp habitat restoration is gaining traction as a management action to support recovery in areas affected by severe disturbances, thereby ensuring the sustainability of ecosystem services. Knowing when and where to restore is a major question. Using a single-species population model, we consider how restoring inside marine protected areas (MPAs) might benefit coastal fish populations and fisheries. We found that MPAs can greatly enhance the population benefits of restoration but at a small cost to fishery yields. Generally, restoring inside MPAs had a better overall gains-loss outcome, especially if the system is under high fishing pressure or severe habitat loss. However, restoring outside became preferable when predatory fish indirectly benefit kelp habitats. In either case, successful restoration actions may be difficult to detect in time-series data due to complex transient dynamics. We provide context for setting management goals and social expectations for the ecosystem service implications of restoration in MPAs.

HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade.

BACKGROUND: Whereas human leukocyte antigen (HLA) class I mutation-associated neoantigen burden has been linked with response to immune checkpoint blockade (ICB), the role of HLA class II-restricted neoantigens in clinical responses to ICB is less studied. We used computational approaches to assess HLA class II immunogenic mutation (IMM) burden in patients with melanoma and lung cancer treated with ICB. PATIENTS AND METHODS: We analyzed whole-exome sequence data from four cohorts of ICB-treated patients with melanoma (n = 110) and non-small-cell lung cancer (NSCLC) (n = 123). MHCnuggets, a neural network-based model, was applied to estimate HLA class II IMM burdens and cellular fractions of IMMs were calculated to assess mutation clonality. We evaluated the combined impact of HLA class II germline genetic variation and class II IMM burden on clinical outcomes. Correlations between HLA class II IMM burden and density of tumor-infiltrating lymphocytes were computed from expression data. RESULTS: Responding tumors harbored a significantly higher HLA class II IMM burden for both melanoma and NSCLC (P ≤ 9.6e-3). HLA class II IMM burden was correlated with longer survival, particularly in the NSCLC cohort and in the context of low intratumoral IMM heterogeneity (P < 0.001). HLA class I and II IMM landscapes were largely distinct suggesting a complementary role for class II IMMs in tumor rejection. A higher HLA class II IMM burden was associated with CD4+ T-cell infiltration and programmed death-ligand 1 expression. Transcriptomic analyses revealed an inflamed tumor microenvironment for tumors harboring a high HLA class II IMM burden. CONCLUSIONS: HLA class II IMM burden identified patients with NSCLC and melanoma that attained longer survival after ICB treatment. Our findings suggest that HLA class II IMMs may impact responses to ICB in a manner that is distinct and complementary to HLA class I-mediated responses.