Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes.

Noncoding genetic variation drives phenotypic diversity, but underlying mechanisms and affected cell types are incompletely understood. Here, investigation of effects of natural genetic variation on the epigenomes and transcriptomes of Kupffer cells derived from inbred mouse strains identified strain-specific environmental factors influencing Kupffer cell phenotypes, including leptin signaling in Kupffer cells from a steatohepatitis-resistant strain. Cell-autonomous and non-cell-autonomous effects of genetic variation were resolved by analysis of F1 hybrid mice and cells engrafted into an immunodeficient host. During homeostasis, non-cell-autonomous trans effects of genetic variation dominated control of Kupffer cells, while strain-specific responses to acute lipopolysaccharide injection were dominated by actions of cis-acting effects modifying response elements for lineage-determining and signal-dependent transcription factors. These findings demonstrate that epigenetic landscapes report on trans effects of genetic variation and serve as a resource for deeper analyses into genetic control of transcription in Kupffer cells and macrophages in vitro.

SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity.

Spalt-like transcription factor 1 (SALL1) is a critical regulator of organogenesis and microglia identity. Here we demonstrate that disruption of a conserved microglia-specific super-enhancer interacting with the Sall1 promoter results in complete and specific loss of Sall1 expression in microglia. By determining the genomic binding sites of SALL1 and leveraging Sall1 enhancer knockout mice, we provide evidence for functional interactions between SALL1 and SMAD4 required for microglia-specific gene expression. SMAD4 binds directly to the Sall1 super-enhancer and is required for Sall1 expression, consistent with an evolutionarily conserved requirement of the TGFß and SMAD homologs Dpp and Mad for cell-specific expression of Spalt in the Drosophila wing. Unexpectedly, SALL1 in turn promotes binding and function of SMAD4 at microglia-specific enhancers while simultaneously suppressing binding of SMAD4 to enhancers of genes that become inappropriately activated in enhancer knockout microglia, thereby enforcing microglia-specific functions of the TGFß-SMAD signaling axis.

Human microglia maturation is underpinned by specific gene regulatory networks.

Microglia phenotypes are highly regulated by the brain environment, but the transcriptional networks that specify the maturation of human microglia are poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia and acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, in cerebral organoids, and following engraftment into humanized mice. Parallel development of computational approaches that considered transcription factor (TF) co-occurrence and enhancer activity allowed prediction of shared and state-specific gene regulatory networks associated with fetal and postnatal microglia. Additionally, many features of the human fetal-to-postnatal transition were recapitulated in a time-dependent manner following the engraftment of iPSC cells into humanized mice. These data and accompanying computational approaches will facilitate further efforts to elucidate mechanisms by which human microglia acquire stage- and disease-specific phenotypes.

Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis.

Tissue-resident and recruited macrophages contribute to both host defense and pathology. Multiple macrophage phenotypes are represented in diseased tissues, but we lack deep understanding of mechanisms controlling diversification. Here, we investigate origins and epigenetic trajectories of hepatic macrophages during diet-induced non-alcoholic steatohepatitis (NASH). The NASH diet induced significant changes in Kupffer cell enhancers and gene expression, resulting in partial loss of Kupffer cell identity, induction of Trem2 and Cd9 expression, and cell death. Kupffer cell loss was compensated by gain of adjacent monocyte-derived macrophages that exhibited convergent epigenomes, transcriptomes, and functions. NASH-induced changes in Kupffer cell enhancers were driven by AP-1 and EGR that reprogrammed LXR functions required for Kupffer cell identity and survival to instead drive a scar-associated macrophage phenotype. These findings reveal mechanisms by which disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct gene expression programs and corresponding functions.

Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity.

Tissue environment plays a powerful role in establishing and maintaining the distinct phenotypes of resident macrophages, but the underlying molecular mechanisms remain poorly understood. Here, we characterized transcriptomic and epigenetic changes in repopulating liver macrophages following acute Kupffer cell depletion as a means to infer signaling pathways and transcription factors that promote Kupffer cell differentiation. We obtained evidence that combinatorial interactions of the Notch ligand DLL4 and transforming growth factor-b (TGF-ß) family ligands produced by sinusoidal endothelial cells and endogenous LXR ligands were required for the induction and maintenance of Kupffer cell identity. DLL4 regulation of the Notch transcriptional effector RBPJ activated poised enhancers to rapidly induce LXRα and other Kupffer cell lineage-determining factors. These factors in turn reprogrammed the repopulating liver macrophage enhancer landscape to converge on that of the original resident Kupffer cells. Collectively, these findings provide a framework for understanding how macrophage progenitor cells acquire tissue-specific phenotypes.

Somatic mosaicism reveals clonal distributions of neocortical development.

The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.

Responsiveness of B cells is regulated by the hinge region of IgD.

Mature B cells express immunoglobulin M (IgM)- and IgD-isotype B cell antigen receptors, but the importance of IgD for B cell function has been unclear. By using a cellular in vitro system and corresponding mouse models, we found that antigens with low valence activated IgM receptors but failed to trigger IgD signaling, whereas polyvalent antigens activated both receptor types. Investigations of the molecular mechanism showed that deletion of the IgD-specific hinge region rendered IgD responsive to monovalent antigen, whereas transferring the hinge to IgM resulted in responsiveness only to polyvalent antigen. Our data suggest that the increased IgD/IgM ratio on conventional B-2 cells is important for preferential immune responses to antigens in immune complexes, and that the increased IgM expression on B-1 cells is essential for B-1 cell homeostasis and function.

How do children with focal epilepsies perceive the moment they realize that they are about to have a seizure? A pilot study.

PROBLEM: A seizure is a challenging situation for children with epilepsy. Little is known regarding the experience of children who perceive in advance that they are about to have a seizure. METHODS: From September 2020 to February 2021, we invited children with focal epilepsies aged 6-18 years to participate in a semi-structured interview. RESULTS: Of 52 children with focal epilepsies, 22 (42 %) said they perceive in advance that they are about to experience a seizure [11 with self-limited epilepsy with centro-temporal spikes (SELECTs), 11 with other focal epilepsies]. All 22/22 (100 %) children described physical symptoms such as headache or a numb feeling in one half of the body. Of those children, 17/22 (77 %) stated they try to do something about the seizure. Those strategies were perceived as helpful by 0/11 (0 %) children with SELECTs and 9/11 (86 %) children with other focal epilepsies (p < 0.001). Of the children with SELECTs 5/11 (45 %), and of those with other focal epilepsies 9/11 (86 %) stated they would like to know in the morning if they are to experience a seizure that day (n.s.). CONCLUSION: Children who perceive in advance that they are about to have a seizure are well able to describe their experience. Most children take measures to manage their seizures. Those measures were regarded as helpful by most children with other focal epilepsies, but by no child with SELECTs. Larger studies are necessary to determine the factors contributing to the child's perception as well as the nature of the support that they require.

Complementary and alternative medicine (CAM) is frequently used by parents for the treatment of functional constipation in children.

OBJECTIVES: Complementary and alternative medicine (CAM) has gained increasing attention as a supportive treatment for chronic diseases such as epilepsy, migraine, autism, and cancer in children. This study aimed to determine the frequency, motivation, and outcomes of CAM in children with functional constipation. METHODS: From January 2018 till September 2019, parents of patients (0-18 years) who were treated for functional constipation (ROME IV-criteria) at our colorectal center were asked to complete a questionnaire on the utilization of CAM. Demographic data and clinical assessments were documented and analyzed for patients with and without CAM treatment. RESULTS: A total of 115 patients were included (mean age: 5.1 years; 49% males), of whom 29 (25%) used CAM as an alternative (4/29,14%) or in addition to conventional therapy (CT), including osteopathy (48%), homeopathy (45%), and natural/herbal remedies (17%). The main reason parents reported for the use of CAM was the urge to leave no treatment option unattempted (76%). Multivariate analysis also identified persistent constipation under CT (72%), adverse effects of CT (24%), and parental use of CAM themselves (83%) as independent variables associated with CAM use. Parents reported positive changes in stool frequency (38%) and fecal incontinence (21%) with CAM. The vast majority (93%) plan to use CAM in the future, and even non-CAM users showed high interest (60%). CONCLUSION: One in four children with functional constipation receives CAM. Significant improvement in stool frequency and continence is missing in the majority. However, parental interest in CAM remains high. Physicians should be aware of CAM when counseling families for functional constipation in children.

Interviews with children and adolescents with epilepsy or asthma about the situation of their healthy siblings.

AIM: Chronic conditions can influence the situation of healthy siblings of affected children. We investigated the opinion of the affected child about the situation of their healthy sibling and the sibling relationship. METHODS: We performed a semi-structured interview with epilepsy or asthma patients aged 6-18 years and asked them to draw a picture: "Epilepsy/Asthma, my siblings and me." RESULTS: Of the 58 children with epilepsy, 67%, and of the 40 children with asthma, 60% thought that their siblings were worried about the condition. Among other aspects, they addressed helplessness during a seizure. Of the children with epilepsy, 83% and of those with asthma, 95% assumed that their siblings were not disadvantaged because of the participant's condition. Of the patients with epilepsy, 91% and of those with asthma, 93% thought that the sibling relationship would not be different without the condition. Of the participants with epilepsy, 86% and of those with asthma, 93% drew a picture; 30% with epilepsy and 14% with asthma visualised an interaction with their siblings in context of a seizure or episode of dyspnoea. CONCLUSION: According to the affected children, the condition worries their siblings but does not affect the siblings' lives or the sibling relationship.

N-linked glycosylation selectively regulates autonomous precursor BCR function.

Developing B cells express distinct classes of B cell antigen receptors (BCRs) that differ in their heavy chain (HC). Although only muHC is expressed in early stages, deltaHC-containing BCRs dominate on the surface of mature B cells. The reason for the tightly regulated expression of these receptors is poorly understood. Here we show that muHC was specifically required for precursor BCR (pre-BCR) function and that deltaHC was unable to form a functional pre-BCR. A conserved asparagine (N)-linked glycosylation site at position 46 (N46) in the first conserved domain of muHC was absolutely required for pre-BCR function, and swapping that domain with deltaHC resulted in a functional deltaHC-containing pre-BCR. When tested in the context of the BCR, muHC with a mutant N46 showed normal function, which indicated that N46-glycosylation is specifically required for pre-BCR function. Our results suggest an unexpected mode of pre-BCR function, in which binding of the surrogate light chain to N46 mediates autonomous crosslinking and, concomitantly, receptor formation.

Heterogeneity of HSCs in a Mouse Model of NASH.

BACKGROUND AND AIMS: In clinical and experimental NASH, the origin of the scar-forming myofibroblast is the HSC. We used foz/foz mice on a Western diet to characterize in detail the phenotypic changes of HSCs in a NASH model. APPROACH AND RESULTS: We examined the single-cell expression profiles (scRNA sequencing) of HSCs purified from the normal livers of foz/foz mice on a chow diet, in NASH with fibrosis of foz/foz mice on a Western diet, and in livers during regression of NASH after switching back to a chow diet. Selected genes were analyzed using immunohistochemistry, quantitative real-time PCR, and short hairpin RNA knockdown in primary mouse HSCs. Our analysis of the normal liver identified two distinct clusters of quiescent HSCs that correspond to their acinar position of either pericentral vein or periportal vein. The NASH livers had four distinct HSC clusters, including one representing the classic fibrogenic myofibroblast. The three other HSC clusters consisted of a proliferating cluster, an intermediate activated cluster, and an immune and inflammatory cluster. The livers with NASH regression had one cluster of inactivated HSCs, which was similar to, but distinct from, the quiescent HSCs. CONCLUSIONS: Analysis of single-cell RNA sequencing in combination with an interrogation of previous studies revealed an unanticipated heterogeneity of HSC phenotypes under normal and injured states.

Medicine and supplement use in infants, children, and adolescents depends on sex, age, and socioeconomic status: results of a German longitudinal population-based cohort study (LIFE Child).

Children and adolescents are exposed to medicines and supplements, but only a few studies have evaluated the actual intake in routine care. Thus, we performed a pharmacoepidemiological evaluation of a longitudinal population-based pediatric cohort study (LIFE Child) conducted at the University Hospital of Leipzig between 2014 and 2019. We analyzed all visits of the participants of the LIFE Child cohort between 1 January 2014 and 31 December 2019. Participants were asked to bring their medicines and supplements to their appointments at the study center. If they had not brought the preparations with them, attempts were made to obtain the relevant information during a telephone call after the visit to the study center. Furthermore, the participants and their parents were interviewed on medicine and supplement use and on sociodemographic and socioeconomic data during their visit to the study center. Associations of medicine and supplement use with age, sex, and socioeconomic status were analyzed using multivariate binary logistic regressions to obtain adjusted odds ratios (aOR) and 95% confidence intervals (95% CI). Furthermore, the number of the respective visit was included as possible confounder in the multivariate model. We included 3602 participants who visited the study center 11,906 times. The intake of 9759 medicines and supplements was recorded. Based on the evaluation of all study visits, 49% of the children and adolescents took at least one medicine or supplement. Self-medication accounted for 28% of the medicines and supplements. The prevalence of overall intake increased from 45% in 2014 to 53% in 2019 (aOR 2.63, 95% CI 2.23, 3.09). The prevalence was the highest (77%) in children aged 0- < 3 years, owing mainly to vitamin D. The prevalence of medicine use was higher in females (40%; aOR 1.18, 95% CI 1.10, 1.28) than in males (35%), owing mainly to the intake of ibuprofen and hormonal contraceptives in adolescent females. A high socioeconomic status was a predictor of lower medicine (aOR 0.80, 95% CI 0.68, 0.95) and higher supplement (aOR 1.47, 95% CI 1.09, 1.98) use. CONCLUSION: Half of all children and adolescents took at least one medicine or supplement. The intake varied depending on age and sex. Furthermore, high socioeconomic status was associated with a decreased probability of medicine intake. WHAT IS KNOWN: • Half of all children and adolescents in Germany are exposed to medicines and supplements. • Data on the actual intake are scarce as most studies focus on prescribed medicines. WHAT IS NEW: • The prevalence of medicine/supplement use rose from 2014 (45%) to 2019 (53%). The prevalence was age-dependent: it was the highest in children aged < 3 years, and the lowest in children aged 6-< 9 years. Females took medicines more frequently than males. • High socioeconomic status was associated with lower medicine and higher supplement use. Self-medication accounted for 28% of all preparations.

Biologicals in the Treatment of Pediatric Atopic Diseases.

The management of atopic diseases such as severe asthma, severe atopic dermatitis, and severe food allergy in childhood is challenging. In particular, there are safety concerns regarding the use of high-dose corticosteroids. The recent development of biologicals and their approval for the treatment of children offer a new, very promising, and more personalized therapy option. Omalizumab, mepolizumab, and dupilumab are currently approved as add-on treatments of severe asthma in children and have been shown to be effective in improvement of asthma control and reduction of exacerbations. Dupilumab is the only biological approved for the treatment of atopic dermatitis in adolescents so far. It has been demonstrated to significantly improve symptoms of atopic dermatitis.However, safety data for biologicals used in atopic diseases in children and adolescents are still very limited. Biologicals are generally considered to be safe in adults. These data are often extrapolated to children. Additionally, data for long-term use are lacking. Thus, the safety profiles of those biologicals cannot yet be conclusively assessed.

Carcass and meat quality characteristics from Iberian wild red deer (Cervus elaphus) hunted at different ages.

BACKGROUND: Deer-meat consumption is increasing in several countries based on claims that it is a healthy red meat. This study assessed the effect of slaughter age (low - 26 months and younger; medium - from 27 months to younger than 42 months; and high - 42 months and older) on carcass characteristics and meat physicochemical properties of 150 Iberian wild red deer. RESULTS: Whole carcass yields of neck, backbone and flank increased (P < 0.001) with age, while yields of shoulder, tenderloin and leg decreased (P < 0.05) with age. The pH measured at 48 h post mortem at 9th rib level was not affected by age, while pH measured at 72 h post mortem at the longissimus thoracis et lumborum muscle decreased (P < 0.05) with age. Meat chemical composition was not affected by slaughter age, except for intramuscular fat (IMF), which increased (P < 0.05) with slaughter age. Finally, cooking loss and shear force were higher (P < 0.05) in meat from older deer. CONCLUSION: Most characteristics of meat from wild red deer depend on age at slaughter. The greater IMF of meat from older animals may render it more palatable. However, meat shear force also increased with age. Additional studies testing palatability seem to be necessary to evaluate the effects of slaughter age on the sensorial quality of meat from Iberian wild red deer. © 2018 Society of Chemical Industry.

Optimizing the use of spineless cactus in the finishing diet of lambs: physicochemical properties and sensory characteristics of meat.

BACKGROUND: The use of spineless cactus in finishing diets for lambs improves the carcass quality. However, data about its influence on meat traits is very scarce. The effects of spineless cactus inclusion in the finishing diet of lambs at four levels (0, 150, 300 and 450 g kg-1 of dry matter, DM) in replacement of Tifton hay on the physicochemical and sensory properties of meat were studied. RESULTS: The spineless cactus modified the chemical composition increasing the protein (P < 0.001) and the fat (P < 0.01) contents of meat, presenting the greatest values in lambs fed diets with 150 and 300 g kg-1 (DM) replacing levels, respectively. However, the spineless cactus did not influence the growth performance from 23.7 to 37.3 kg of body weight (on average). In addition, colour parameters of the meat were not affected by the inclusion of spineless cactus in the finishing diet of lambs, resulting in mean values of 37.55, 14.96 and 8.49 for lightness, redness and yellowness, respectively. There were no statistical differences among treatments for cooking loss and shear force, with mean values of 34.8% and 14.8 N, respectively. Finally, the sensorial properties were not affected by the inclusion of spineless cactus in the finishing diet of lambs. CONCLUSION: Spineless cactus could be included up to the level of 300 g kg-1 DM in the finishing diets of lambs to increase the fat content of meat without compromising its sensorial properties. However, further studies about the fatty acid composition of meat from lambs fed diets containing spineless cactus are necessary. © 2019 Society of Chemical Industry.

Chronic lymphocytic leukaemia is driven by antigen-independent cell-autonomous signalling.

B-cell antigen receptor (BCR) expression is an important feature of chronic lymphocytic leukaemia (CLL), one of the most prevalent B-cell neoplasias in Western countries. The presence of stereotyped and quasi-identical BCRs in different CLL patients suggests that recognition of specific antigens might drive CLL pathogenesis. Here we show that, in contrast to other B-cell neoplasias, CLL-derived BCRs induce antigen-independent cell-autonomous signalling, which is dependent on the heavy-chain complementarity-determining region (HCDR3) and an internal epitope of the BCR. Indeed, transferring the HCDR3 of a CLL-derived BCR provides autonomous signalling capacity to a non-autonomously active BCR, whereas mutations in the internal epitope abolish this capacity. Because BCR expression was required for the binding of secreted CLL-derived BCRs to target cells, and mutations in the internal epitope reduced this binding, our results indicate a new model for CLL pathogenesis, with cell-autonomous antigen-independent signalling as a crucial pathogenic mechanism.

Antibody repertoire diversification through VH gene replacement in mice cloned from an IgA plasma cell.

In mammals, VDJ recombination is responsible for the establishment of a highly diversified preimmune antibody repertoire. Acquisition of a functional Ig heavy (H) chain variable (V) gene rearrangement is thought to prevent further recombination at the IgH locus. Here, we describe VHQ52(NT); Vκgr32(NT) Ig monoclonal mice reprogrammed from the nucleus of an intestinal IgA(+) plasma cell. In VHQ52(NT) mice, IgA replaced IgM to drive early B-cell development and peripheral B-cell maturation. In VHQ52(NT) animals, over 20% of mature B cells disrupted the single productive, nonautoimmune IgH rearrangement through VH replacement and exchanged it with a highly diversified pool of IgH specificities. VH replacement occurred in early pro-B cells, was independent of pre-B-cell receptor signaling, and involved predominantly one adjacent VH germ-line gene. VH replacement was also identified in 5% of peripheral B cells of mice inheriting a different productive VH rearrangement expressed in the form of an IgM H chain. In summary, editing of a productive IgH rearrangement through VH replacement can account for up to 20% of the IgH repertoire expressed by mature B cells.

Proteomic analysis reveals a role for Bcl2-associated athanogene 3 and major vault protein in resistance to apoptosis in senescent cells by regulating ERK1/2 activation.

Senescence is a prominent solid tumor response to therapy in which cells avoid apoptosis and instead enter into prolonged cell cycle arrest. We applied a quantitative proteomics screen to identify signals that lead to therapy-induced senescence and discovered that Bcl2-associated athanogene 3 (Bag3) is up-regulated after adriamycin treatment in MCF7 cells. Bag3 is a member of the BAG family of co-chaperones that interacts with Hsp70. Bag3 also regulates major cell-signaling pathways. Mass spectrometry analysis of the Bag3 Complex revealed a novel interaction between Bag3 and Major Vault Protein (MVP). Silencing of Bag3 or MVP shifts the cellular response to adriamycin to favor apoptosis. We demonstrate that Bag3 and MVP contribute to apoptosis resistance in therapy-induced senescence by increasing the level of activation of extracellular signal-regulated kinase1/2 (ERK1/2). Silencing of either Bag3 or MVP decreased ERK1/2 activation and promoted apoptosis in adriamycin-treated cells. An increase in nuclear accumulation of MVP is observed during therapy-induced senescence and the shift in MVP subcellular localization is Bag3-dependent. We propose a model in which Bag3 binds to MVP and facilitates MVP accumulation in the nucleus, which sustains ERK1/2 activation. We confirmed that silencing of Bag3 or MVP shifts the response toward apoptosis and regulates ERK1/2 activation in a panel of diverse breast cancer cell lines. This study highlights Bag3-MVP as an important complex that regulates a potent prosurvival signaling pathway and contributes to chemotherapy resistance in breast cancer.