An orthologous non-MHC locus in rats and mice is linked to CD4+ and CD8+ T-cell proportion.

CD4+ and CD8+ T cells have a central role in the immune system due to their ability to protect against infection and cancer development without targeting self. Consequently, changes in CD4+ and CD8+ T-cell homeostasis can be indicative of an array of serious illnesses, ranging from viral infections to autoimmune diseases. In addition to environmental influences, there is evidence for a genetic component regulating the proportion of CD4+ and CD8+ T cells in lymphoid organs. Indeed, identifying the genetic determinants defining the frequency of the T-cell subsets is critical as it may reveal a targetable genetic pathway to modulate CD4+ and CD8+ T-cell numbers, which could be of clinical relevance for multiple disease settings. In this study, we aim to uncover non-MHC genetic factors regulating the proportion of CD4+ and CD8+ T cells in lymphoid tissues. By investigating linkage analyses on three independent F2 cohorts, namely a rat F2 (BBDP × ACI.1U.LYP) cohort, a mouse 3A9 TCR transgenic F2 (B10.BR × NOD.H2k) cohort and a mouse F2 (C57BL/6 × FVB/N) cohort, we uncover an orthologous non-MHC locus on rat chromosome 1 and mouse chromosome 7 that is linked to T-cell proportion amongst total lymphocytes.

Programmed cell death-1 expression correlates with disease severity and IL-5 in chronic rhinosinusitis with nasal polyps.

BACKGROUND: Programmed cell death-1 (PD-1) is a negative regulator of T-cell responses. Expression of PD-1 and its ligands PD-L1 and PD-L2 in chronic rhinosinusitis with nasal polyps (CRSwNP) is poorly studied. METHODS: Expression of PD-1, PD-L1, PD-L2, TGF-ß, IL-5, and IL-10 mRNA was measured by real-time quantitative PCR on tissue homogenates of patients with CRSwNP (n = 21) and healthy controls (n = 21) and on primary epithelial cells. Disease severity was scored using the Lund-Mackay scores of maxillofacial computed tomography (CT) scans. Expression of PD-1 and PD-L1/L2 was evaluated at the cellular and tissue levels (n = 6) by flow cytometry and immunohistochemistry. RESULTS: Programmed cell death-1 mRNA expression was increased in tissue homogenates from patients with CRSwNP compared with controls, irrespective of the atopy status. Importantly, expression of PD-1 correlated with the total CT scan scores (r = 0.5, P = 0.02). Additionally, a significant association was found between PD-1 mRNA and expression of IL-5 mRNA in control nasal tissue (r = 0.95, P < 0.0001) and in CRSwNP (r = 0.63, P = 0.002). PD-1 was expressed on different subsets of T cells and CD11b- dendritic cells. Both PD-1 and its ligands were expressed on primary epithelial cells from control nasal tissue and nasal polyp tissue. CONCLUSIONS: Higher PD-1 expression was found in CRSwNP than in nasal tissue from controls. This was associated with disease severity and tissue IL-5 expression but unrelated to the patients' atopy status.

Idd13 is involved in determining immunoregulatory DN T-cell number in NOD mice.

Immunoregulatory T cells have been identified as key modulators of peripheral tolerance and participate in preventing autoimmune diseases. CD4(-)CD8(-) (double negative, DN) T cells compose one of these immunoregulatory T-cell subsets, where the injection of DN T cells confers protection from autoimmune diabetes progression. Interestingly, genetic loci defining the function and number of CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs) coincide with at least some autoimmune disease susceptibility loci. Herein, we investigate the impact of major insulin-dependent diabetes (Idd) loci in defining the number of DN T cells. We demonstrate that although Idd3, Idd5 and Idd9 loci do not regulate DN T-cell number, NOD mice congenic for diabetes resistance alleles at the Idd13 locus show a partial restoration in DN T-cell number. Moreover, competitive and non-competitive bone marrow chimera experiments reveal that DN T-cell number is defined by a bone marrow-intrinsic, but DN T-cell-extrinsic, factor. This suggests that non-autonomous candidate genes define DN T-cell number in secondary lymphoid organs. Together, our results show that the regulation of DN T-cell number in NOD mice is at least partially conferred by alleles at the Idd13 locus.

Anti-CD4 treatment inhibits autoimmunity in scurfy mice through the attenuation of co-stimulatory signals.

A major concept in autoimmunity is that disruption of Foxp3(+) regulatory T cells (Tregs) predisposes to breach of tolerance. This is exemplified by the Foxp3-linked disorder termed IPEX (immunodysregulation, polyendocrinopathy, enteropathy, X-linked) which affects newborn children. There has been considerable clinical interest in the role of non-depleting anti-CD4 antibodies as a means of upregulating the function of Foxp3(+) Tregs in order to control detrimental inflammatory responses such as transplant rejection. However, according to the paradigm of a Treg-dependent mechanism of action, the effectiveness of anti-CD4 antibodies as a therapy for human autoimmune diseases is unclear considering that Treg function might be intrinsically impaired. Specifically, anti-CD4 therapy is expected to fail in patients suffering from the IPEX syndrome due to the lack of functional Foxp3(+) Tregs. Taking advantage of natural Foxp3 mutant scurfy (sf) mice closely resembling the IPEX syndrome, and genetically engineered mice depleted of Foxp3(+) Tregs, we report here that anti-CD4 treatment induces tolerance independent of Foxp3(+) Tregs. This so far undefined mechanism is dependent on the recessive non-infectious tolerization of autoreactive T cells. Treg-independent tolerance alone is powerful enough to suppress both the onset and severity of autoimmunity and reduces clinically relevant autoantibody levels and liver fibrosis. Mechanistically, tolerance induction requires the concomitant activation of autoreactive T cells and is associated with the down-regulation of the co-stimulatory TNF-receptor superfamily members OX40 and CD30 sustaining CD4(+) T cell survival. In the light of ongoing clinical trials, our results highlight an unexpected potency of anti-CD4 antibodies for the treatment of autoimmune diseases. Particularly, CD4 blockade might represent a novel therapeutic option for the human IPEX syndrome.

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia.

We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or both maternal species, (2) the sex-determining chromosome of the hybrid reflects the location of male sterility within the maternal donor species and (3) crosses from the hybrid species show less sexual dimorphism than the parental species. We found that F. × ananassa subsp. cuneifolia populations consisted of both parental cytotypes but one predominated within each population. Genetic linkage mapping of two crosses showed dominance of male sterility similar to the parental species, however, the map location of male sterility reflected the maternal donor in one cross, but not the other. Moreover, female function mapped to a single region in the first cross, but to two regions in the second cross. Aside from components of female function (fruit set and seed set), other traits that have been found to be significantly sexually dimorphic in the pure species were either not dimorphic or were dimorphic in the opposite direction to the parental species. These results suggest that hybrids experience some disruption of dimorphism in secondary sexual traits, as well as novel location and number of quantitative trait locus (QTL) affecting sex function.

Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity.

Epidemiological and clinical reports indicate that SARS-CoV-2 virulence hinges upon the triggering of an aberrant host immune response, more so than on direct virus-induced cellular damage. To elucidate the immunopathology underlying COVID-19 severity, we perform cytokine and multiplex immune profiling in COVID-19 patients. We show that hypercytokinemia in COVID-19 differs from the interferon-gamma-driven cytokine storm in macrophage activation syndrome, and is more pronounced in critical versus mild-moderate COVID-19. Systems modelling of cytokine levels paired with deep-immune profiling shows that classical monocytes drive this hyper-inflammatory phenotype and that a reduction in T-lymphocytes correlates with disease severity, with CD8+ cells being disproportionately affected. Antigen presenting machinery expression is also reduced in critical disease. Furthermore, we report that neutrophils contribute to disease severity and local tissue damage by amplification of hypercytokinemia and the formation of neutrophil extracellular traps. Together our findings suggest a myeloid-driven immunopathology, in which hyperactivated neutrophils and an ineffective adaptive immune system act as mediators of COVID-19 disease severity.

Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines.

Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.

Evidence for long-term sensitization of the bowel in patients with post-infectious-IBS.

Post-infectious irritable bowel syndrome (PI-IBS) is a common gastrointestinal disorder characterized by persistent abdominal pain despite recovery from acute gastroenteritis. The underlying mechanisms are unclear, although long-term changes in neuronal function, and low grade inflammation of the bowel have been hypothesized. We investigated the presence and mechanism of neuronal sensitization in a unique cohort of individuals who developed PI-IBS following exposure to contaminated drinking water 7 years ago. We provide direct evidence of ongoing sensitization of neuronal signaling in the bowel of patients with PI-IBS. These changes occur in the absence of any detectable tissue inflammation, and instead appear to be driven by pro-nociceptive changes in the gut micro-environment. This is evidenced by the activation of murine colonic afferents, and sensitization responses to capsaicin in dorsal root ganglia (DRGs) following application of supernatants generated from tissue biopsy of patients with PI-IBS. We demonstrate that neuronal signaling within the bowel of PI-IBS patients is sensitized 2 years after the initial infection has resolved. This sensitization appears to be mediated by a persistent pro-nociceptive change in the gut micro-environment, that has the capacity to stimulate visceral afferents and facilitate neuronal TRPV1 signaling.

C-kit is important for SOD1(G93A) mouse survival independent of mast cells.

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease leading to progressive and lethal paralysis. The disease process is multi-factorial and is characterized by selective motor neuron degeneration. Previous work demonstrated that the local concentration of various growth factors can influence motor neuron survival and disease progression. A potential role for c-kit, a growth factor receptor present in the spinal cord, in ALS is unknown. To dissect the role of c-kit in ALS we interbred SOD1(G93A) mice with kit(w-sh/w-sh) mice, which have a 70% decrease in c-kit expression in the spinal cord. kit(w-sh/w-sh) SOD1(G93A) mice have a reduced survival compared to SOD1(G93A) mice, while the amount of motor neurons at end stage is similar. By means of grip strength and nerve conductance analysis we show that kit(w-sh/w-sh) mice have diminished strength and slightly impaired compound muscle action potential latency, although the number of neurons is similar across genotypes. Decreasing kit gene expression in SOD1(G93A) mice is detrimental and our results imply that this effect is independent of mast cells, as tested by ketotifen administration. To conclude, our data expand on the protective role of growth factors in ALS, as decreasing c-kit by approximately 70% is detrimental in SOD1(G93A) mice.

The effect of layers in imaging brain function using electrical impedance tomograghy.

Electrical impedance tomography (EIT) has promise for imaging brain function with rings of scalp electrodes, but hitherto human images have been collected and reconstructed using a simple algorithm in which the head was modelled as a homogeneous sphere. The purpose of this work was to assess the improvement in image quality which could be achieved by adding layers to represent the cerebro-spinal fluid (CSF), skull and scalp in the forward model employed by the reconstruction algorithm. Solutions to the forward model were produced analytically and using the linear finite element method (FEM). This was undertaken for computer simulated data when a spherical conductivity change of 10%, radius 5 mm, was moved through 29 positions within a head modelled as four concentric spheres of radius 80-92 mm in order to verify the accuracy of the linear FEM by comparison with the analytical method. Test data were also recorded in a 93.5 mm, spherical, saline-filled tank in which the skull was simulated by a hollow sphere of plaster of Paris, 5 mm thick and a 20 x 20 mm right-cylindrical Perspex object, a 100% conductivity decrease, was moved through 39 positions. The best images were achieved by reconstruction with a four- or three-shell analytical model, giving a spatial accuracy of 5.8 +/- 2.2 mm for computer simulated or 14.0 +/- 5.8 mm for tank data. Mean FWHM was 57 mm and 91 mm in the XY-plane and along the z-axis, respectively. Reconstruction with a homogeneous analytical model gave localization errors greater by about 50-300%, but a reduction in FWHM of about 5% of the image diameter. Unexpectedly, reconstruction with FEM models gave poorer results similar to the analytical homogeneous case. This confirms that addition of shells to the forward model improves image quality as expected with an analytical model for reconstruction, but that the FEM method employed, which used a medium mesh and a linear element computation, requires improvement in order to yield the expected benefits.

A multi-shell algorithm to reconstruct EIT images of brain function.

Electrical impedance tomography (EIT) may be used to image brain function, but an important consideration is the effect of the highly resistive skull and other extracerebral layers on the flow of injected current. We describe a new reconstruction algorithm, based on a forward solution which models the head as four concentric, spherical shells, with conductivities of the brain, cerebrospinal fluid, skull and scalp. The model predicted that the mean current travelling in the brain in the diametric plane for current injection from polar electrodes was 5.6 times less than if the head was modelled as a homogeneous sphere; this suggests that an algorithm based on this should be more accurate than one based on a homogeneous sphere model. In images reconstructed from computer-simulated data or data from a realistic saline-filled tank containing a real skull, a Perspex rod was localized to within 17% or 20% of the tank diameter of its true position, respectively. Contrary to expectation, the tank images were less accurate than those obtained with a reconstruction algorithm based on a homogeneous sphere. It is not yet clear if the theoretical advantages of this algorithm will yield practical advantages for head EIT imaging; it may be necessary to proceed to more complex algorithms based on numerical models which incorporate realistic head geometry. If so, this analytical forward model and algorithm may be used to validate numerical solutions.

Neuromagnetic field strength outside the human head due to impedance changes from neuronal depolarization.

The holy grail of neuroimaging would be to have an imaging system, which could image neuronal electrical activity over milliseconds. One way to do this would be by imaging the impedance changes associated with ion channels opening in neuronal membranes in the brain during activity. In principle, we could measure this change by using electrical impedance tomography (EIT) but it is close to its threshold of detectability. With the inherent limitation in the use of electrodes, we propose a new scheme based on recording the magnetic field resulting from an injected current with superconducting quantum interference devices (SQUIDs), used in magnetoencephalography (MEG). We have performed a feasibility study using computer simulation. The head was modelled as concentric spheres to mimic the scalp, skull, cerebrospinal fluid and brain using the finite element method. The magnetic field 1 cm away from the scalp was estimated. An impedance change of 1% in a 2 cm radius volume in the brain was modelled as the region of depolarization. A constant current of 100 microA was injected into the head from diametrically opposite electrodes. The model predicts that the standing magnetic field is about 10 pT and changed by about 3 fT (0.03%) on depolarization. The spectral noise density in a typical MEG system in the frequency band 1-100 Hz is about 7 fT, so this places the change at the limit of detectability. This is similar to electrical recording, as in conventional EIT systems, but there may be advantages to MEG in that the magnetic field directly traverses the skull and instrumentation errors from the electrode-skin interface will be obviated.

Modelling cardiac signal as a confound in EEG-fMRI and its application in focal epilepsy studies.

Cardiac noise has been shown to reduce the sensitivity of functional Magnetic Resonance Imaging (fMRI) to an experimental effect due to its confounding presence in the blood oxygenation level-dependent (BOLD) signal. Its effect is most severe in particular regions of the brain and a method is yet to take it into account in routine fMRI analysis. This paper reports the development of a general and robust technique to improve the reliability of EEG-fMRI studies to BOLD signal correlated with interictal epileptiform discharges (IEDs). In these studies, ECG is routinely recorded, enabling cardiac effects to be modelled, as effects of no interest. Our model is based on an over-complete basis set covering a linear relationship between cardiac-related MR signal and the phase of the cardiac cycle or time after pulse (TAP). This method showed that, on average, 24.6 +/- 10.9% of grey matter voxels contained significant cardiac effects and 22.3 +/- 24.1% of those voxels exhibiting significantly IED-correlated BOLD signal also contained significant cardiac effects. We quantified the improvement of the TAP model over the original model, without cardiac effects, by evaluating changes in efficiency, with respect to estimating the contrast of the effects of interest. Over voxels containing significant, cardiac-related signal, efficiency was improved by 18.5 +/- 4.8%. Over the remaining voxels, no improvement was demonstrated. This suggests that, while improving sensitivity in particular regions of the brain, there is no risk that the TAP model will reduce sensitivity elsewhere.