Transposable elements regulate thymus development and function

Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.

On Net Water Uptake in Posttraumatic Ischemia Foci

BACKGROUND

The influence of cerebral edema and resultant secondary complications on the clinical outcome of traumatic brain injury (TBI) is well known. Clinical studies of brain water homeostasis dynamics in TBI are limited, which determines the relevance of our work. The purpose is to study changes in brain water homeostasis after TBI of varying severity compared to corresponding cerebral microcirculation parameters.

MATERIALS

This non-randomized retrospective single-center study complies with the Helsinki Declaration for patient's studies. The study included 128 patients with posttraumatic ischemia (PCI) after moderate-to-severe TBI in the middle cerebral artery territory who were admitted to the hospital between July 2015 and February 2022. PCI was evaluated by perfusion computed tomography (CT), and brain edema was determined using net water uptake (NWU) on baseline CT images. The patients were allocated according to Marshall's classification. Multivariate linear regression models were performed to analyze data.

RESULTS

NWU in PCI areas were significantly higher than in patients with its absence (8.1% vs. 4.2%, accordingly; p < 0.001). In the multivariable regression analysis, the mean transit time increase was significantly and independently associated with higher NWU (R2 = 0.089, p < 0.01). In the PCI zone, cerebral blood flow, cerebral blood volume, and time to peak were not significantly associated with NWU values (p > 0.05). No significant differences were observed between the NWU values in PCI foci in different Marshall groups (p = 0.308).

CONCLUSION

Marshall's classification does not predict the progression of posttraumatic ischemia. The blood passage delays through the cerebral microvascular bed is associated with brain tissue water content increase in the PCI focus.

Two types of human TCR differentially regulate reactivity to self and non-self antigens

Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are reported as disease-associated. Thus, 10%–30% of most frequent cord blood TCRs are associated with common pathogens and autoantigens. TDT-dependent TCRs present distinct structural features and are less shared among subjects. TDT-dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.

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Over 10⁸ TCR CDR3 sequences from ∼10³ individuals and 7 cohorts were analyzed

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The TCR repertoire is composed of two layers: neonatal and TDT-dependent layer

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∼70% of frequent cord blood TCRs are associated with common pathogens

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Acute graft-vs-host disease correlates with a high proportion of TDT-dependent TCRs

UM171-Expanded Cord Blood Transplants Support Robust T Cell Reconstitution with Low Rates of Severe Infections

Rapid T cell reconstitution following hematopoietic stem cell transplantation (HSCT) is essential for protection against infections and has been associated with lower incidence of chronic graft-versus-host disease (cGVHD), relapse, and transplant-related mortality (TRM). While cord blood (CB) transplants are associated with lower rates of cGVHD and relapse, their low stem cell content results in slower immune reconstitution and higher risk of graft failure, severe infections, and TRM. Recently, results of a phase I/II trial revealed that single UM171-expanded CB transplant allowed the use of smaller CB units without compromising engraftment (www.clinicaltrials.gov, NCT02668315). We assessed T cell reconstitution in patients who underwent transplantation with UM171-expanded CB grafts and retrospectively compared it to that of patients receiving unmanipulated CB transplants. While median T cell dose infused was at least 2 to 3 times lower than that of unmanipulated CB, numbers and phenotype of T cells at 3, 6, and 12 months post-transplant were similar between the 2 cohorts. T cell receptor sequencing analyses revealed that UM171 patients had greater T cell diversity and higher numbers of clonotypes at 12 months post-transplant. This was associated with higher counts of naive T cells and recent thymic emigrants, suggesting active thymopoiesis and correlating with the demonstration that UM171 expands common lymphoid progenitors in vitro. UM171 patients also showed rapid virus-specific T cell reactivity and significantly reduced incidence of severe infections. These results suggest that UM171 patients benefit from rapid T cell reconstitution, which likely contributes to the absence of moderate/severe cGVHD, infection-related mortality, and late TRM observed in this cohort.

Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition

MOTIVATION

The recent development of sequencing technologies revolutionized our understanding of the inner workings of the cell as well as the way disease is treated. A single RNA sequencing (RNA-Seq) experiment, however, measures tens of thousands of parameters simultaneously. While the results are information rich, data analysis provides a challenge. Dimensionality reduction methods help with this task by extracting patterns from the data by compressing it into compact vector representations.

RESULTS

We present the factorized embeddings (FE) model, a self-supervised deep learning algorithm that learns simultaneously, by tensor factorization, gene and sample representation spaces. We ran the model on RNA-Seq data from two large-scale cohorts and observed that the sample representation captures information on single gene and global gene expression patterns. Moreover, we found that the gene representation space was organized such that tissue-specific genes, highly correlated genes as well as genes participating in the same GO terms were grouped. Finally, we compared the vector representation of samples learned by the FE model to other similar models on 49 regression tasks. We report that the representations trained with FE rank first or second in all of the tasks, surpassing, sometimes by a considerable margin, other representations.

AVAILABILITY AND IMPLEMENTATION

A toy example in the form of a Jupyter Notebook as well as the code and trained embeddings for this project can be found at: https://github.com/TrofimovAssya/FactorizedEmbeddings.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

BACKGROUND

Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed in embryonic stem cells (ESCs) and germline cells but are repressed in differentiated somatic cells. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a system-level evaluation of their expression in human tissues is lacking.

METHODS

Using RNA sequencing data, we analyzed ERE expression in 32 human tissues and cell types, including medullary thymic epithelial cells (mTECs). A tissue specificity index was computed to identify tissue-restricted ERE families. We also analyzed the transcriptome of mTECs in wild-type and autoimmune regulator (AIRE)-deficient mice. Finally, we developed a proteogenomic workflow combining RNA sequencing and mass spectrometry (MS) in order to evaluate whether EREs might be translated and generate MHC I-associated peptides (MAP) in B-lymphoblastoid cell lines (B-LCL) from 16 individuals.

RESULTS

We report that all human tissues express EREs, but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. ERE expression was particularly high in two MHC I-deficient tissues (ESCs and testis) and one MHC I-expressing tissue, mTECs. In mutant mice, we report that the exceptional expression of EREs in mTECs was AIRE-independent. MS analyses identified 103 non-redundant ERE-derived MAPs (ereMAPs) in B-LCLs. These ereMAPs preferentially derived from sense translation of intronic EREs. Notably, detailed analyses of their amino acid composition revealed that ERE-derived MAPs presented homology to viral MAPs.

CONCLUSIONS

This study shows that ERE expression in somatic tissues is more pervasive and heterogeneous than anticipated. The high and diversified expression of EREs in mTECs and their ability to generate MAPs suggest that EREs may play an important role in the establishment of self-tolerance. The viral-like properties of ERE-derived MAPs suggest that those not expressed in mTECs can be highly immunogenic.

Molecular-Physiological Aspects of Regulatory Effect of Peptide Retinoprotectors

Retinal diseases were always difficult problem for clinical ophthalmology. Modern methods of their treatment only decrease risk of complications, however in Russia was created better technology for this purpose: peptide bioregulators, which were made by sequential adding of amino acids one to another, binding with the promoter region of genes, and promoting retinoprotective effect by regulation of their expression, improving the state of the retina.

Validation of a deformable image registration technique for cone beam CT-based dose verification

PURPOSE

As radiation therapy evolves toward more adaptive techniques, image guidance plays an increasingly important role, not only in patient setup but also in monitoring the delivered dose and adapting the treatment to patient changes. This study aimed to validate a method for evaluation of delivered intensity modulated radiotherapy (IMRT) dose based on multimodal deformable image registration (dir) for prostate treatments.

METHODS

A pelvic phantom was scanned with CT and cone-beam computed tomography (CBCT). Both images were digitally deformed using two realistic patient-based deformation fields. The original CT was then registered to the deformed CBCT resulting in a secondary deformed CT. The registration quality was assessed as the ability of the dir method to recover the artificially induced deformations. The primary and secondary deformed CT images as well as vector fields were compared to evaluate the efficacy of the registration method and it's suitability to be used for dose calculation. plastimatch, a free and open source software was used for deformable image registration. A B-spline algorithm with optimized parameters was used to achieve the best registration quality. Geometric image evaluation was performed through voxel-based Hounsfield unit (HU) and vector field comparison. For dosimetric evaluation, IMRT treatment plans were created and optimized on the original CT image and recomputed on the two warped images to be compared. The dose volume histograms were compared for the warped structures that were identical in both warped images. This procedure was repeated for the phantom with full, half full, and empty bladder.

RESULTS

The results indicated mean HU differences of up to 120 between registered and ground-truth deformed CT images. However, when the CBCT intensities were calibrated using a region of interest (ROI)-based calibration curve, these differences were reduced by up to 60%. Similarly, the mean differences in average vector field lengths decreased from 10.1 to 2.5 mm when CBCT was calibrated prior to registration. The results showed no dependence on the level of bladder filling. In comparison with the dose calculated on the primary deformed CT, differences in mean dose averaged over all organs were 0.2% and 3.9% for dose calculated on the secondary deformed CT with and without CBCT calibration, respectively, and 0.5% for dose calculated directly on the calibrated CBCT, for the full-bladder scenario. Gamma analysis for the distance to agreement of 2 mm and 2% of prescribed dose indicated a pass rate of 100% for both cases involving calibrated CBCT and on average 86% without CBCT calibration.

CONCLUSIONS

Using deformable registration on the planning CT images to evaluate the IMRT dose based on daily CBCTs was found feasible. The proposed method will provide an accurate dose distribution using planning CT and pretreatment CBCT data, avoiding the additional uncertainties introduced by CBCT inhomogeneity and artifacts. This is a necessary initial step toward future image-guided adaptive radiotherapy of the prostate.

Differential Features of AIRE-Induced and AIRE-Independent Promiscuous Gene Expression in Thymic Epithelial Cells

Establishment of self-tolerance in the thymus depends on promiscuous expression of tissue-restricted Ags (TRA) by thymic epithelial cells (TEC). This promiscuous gene expression (pGE) is regulated in part by the autoimmune regulator (AIRE). To evaluate the commonalities and discrepancies between AIRE-dependent and -independent pGE, we analyzed the transcriptome of the three main TEC subsets in wild-type and Aire knockout mice. We found that the impact of AIRE-dependent pGE is not limited to generation of TRA. AIRE decreases, via non-cell autonomous mechanisms, the expression of genes coding for positive regulators of cell proliferation, and it thereby reduces the number of cortical TEC. In mature medullary TEC, AIRE-driven pGE upregulates non-TRA coding genes that enhance cell-cell interactions (e.g., claudins, integrins, and selectins) and are probably of prime relevance to tolerance induction. We also found that AIRE-dependent and -independent TRA present several distinctive features. In particular, relative to AIRE-induced TRA, AIRE-independent TRA are more numerous and show greater splicing complexity. Furthermore, we report that AIRE-dependent versus -independent TRA project nonredundant representations of peripheral tissues in the thymus.

Immunoproteasomes shape the transcriptome and regulate the function of dendritic cells (IRM7P.476)

Background: By regulating protein degradation, constitutive proteasomes (CPs) regulate practically all fundamental cellular processes. Vertebrates also express immunoproteasomes (IPs), but the only well-established non-redundant role for IPs is their enhanced ability to generate peptides for MHC-I presentation. Results: Here we show that IPs regulate the expression of 8,104 genes in maturing bone marrow-derived dendritic cells (DCs). IPs regulated transcription of many mRNAs and maturation of a subset of them. These genes were separated into 15 different kinetic patterns, and Gene-Ontology analysis revealed enrichment linked to immune functions and housekeeping cellular processes, highlighting the complexity of the transcriptional cascade regulated by IPs. Notably, IPs’ impact on transcription was mediated through the non-redundant regulation of critical immune-related pathways, such as Nf-kB, STATs and IRFs. Furthermore, even when loaded with optimal amounts of SIINFEKL, IP-deficient DCs were inefficient for in vivo priming of OT-1 T cells. Conclusion: Our study shows that the role of IPs is not limited to antigen processing and highlights a new and critical role for IPs in regulation of gene expression. The dramatic impact of IPs on the transcriptional landscape could explain the various immune and non-immune phenotypes observed in vertebrates with IP-deficiency or -mutation.

Rejection of leukemic cells requires antigen-specific T cells with high functional avidity

In a context where injection of antigen (Ag)-specific T cells probably represents the future of leukemia immunotherapy, identification of optimal target Ags is crucial. We therefore sought to discover a reliable marker for selection of the most potent Ags. To this end, (1) we immunized mice against 8 individual Ags: 4 minor histocompatibility Ags (miHAs) and 4 leukemia-associated Ags (LAAs) that were overexpressed on leukemic relative to normal thymocytes; (2) we assessed their ability to reject EL4 leukemic cells; and (3) we correlated the properties of our Ags (and their cognate T cells) with their ability to induce protective antileukemic responses. Overall, individual miHAs instigated more potent antileukemic responses than LAAs. Three features had no influence on the ability of primed T cells to reject leukemic cells: (1) MHC-peptide affinity; (2) the stability of MHC-peptide complexes; and (3) epitope density at the surface of leukemic cells, as assessed using mass spectrometry. The cardinal feature of successful Ags is that they were recognized by high-avidity CD8 T cells that proliferated extensively in vivo. Our work suggests that in vitro evaluation of functional avidity represents the best criterion for selection of Ags, which should be prioritized in clinical trials of leukemia immunotherapy.

The rationale for intensity-modulated proton therapy in geometrically challenging cases

Intensity-modulated proton therapy (IMPT) delivered with beam scanning is currently available at a limited number of proton centers. However, a simplified form of IMPT, the technique of field 'patching', has long been a standard practice in proton therapy centers. In field patching, different parts of the target volume are treated from different directions, i.e., a part of the tumor gets either full dose from a radiation field, or almost no dose. Thus, patching represents a form of binary intensity modulation. This study explores the limitations of the standard binary field patching technique, and evaluates possible dosimetric advantages of continuous dose modulations in IMPT. Specifics of the beam delivery technology, i.e., pencil beam scanning versus passive scattering and modulation, are not investigated. We have identified two geometries of target volumes and organs at risk (OAR) in which the use of field patching is severely challenged. We focused our investigations on two patient cases that exhibit these geometries: a paraspinal tumor case and a skull-base case. For those cases we performed treatment planning comparisons of three-dimensional conformal proton therapy (3DCPT) with field patching versus IMPT, using commercial and in-house software, respectively. We also analyzed the robustness of the resulting plans with respect to systematic setup errors of ±1 mm and range errors of ±2.5 mm. IMPT is able to better spare OAR while providing superior dose coverage for the challenging cases identified above. Both 3DCPT and IMPT are sensitive to setup errors and range uncertainties, with IMPT showing the largest effect. Nevertheless, when delivery uncertainties are taken into account IMPT plans remain superior regarding target coverage and OAR sparing. On the other hand, some clinical goals, such as the maximum dose to OAR, are more likely to be unmet with IMPT under large range errors. IMPT can potentially improve target coverage and OAR sparing in challenging cases, even when compared with the relatively complicated and time consuming field patching technique. While IMPT plans tend to be more sensitive to delivery uncertainties, their dosimetric advantage generally holds. Robust treatment planning techniques may further reduce the sensitivity of IMPT plans.

Search for Lorentz and CPT violation effects in Muon spin precession

The spin precession frequency of muons stored in the (g-2) storage ring has been analyzed for evidence of Lorentz and CPT violation. Two Lorentz and CPT violation signatures were searched for a nonzero delta omega a(=omega a mu+ - omega a mu-) and a sidereal variation of omega a mu+/-). No significant effect is found, and the following limits on the standard-model extension parameters are obtained: bZ = -(1.0+/-1.1) x 10(-23) GeV; (m mu dZ0 + HXY)=(1.8+/-6.0) x 10(-23) GeV; and the 95% confidence level limits b perpendicular mu+ <1.4 x 10(-24) GeV and b perpendicular mu- <2.6 x 10(-24) GeV.