Functional Subsets Research Articles

Characterizing Inferred Functional and Phenotypical States of Newly Diagnosed Acute Myeloid Leukemia from Single Cell Transcriptomic Profiling

Background: Acute myeloid leukemia (AML) is a heterogeneous disease, marked by leukemia stem cells (LSCs), which significantly contribute to treatment resistance and dismal prognosis. While appreciable efforts have been made to study the diversity of functional and phenotypic states of LSCs, integrating these states from inferred single cell profiling has not been explored. Moreover, the spatial distribution and variability of hierarchical leukemic states within diverse cytogenetic groups, and their potential connection to transcriptional profiles, remain understudied, highlighting a gap in our understanding of this complex disease. Methods: To investigate the heterogeneity across different cytogenetics,we performed single cell RNA profiling (scRNA) of bone marrow (BM) mononulear cells from 20 newly diagnosed adult AML patients with diploid (n=7), del5/5q (n=5), del7/7q (n=5) and double deletion (del5/5q & del7/7q; n=3). A total of 111,130 cells passed quality assessment, of which 56,168 (50.5%) cells were identified as AML cells by integrating flow cytometry, immunohistochemistry, copy number variation, and FISH with the scRNA expression profiles. Functional states of AML cells were predicted by a recently proposed hierarchy of AML LSCs representing distinct maturation states (Zeng et al Nat Med 2022). Phenotypical states were annotated by Symphony using a healthy BM and validated in newly sequenced healthy BM samples. We also applied deconvolution scRNA analysis with spatial GeoMx profiling to identify spatial location of primitive versus differentiated AML cells. Results: Differential gene expression and gene set enrichment analysis (GSEA) revealed transcriptional and biological diversity across cytogenetic groups. Del7/7q cells showed high expression of human leukocyte antigen (HLA) genes and CD74, consistent with enrichment for a inflammatory phenotype revealed by GSEA. Del5/5q group demonstrated enrichment in proliferative pathways and heat shock proteins. Some diploid cells showed high expression of monocytic markers, while the others were highly expressing GMP markers, indicating the co-existence of different subclones. Differentiation states of leukemic cells are reflected in the hierarchy of cellular compositions. There is a diverse spectrum of cell types within each cytogenetic group and each patient. However, AML cells from diploid patients were enriched for GMP-like and monocyte-like cells, while phenotypically HSC-like cells showed an incremental trend in the sequence of diploid, del5/5q, del7/7q, and double deletion (Figure 1A). The inferred functional LSC states in our data also showed diverse distribution across cytogenetic groups, with nondiploid cells harboring more LSC. We also evaluated the biological differences of cytogenetic groups within each phenotypical and functional subset. Our data revealed consistent upregulation of proliferation in del5/5q and inflammation in del7/7q with double deletion preserving both features. However, diploid cells were downregulated in almost all. These data suggest cytogenetics as a major driver of ITH even for phenotypically or functionally similar AML cells. By correlating phenotypical axis with LSC states, we found a shared transcriptional program in LSC-like states across phenotypical axis except for Mono-like and DC-like cells, demonstrating the broad distribution of inferred functional LSC spanning the phenotypical axis from primitive to differentiated cells (Figure 1B). This was also observed in other LSC signatures, suggesting that AML cells with LSC capacity exist across the phenotypic of HSC-like cells to more phenotypically differentiated cells. We then performed spatial deconvolution using GeoMx of CD34 + or CD68 + myeloid areas of interest using the phenotypical signature. GeoMx revealed that primitive cells were more likely to be proximal to bone, while more differentiated states were enriched in distal region from the bone, indicating a spatial migration at time of differentiation. Conclusions: ScRNA profiling of newly diagnosed AML revealed the existence of heterogeneous LSC functional states underlying varying degrees of differentiation. We identified cytogenetics as a major source of ITH. Also, primitive cells were likely to localize to bone regions. These findings provide new insights in developing specific therapeutic strategies to improve clinical outcomes.

Inoculation with plant growth-promoting rhizobacteria improves seagrass Thalassia hemprichii photosynthesis performance and shifts rhizosphere microbiome

Plant growth-promoting rhizobacteria (PGPR) inoculation is a crucial strategy for maintaining the sustainability of agriculture and presents a promising solution for seagrass ecological restoration in the face of disturbances. However, the possible roles and functions of PGPRs in the seagrass rhizosphere remain unclear. Here, we isolated rhizosphere bacterial strains from both reef and coastal regions and screened two PGPR isolates regarding their in vivo functional traits. Subsequently, we conducted microcosm experiments to elucidate how PGPR inoculation affected seagrass photosynthesis and shape within each rhizosphere microbiome. Both screened PGPR strains, Raoultella terrigena NXT28 and Bacillus aryabhattai XT37, excelled at expressing a specific subset of plant-beneficial functions and increased the photosynthetic rates of the seagrass host. PGPR inoculation not only decreased the abundance of sulfur-cycling bacteria, it also improved the abundance of putative iron-cycling bacteria in the seagrass rhizosphere. Strain XT37 successfully colonized the seagrass rhizosphere and displayed a leading role in microbial network structure. As a nitrogen-fixing bacteria, NXT28 showed potential to change the microbial nitrogen cycle with denitrification in the rhizosphere and alter dissimilatory and assimilatory nitrate reduction in bulk sediment. These findings have implications for the development of eco-friendly strategies aimed at exploiting microbial communities to confer sulfide tolerance in coastal seagrass ecosystem.

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.

Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complexes. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their motifs at near-fixed distances from a reference point, such as TSS. When combined with experimental data from CAGE, seqArchR can efficiently identify TSS-directing motifs, including known ones like TATA, DPE, and nucleosome positioning signal, as well as novel lineage-specific motifs and the function of genes associated with them. By using seqArchR on developmental time courses, we reveal how relative use of promoter architectures changes over time with stage-specific expression. seqArchR is a powerful tool for initial genome-wide classification and functional characterisation of promoters. Its use cases are more general: it can also be used to discover any motifs at near-fixed distances from a reference point, even if they are present in only a small subset of sequences.

Characterization of polarization states of canine monocyte derived macrophages.

Macrophages can reversibly polarize into multiple functional subsets depending on their micro-environment. Identification and understanding the functionality of these subsets is relevant for the study of immune‑related diseases. However, knowledge about canine macrophage polarization is still in its infancy. In this study, we polarized canine monocytes using GM-CSF/IFN- γ and LPS towards M1 macrophages or M-CSF and IL-4 towards M2 macrophages and compared them to undifferentiated monocytes (M0). Polarized M1 and M2 macrophages were thoroughly characterized for morphology, surface marker features, gene profiles and functional properties. Our results showed that canine M1-polarized macrophages obtained a characteristic large, roundish, or amoeboid shape, while M2-polarized macrophages were smaller and adopted an elongated spindle-like morphology. Phenotypically, all macrophage subsets expressed the pan-macrophage markers CD14 and CD11b. M1-polarized macrophages expressed increased levels of CD40, CD80 CD86 and MHC II, while a significant increase in the expression levels of CD206, CD209, and CD163 was observed in M2-polarized macrophages. RNAseq of the three macrophage subsets showed distinct gene expression profiles, which are closely associated with immune responsiveness, cell differentiation and phagocytosis. However, the complexity of the gene expression patterns makes it difficult to assign clear new polarization markers. Functionally, undifferentiated -monocytes, and M1- and M2- like subsets of canine macrophages can all phagocytose latex beads. M2-polarized macrophages exhibited the strongest phagocytic capacity compared to undifferentiated monocytes- and M1-polarized cells. Taken together, this study showed that canine M1 and M2-like macrophages have distinct features largely in parallel to those of well-studied species, such as human, mouse and pig. These findings enable future use of monocyte derived polarized macrophages particularly in studies of immune related diseases in dogs.

Data-driven turbulence modelling of inherently unsteady flow in stratified water storage tanks

The flow and thermal characteristics of thermal stratification appears in a wide range of industrial applications related to energy storage. In a previous study (Xu et al. submitted to Flow, Turbulence and Combustion), it has been shown that linear closure models in unsteady Reynolds averaged Navier–Stokes (RANS) calculations are unable to accurately capture the transient flow and thermal characteristics occurring in stratified water storage tank configurations. In the current study, we extend a data-driven framework to develop turbulence and heat flux closures for a three-dimensional (3D) geometry of a stratified water storage tank, using data from a highly resolved large eddy simulation. The transient high-fidelity data set is partitioned into several time-intervals used for closure development and testing. In detail, we first present the model formulations for 3D buoyant flow. We then use the reference data to extract the most suitable input features, i.e. variables used to regress the data driven model. In order to reduce the complexity of the resulting models and accelerate the training process, a recursive basis function elimination is performed, using alignment of the different basis functions with the target turbulence stress and heat flux as metric. Using the identified features and the subsets of basis functions, novel closures are then developed using a symbolic regression framework, based on Gene Expression Programming (GEP). Models are developed either for each time interval or for all intervals at once. The different machine-learnt turbulence and heat-flux closure models are then tested for two different tank configurations where the thermal stratification is affected by positively/negatively buoyant jets within simple or complex three-dimensional geometries. It is demonstrated that the extended GEP-based data-driven turbulence modelling approach is able to create models that can accurately predict flow with inherent unsteadiness in three dimensional complex-geometry cases.

The consensus of Chinese experts on refined analysis of immune cell subsets in peripheral blood by multi-parameter flow cytometry

The detection of immune cell subsets plays a very important role in the clinical diagnosis and treatment of various benign and malignant diseases and health management. In order to better carry out in-depth research on different functional immune cell subsets, establish reference intervals for clonality related indicators, establish special reference intervals for immune aging, individualized dynamic monitoring and treatment recovery, and discover the clinical significance of immune cells other than lymphocytes, it is urgent to analyze the peripheral blood immune cell subsets in a refined way. Multiparameter flow cytometry is an important technical method to detect immune cell subsets and evaluate immune function. In order to standardize the refined detection methods and protocols of peripheral blood immune cell subsets by flow cytometry, and further promote its application in clinical diagnosis and treatment of diseases and health management, Laboratory Medicine Committee of Chinese Association of Integrative Medicine (LMC-CAIM) organized experts to formulate this expert consensus.

Functional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation

Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.

Habenular functional connections are associated with depression state and modulated by ketamine

BackgroundDepression is a widespread mental health disorder with complex neurobiological underpinnings. The habenula, known as the ‘anti-reward center’, is thought to play a pivotal role in the pathophysiology of depression. This study aims to elucidate the association between the functional connections of the habenula and depression severity and to explore the modulation of these connections by ketamine. MethodsWe studied 177 participants from a 7-T resting-state functional magnetic resonance imaging subset of the Human Connectome Project dataset to determine the associations between the functional connections of the habenula and depression. Additionally, we analyzed 60 depressed patients from our ketamine database to conduct a preliminary study on alterations in the functional connections of the habenula after ketamine infusions. We also investigated whether the baseline functional connectivity of the habenula is linked to subsequent improvement in depression. ResultsWe found that functional connections between the habenula and the substantia nigra, as well as the ventral tegmental area were negatively correlated with depression scores and elevated after ketamine infusions. Furthermore, the connection between the right habenula and the right substantia nigra was negatively associated with the improvement of depression. LimitationsThe Human Connectome Project dataset primarily consists of data from healthy participants, with varying levels of depression scores. ConclusionThese results suggest that the habenula may facilitate depression by suppressing dopamine reward centers, and ketamine may relieve depression by disinhibiting these dopaminergic regions. This study may enhance our understanding of the neural underpinnings of depression and ketamine's antidepressant effects.

The change of Siglec-9 expression in peripheral blood NK cells of SFTS patients can affect the function of NK cells

ObjectivesTo investigate the changes and mechanism of Siglec-9 on NK cells in peripheral blood of patients with severe fever with thrombocytopenia syndrome (SFTS). MethodsFirst, we used single-cell RNA sequencing to analyze the frequency of NK cells in Peripheral Blood Mononuclear Cells (PBMCs) of SFTS patients and healthy controls (HCs), as well as the differences in the genes on NK cells. Secondly, we analyzed the expression of Siglec-9 and other receptors on NK cells by flow cytometry. Thirdly, we analyzed the correlation between Siglec-9 on NK cells and DBV viral load in plasma. ResultsCompared with HCs, the frequency of NK cells in peripheral blood of SFTS patients was significantly decreased, and the activating receptors on NK cells were reduced. The expression of Siglec-9 on NK cells and the frequency of Siglec-9+NK cells decreased significantly in SFTS patients. The expression of Siglec-9 on CD16+CD56dim NK cells was negatively correlated with DBV viral load. In addition, Siglec-9+NK cells expressed higher levels of activating receptors and exhibited stronger effector functions than Siglec-9−NK cells. ConclusionsThe decreased expression of Siglec-9 on NK cells predicts NK cell dysfunction in SFTS patients, suggesting that Siglec-9 may be a potential marker for functional NK cell subsets in SFTS patients.

Functional and transcriptional heterogeneity within the massively expanding HLADR+CD38+ CD8 T cell population in acute febrile dengue patients.

CD8 T cells play a crucial role in protecting against intracellular pathogens such as viruses by eliminating infected cells and releasing anti-viral cytokines such as interferon gamma (IFNγ). Consequently, there is significant interest in comprehensively characterizing CD8 T cell responses in acute dengue febrile patients. Previous studies, including our own, have demonstrated that a discrete population of CD8 T cells with HLADR+ CD38+ phenotype undergoes massive expansion during the acute febrile phase of natural dengue virus infection. Although about a third of these massively expanding HLADR+ CD38+ CD8 T cells were also CD69high when examined ex vivo, only a small fraction of them produced IFNγ upon in vitro peptide stimulation. Therefore, to better understand such functional diversity of CD8 T cells responding to dengue virus infection, it is important to know the cytokines/chemokines expressed by these peptide-stimulated HLADR+CD38+ CD8 T cells and the transcriptional profiles that distinguish the CD69+IFNγ+, CD69+IFNγ-, and CD69-IFNγ- subsets.

Diverging Maternal and Cord Antibody Functions From SARS-CoV-2 Infection and Vaccination in Pregnancy.

Maternal immunity impacts the infant, but how is unclear. To understand the implications of the immune exposures of vaccination and infection in pregnancy for neonatal immunity, we evaluated antibody functions in paired peripheral maternal and cord blood. We compared those who in pregnancy received mRNA coronavirus disease 2019 (COVID-19) vaccine, were infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the combination. We found that vaccination enriched a subset of neutralizing activities and Fc effector functions that was driven by IgG1 and was minimally impacted by antibody glycosylation in maternal blood. In paired cord blood, maternal vaccination also enhanced IgG1. However, Fc effector functions compared to neutralizing activities were preferentially transferred. Moreover, changes in IgG posttranslational glycosylation contributed more to cord than peripheral maternal blood antibody functional potency. These differences were enhanced with the combination of vaccination and infection as compared to either alone. Thus, Fc effector functions and antibody glycosylation highlight underexplored maternal opportunities to safeguard newborns.

Developmental adaptations of γδ T cells and B cells in blood and intestinal mucosa from birth until weaning in Holstein bull calves

This study aimed to characterize the development of systemic and colon tissue resident B and γδ T cells in newborn calves from birth until weaning. At birth, calves have limited capacity to initiate immune responses, and the immune system gradually matures over time. Gamma delta (γδ) T cells are an important lymphocyte subset in neonatal calves that confer protection and promote immune tolerance. A total of 36 newborn calves were enrolled in a longitudinal study to characterize how systemic and colon tissue resident B and γδ T cells develop from birth until weaning. Blood and colon biopsy samples were collected on d 2, 28, and 42 to determine the proportions of various B and γδ T cell subsets by flow cytometry. We classified γδ T cells into different functional subsets according to the level of expression intensity of the coreceptors WC1.1 (effector function) and WC1.2 (regulatory function). Furthermore, naive B cells were classified based on the expression IgM receptor, and activation state was determined based on expression of CD21 and CD32, 2 receptors with opposing signals involved in B cell activation in early life. Additional colon biopsy samples were used for 16S sequencing, and microbial diversity data are reported. At birth, γδ T cells were the most abundant lymphocyte population in blood, accounting for 58.5% of the lymphocyte pool, after which the proportions of these cells declined to 38.2% after weaning. The proportion of γδ T cells expressing WC1.1 decreased by 50% from d 2 to d 28, whereas no change was observed in the expression of WC1.2. In the colon, there was a 50% increase of γδ T cells after weaning and the proportion of WC1.2+ γδ T cells doubled from d 28 to 42. The proportion of IgM+ B lymphocytes in blood increased from 23.6% at birth to 30% after weaning, were the proportion of B cells expressing CD21 increased by 25%, while the proportion of B cells expressing CD32 decreased by 30%. While no changes were observed for the overall proportion of IgM+ B lymphocytes in the colon, there was a 6-fold increase in the proportion of CD21+ B cells from pre- (d 28) to postweaning (d 42). Microbial diversity increased from d 2 of life to 28 and declined abruptly after weaning. The reduction in microbial diversity during weaning was negatively correlated with the increase in all γδ T cell subsets and CD21+ B cells. These data suggest that developmental adaptations after birth coordinate expansion of γδ T cells to provide early systemic protection, as well as to steer immune tolerance, while B cells mature over time. Additionally, the increase of colonic γδ T cells on d 42 suggests a protective role of these cells during weaning.

OMIP-095: 40-Color spectral flow cytometry delineates all major leukocyte populations in murine lymphoid tissues.

High-dimensional immunoprofiling is essential for studying host response to immunotherapy, infection, and disease in murine model systems. However, the difficulty of multiparameter panel design combined with a lack of existing murine tools has prevented the comprehensive study of all major leukocyte phenotypes in a single assay. Herein, we present a 40-color flow cytometry panel for deep immunophenotyping of murine lymphoid tissues, including the spleen, blood, Peyer's patches, inguinal lymph nodes, bone marrow, and thymus. This panel uses a robust set of surface markers capable of differentiating leukocyte subsets without the use of intracellular staining, thus allowing for the use of cells in downstream functional experiments or multiomic analyses. Our panel classifies T cells, B cells, natural killer cells, innate lymphoid cells, monocytes, macrophages, dendritic cells, basophils, neutrophils, eosinophils, progenitors, and their functional subsets by using a series of co-stimulatory, checkpoint, activation, migration, and maturation markers. This tool has a multitude of systems immunology applications ranging from serial monitoring of circulating blood signatures to complex endpoint analysis, especially in pre-clinical settings where treatments can modulate leukocyte abundance and/or function. Ultimately, this 40-color panel resolves a diverse array of immune cells on the axes of time, tissue, and treatment, filling the niche for a modern tool dedicated to murine immunophenotyping.

An exact estimate of the third Hankel determinants for functions inverse to convex functions

Invesigation of bounds for Hankel determinat of analytic univalent functions is prominent intrest of many researcher from early twenth century to study geometric properties. Many authors obtained non sharp upper bound of third Hankel determinat for different subclasses of analytic univalent functions until Kwon et al. obtained exact estimation of the fourth coefficeient of Caratheodory class. Recently authors made use of an exact estimation of the fourth coefficient, well known second and third coefficient of Caratheodory class obtained sharp bound for the third Hankel determinant associated with subclasses of analytic univalent functions. Let $w=f(z)=z+a_{2}z^{2}+\cdots$ be analytic in the unit disk $\mathbb{D}=\{z\in\mathbb{C}:|z|<1\}$, and $\mathcal{S}$ be the subclass of normalized univalent functions with $f(0)=0$, and $f'(0)=1$. Let $z=f^{-1}$ be the inverse function of $f$, given by $f^{-1}(w)=w+t_2w^2+\cdots$ for some $|w|<r_o(f)$. Let $\mathcal{S}^c\subset\mathcal{S}$ be the subset of convex functions in $\mathbb{D}$. In this paper, we estimate the best possible upper bound for the third Hankel determinant for the inverse function $z=f^{-1}$ when $f\in \mathcal{S}^c$.Let $\mathcal{S}^c$ be the class of convex functions. We prove the following statements (Theorem):If $f\in$ $\mathcal{S}^c$, then\begin{equation*}\big|H_{3,1}(f^{-1})\big| \leq \frac{1}{36}\end{equation*} and the inequality is attained for $p_0(z)=(1+z^3)/(1-z^3).$

Multi-objective and machine learning strategies for addressing the Water–Energy–Waste nexus in the design of energy systems

This paper presents a multi-objective strategy coupled with fuzzy C-means to address synergies and conflicts around the water–energy–waste nexus. The proposal deals with an optimal design and operation scheme in a multi-objective framework where the objective functions are linked to the nexus. The objective functions are normalized to obtain subsets of functions that are used to assess the performance of the nexus and compute trade-off optimal solutions. The soft clustering algorithm is used to determine levels of synergy among Pareto optimal solutions. The proposed strategy has the potential to address problems with many-objective functions, in which the Pareto front has representation limitations, allowing for the identification of conflicts. The soft clustering algorithm indicates different levels of synergy among the Pareto optimal solutions based on the level of membership. The focus of the analysis is on distributed generation systems. As a demonstration, the coupling of a combined heat and power unit with a biodigester and a thermal storage system, interconnected to the local grid. The objective functions, used as descriptors of the nexus, are the use of waste, energy efficiency and water consumption, which are used with the economic performance of the system to configure a problem of many-objective functions.

A Constructive Approach for Threshold Function Identification

Threshold Function (TF) is a subset of Boolean function that can be represented with a single linear threshold gate (LTG). In the research about threshold logic, the identification of TF is an important task that determines whether a given function is a TF or not. In this article, we propose a sufficient and necessary condition for a function being a TF. With the proposed sufficient and necessary condition, we devise a TF identification algorithm. The experimental results show that the proposed approach saves 80% CPU time for identifying all the 8-input NP-class TFs as compared with the state-of-the-art. Furthermore, the LTGs corresponding to the identified TFs obtained by the proposed approach have smaller weights and threshold values than the state-of-the-art.

Bernstein–Remez inequality for algebraic functions: A topological approach

By taking full advantage of the structure of complex algebraic curves and by using compactness arguments, in this paper we give a self-contained proof that holomorphic algebraic functions verify a uniform Bernstein–Remez inequality. Namely, their growth over a bounded, open, complex set is uniformly controlled by their size on a compact complex subset of sufficiently high cardinality. Up to our knowledge, the first known demonstration on the existence of such an inequality for a specific subset of algebraic functions is contained in Nekhoroshev’s 1973 breakthrough on the genericity of close-to-integrable Hamiltonian systems that are stable over long time. Despite its pivotal rôle, this passage of Nekhoroshev’s proof has remained unnoticed so far. This work aims at extending and generalizing Nekhoroshev’s arguments to a modern framework. We stress the fact that our proof is different from the one contained in Roytwarf and Yomdin’s seminal work (1998), where Bernstein-type inequalities are proved for several classes of functions.

Complement C1q essential for aeroallergen sensitization via CSF1R+ conventional dendritic cells type 2

Dendritic cells (DCs) are heterogeneous, comprising multiple subsets with unique functional specifications. Our previous work has demonstrated that the specific conventional type 2 DC subset, CSF1R+cDC2s, plays a critical role in sensing aeroallergens. It remains to be understood how CSF1R+cDC2s recognize inhaled allergens. We sought to elucidate the transcriptomic programs and receptor-ligand interactions essential for function of this subset in allergen sensitization. We applied single-cell RNA sequencing to mouse lung DCs. Conventional DC-selective knockout mouse models were employed, and mice were subjected to inhaled allergen sensitization with multiple readouts of asthma pathology. Under the clinical arm of this work, human lung transcriptomic data were integrated with mouse data, and bronchoalveolar lavage (BAL) specimens were collected from subjects undergoing allergen provocation, with samples assayed for C1q. We found that C1q is selectively enriched in lung CSF1R+cDC2s, but not in other lung cDC2 or cDC1 subsets. Depletion of C1q in conventional DCs significantly attenuates allergen sensing and features of asthma. Additionally, we found that C1q binds directly to human dust mite allergen, and the C1q receptor CD91 (LRP1) is required for lung CSF1R+cDC2s to recognize the C1q-allergen complex and induce allergic lung inflammation. Lastly, C1q is enriched in human BAL samples following subsegmental allergen challenge, and human RNA sequencing data demonstrate close homology between lung IGSF21+DCs and mouse CSF1R+cDC2s. C1q is secreted from the CSF1R+cDC2 subset among conventional DCs. Our data indicate that the C1q-LRP1 axis represents a candidate for translational therapeutics in the prevention and suppression of allergic lung inflammation.

Longitudinal analysis of memory Tfh cells and antibody response following CoronaVac vaccination.

The inactivated vaccine CoronaVac is one of the most widely used COVID-19 vaccines globally. However, the longitudinal evolution of the immune response induced by CoronaVac remains elusive compared with other vaccine platforms. Here, we recruited 88 healthy individuals who received 3 doses of CoronaVac vaccine. We longitudinally evaluated their polyclonal and antigen-specific CD4+ T cells and neutralizing antibody response after receiving each dose of vaccine for over 300 days. Both the second and third doses of vaccine induced robust spike-specific neutralizing antibodies, with a third vaccine further increasing the overall magnitude of antibody response and neutralization against Omicron sublineages B.1.1.529, BA.2, BA.4/BA.5, and BA.2.75.2. Spike-specific CD4+ T cells and circulating T follicular helper (cTfh) cells were markedly increased by the second and third dose of CoronaVac vaccine, accompanied by altered composition of functional cTfh cell subsets with distinct effector and memory potential. Additionally, cTfh cells were positively correlated with neutralizing antibody titers. Our results suggest that CoronaVac vaccine-induced spike-specific T cells are capable of supporting humoral immunity for long-term immune protection.

Encoding of data sets and algorithms

In many high-impact applications, it is important to ensure the quality of the output of a machine learning algorithm as well as its reliability in comparison to the complexity of the algorithm used. In this paper, we have initiated a mathematically rigorous theory to decide which models (algorithms applied on data sets) are close to each other in terms of certain metrics, such as performance and the complexity level of the algorithm. This involves creating a grid on the hypothetical spaces of data sets and algorithms so as to identify a finite set of probability distributions from which the data sets are sampled and a finite set of algorithms. A given threshold metric acting on this grid will express the nearness (or statistical distance) of each algorithm and data set of interest to any given application. A technically difficult part of this project is to estimate the so-called metric entropy of a compact subset of functions of infinitely many variables that arise in the definition of these spaces.