Discrete Cell Research Articles

Evolution of plant cell-type-specific cis-regulatory elements.

Cis-regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa, integrating data from 103,911 nuclei representing 126 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, and Urochloa fusca). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1-derived epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially silencer-like CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of plant cell-type-specific CRE evolution.

Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data.

Single-cell RNA-sequencing has transformed the study of biological tissues by enabling transcriptomic characterizations of their constituent cell states. Computational methods for gene expression deconvolution use this information to infer the cell composition of related tissues profiled at the bulk level. However, current deconvolution methods are restricted to discrete cell types and have limited power to make inferences about continuous cellular processes like cell differentiation or immune cell activation. We present ConDecon, a clustering-independent method for inferring the likelihood for each cell in a single-cell dataset to be present in a bulk tissue. ConDecon represents an improvement in phenotypic resolution and functionality with respect to regression-based methods. Using ConDecon, we discover the implication of neurodegenerative microglia inflammatory pathways in the mesenchymal transformation of pediatric ependymoma and characterize their spatial trajectories of activation. The generality of this approach enables the deconvolution of other data modalities such as bulk ATAC-seq data.

Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS.

Reproducible definition and identification of cell types is essential to enable investigations into their biological function and to understand their relevance in the context of development, disease and evolution. Current approaches model variability in data as continuous latent factors, followed by clustering as a separate step, or immediately apply clustering on the data. We show that such approaches can suffer from qualitative mistakes in identifying cell types robustly, particularly when the number of such cell types is in the hundreds or even thousands. Here we propose an unsupervised method, Mixture Model Inference with Discrete-coupled AutoencoderS (MMIDAS), which combines a generalized mixture model with a multi-armed deep neural network to jointly infer the discrete type and continuous type-specific variability. Using four recent datasets of brain cells spanning different technologies, species and conditions, we demonstrate that MMIDAS can identify reproducible cell types and infer cell type-dependent continuous variability in both unimodal and multimodal datasets.

Pseudoinvasion and squamous metaplasia/morules in colorectal adenomatous polyp: a case report and literature review

BackgroundSubmucosal pseudoinvasion and squamous metaplasia (SM) are incidental and special morphological findings in colorectal adenomas, and both can mimic invasive carcinoma. The coexistence of these two findings further increases the risk of misdiagnosis, posing a great diagnostic challenge to pathologists. From 1979 to 2022, only 8 cases have been reported, which was extremely rare. In this report, we presented a case of sigmoid colon adenoma accompanied by pseudoinvasion and SM. Additionally, relevant literature was analyzed to summarize the clinical and pathological characteristics.Case presentationA 51-year-old Chinese male patient presented with fresh blood after defecation. Electronic colonoscopy revealed multiple polyps, which were removed using a snare and subjected to high-frequency electrocoagulation resection. The largest polyp, located in the sigmoid colon, was a thick pedunculated and lobulated polyp with a maximum diameter of 2.8 cm. The surface of the polyp showed slight ruggedness and redness, and it was sent for pathological examination. Grossly, the polyp had a lobulated and slightly rough surface. Microscopically, it showed a tubulovillous adenoma with focal high-grade dysplasia and mucosal muscle hyperplasia. Glandular elements were observed in the submucosal layer, forming a well-defined lobular structure. Some of the glands displayed cystic change, and focal SM could be seen within the adenoma. SM could manifest as discrete solid cell nests of varying sizes or cribriform-morular-like structures. Immunohistochemical staining showed that SM cells were diffusely positive for cytokeratin 5/6 (CK5/6); p40, p63, and cytokeratin 20 (CK20) were negative; while caudal type homeobox 2 (CDX2) was weakly positive. β-catenin showed abnormal nuclear expression, and an extremely low Ki67 proliferation index was observed.ConclusionsCoexistence of SM and pseudoinvasion in colorectal adenomas is highly rare. It is more commonly observed in males and tends to occur in the sigmoid colon. It primarily manifests in tubulovillous adenoma and tubular adenoma, with a majority of cases exhibiting a pedicle. Histologically, it is similar to invasive lesions. The cystic dilation of the submucosal glands, hemosiderin deposition, and the presence of a lamina propria around the submucosal glands without adjacent desmoplastic reaction, suggest pseudoinvasion rather than cancer. The bland cytological morphology and Immunohistochemical markers play a crucial role in distinguishing SM from true invasive lesions.

SpatialCTD: A Large-Scale Tumor Microenvironment Spatial Transcriptomic Dataset to Evaluate Cell Type Deconvolution for Immuno-Oncology.

Recent technological advancements have enabled spatially resolved transcriptomic profiling but at a multicellular resolution that is more cost-effective. The task of cell type deconvolution has been introduced to disentangle discrete cell types from such multicellular spots. However, existing benchmark datasets for cell type deconvolution are either generated from simulation or limited in scale, predominantly encompassing data on mice and are not designed for human immuno-oncology. To overcome these limitations and promote comprehensive investigation of cell type deconvolution for human immuno-oncology, we introduce a large-scale spatial transcriptomic deconvolution benchmark dataset named SpatialCTD, encompassing 1.8 million cells and 12,900 pseudo spots from the human tumor microenvironment across the lung, kidney, and liver. In addition, SpatialCTD provides more realistic reference than those generated from single-cell RNA sequencing (scRNA-seq) data for most reference-based deconvolution methods. To utilize the location-aware SpatialCTD reference, we propose a graph neural network-based deconvolution method (i.e., GNNDeconvolver). Extensive experiments show that GNNDeconvolver often outperforms existing state-of-the-art methods by a substantial margin, without requiring scRNA-seq data. To enable comprehensive evaluations of spatial transcriptomics data from flexible protocols, we provide an online tool capable of converting spatial transcriptomic data from various platforms (e.g., 10× Visium, MERFISH, and sci-Space) into pseudo spots, featuring adjustable spot size. The SpatialCTD dataset and GNNDeconvolver implementation are available at https://github.com/OmicsML/SpatialCTD, and the online converter tool can be accessed at https://omicsml.github.io/SpatialCTD/.

On the equivalence of demagnetization tensors as discrete cell size approaches zero in three-dimensional space.

The calculation of the demagnetization field is crucial in various disciplines, including magnetic resonance imaging and micromagnetics. A standard method involves discretizing the spatial domain into finite difference cells and using demagnetization tensors to compute the field. Different demagnetization tensors can result in contributions from adjacent cells that do not approach zero, nor do their differences, even as the cell size decreases. This work demonstrates that in three-dimensional space, a specific set of magnetization tensors produces the same total demagnetization field as the Cauchy principal value when the cell size approaches zero. Additionally, we provide a lower bound for the convergence speed, validated through numerical experiments.

Chronic aluminium chloride exposure induces redox imbalance, metabolic distress, DNA damage, and histopathologic alterations in Wistar rat liver.

Aluminium, a ubiquitous environmental toxicant, is distinguished for eliciting a broad range of physiological, biochemical, and behavioural alterations in laboratory animals and humans. The present work was conducted to study the functional and structural changes induced by aluminium in rat liver. Twenty five adult male Wistar rats (150-200 g) were randomly divided into five groups; control group and four Al-treated groups viz: Al 1 (25mg AlCl3/kg b.wt), Al 2 (35mg AlCl3/kg b.wt), Al 3 (45mg AlCl3/kg b.wt), and Al 4 (55mg AlCl3/kg b.wt). Rats in the aluminium-treated groups were administered AlCl3 for 30 days through oral gavage. Aluminium significantly increased the serum levels of liver function markers (ALT, AST, and ALP), phospholipids, and cholesterol. The activities of hepatocyte membrane (ALP, GGT, and LAP) and carbohydrate metabolic (G6P, F16BP, HK, LDH, MDH, ME, and G6PDH) enzymes were significantly altered by AlCl3 administration. Prolonged Al exposure induced oxidative stress in the liver, as evident by significant hepatocellular DNA damage, increased lipid peroxidation, and decreased non-enzymatic and enzymatic antioxidants. The toxic effects observed in this study were AlCl3 dose-dependent. Histopathological examination of liver sections revealed enlargement of sinusoidal spaces, derangement of the hepatic chord, loss of discrete hepatic cell boundaries, congestion of hepatic sinusoids, and degeneration of hepatocytes in Al-intoxicated rats. In conclusion, aluminium causes severe hepatotoxicity by inhibiting the hepatocyte membrane enzymes and disrupting the liver's energy metabolism and antioxidant defence.

Identifying dysfunctional cell types and circuitsin animal models for psychiatric disorders with calcium imaging.

A central goal of neuroscience is to understand how the brain transforms external stimuli and internal bodily signals into patterns of activity that underlie cognition, emotional states, and behavior. Understanding how these patterns of activity may be disrupted in mental illness is crucial for developing novel therapeutics. It is well appreciated that psychiatric disorders are complex, circuit-based disorders that arise from dysfunctional activity patterns generated in discrete cell types and their connections. Recent advances in large-scale, cell-type specific calcium imaging approaches have shed new light on the cellular, circuit, and network-level dysfunction in animal models for psychiatric disorders. Here, we highlight a series of recent findings over the last ~10 years from in vivo calcium imaging studies that show how aberrant patterns of activity in discrete cell types and circuits may underlie behavioral deficits in animal models for several psychiatric disorders, including depression, anxiety, autism spectrum disorders, and schizophrenia. These advances in calcium imaging in pre-clinical models demonstrate the power of cell-type-specific imaging tools in understanding the underlying dysfunction in cell types, activity patterns, and neural circuits that may contribute to disease and provide new blueprints for developing more targeted therapeutics and treatment strategies.

Assessing the relationship of agger nasi pneumatization to the lacrimal sac: a dynamic computed tomography-dacryocystography analysis.

An understanding of the anatomical structure is crucial for completing successful endoscopic dacryocystorhinostomy (DCR) surgery. This study aimed to precisely delineate the spatial relationship between the lacrimal sac and the agger nasi cell (ANC) and evaluate the impact of ANC on surgical strategies in endoscopic DCR. This retrospective cross-sectional study included 110 Han Chinese patients diagnosed with unilateral primary acquired nasolacrimal duct obstruction (PANDO) from January 2021 to June 2023. This study was conducted in Eye, Ear, Nose, and Throat Hospital of Fudan University and involved inpatient participants who were scheduled for DCR surgery under general anesthesia. Patients were consecutively enrolled. The patients underwent preoperative computed tomography-dacryocystography (CT-DCG), and contrast-enhanced images were used to locate the positions of the lacrimal sac and the common canaliculus. A dynamic approach was adopted to analyze the multiplanar CT imaging, facilitating a detailed assessment of the morphology of the lacrimal drainage system and potential overlap of the lacrimal sac. Patient ages and measured values are presented as the mean ± standard deviation, which were measured three times by the same observer and averaged for statistical analysis. The prevalence of ANC in this study was 90.9% (100/110). Dynamic examination revealed that only 42.7% (47/110) of ANCs appeared as discrete cells, while the majority were connected to nearby sinus openings. Spatial analysis showed that in 57 out of 110 cases, ANCs were situated below the common canaliculus and not posterior to the lacrimal sac, indicating an overlap rate of 51.8%. Notably, our dynamic approach identified five critical cases of overlap below the level of the common canaliculus, which might have been missed by prior studies that used different methodologies. More than half of the ANCs exhibited overlap with the lacrimal sac, suggesting a significant proportion may necessitate opening during endoscopic DCR procedures. ANCs are often interconnected with adjacent nasal sinuses, necessitating careful consideration in the decision to open the ANCs during surgery. The dynamic evaluation employed in CT-DCG effectively assessed the extent of ANC coverage over the lacrimal sac.

Single cell transcriptomic profiling identifies tumor-acquired and therapy-resistant cell states in pediatric rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is a pediatric tumor that resembles undifferentiated muscle cells; yet the extent to which cell state heterogeneity is shared with human development has not been described. Using single-cell/nucleus RNA sequencing from patient tumors, patient-derived xenografts, primary in vitro cultures, and cell lines, we identify four dominant muscle-lineage cell states: progenitor, proliferative, differentiated, and ground cells. We stratify these RMS cells/nuclei along the continuum of human muscle development and show that they share expression patterns with fetal/embryonal myogenic precursors rather than postnatal satellite cells. Fusion-negative RMS (FN-RMS) have a discrete stem cell hierarchy that recapitulates fetal muscle development and contain therapy-resistant FN-RMS progenitors that share transcriptomic similarity with bipotent skeletal mesenchymal cells. Fusion-positive RMS have tumor-acquired cells states, including a neuronal cell state, that are not found in myogenic development. This work identifies previously underappreciated cell state heterogeneity including unique treatment-resistant and tumor-acquired cell states that differ across RMS subtypes.

Genetic Identity of Neural Crest Cell Differentiation in Tissue and Organ Development.

The neural crest (NC), also known as the "fourth germ layer", is an embryonic structure with important contributions to multiple tissue and organ systems. Neural crest cells (NCCs) are subjected to epithelial to mesenchymal transition and migrate throughout the embryo until they reach their destinations, where they differentiate into discrete cell types. Specific gene expression enables this precise NCCs delamination and colonization potency in distinct and diverse locations therein. This review aims to summarize the current experimental evidence from multiple species into the NCCs specifier genes that drive this embryo body axes segmentation. Additionally, it attempts to filter further into the genetic background that produces these individual cell subpopulations. Understanding the multifaceted genetic makeup that shapes NC-related embryonic structures will offer valuable insights to researchers studying organogenesis and disease phenotypes arising from dysmorphogenesis.

IMmuneCite: an integrated workflow for analysis of immune enriched spatial proteomic data.

Spatial proteomics enable detailed analysis of tissue at single cell resolution. However, creating reliable segmentation masks and assigning accurate cell phenotypes to discrete cellular phenotypes can be challenging. We introduce IMmuneCite, a computational framework for comprehensive image pre-processing and single-cell dataset creation, focused on defining complex immune landscapes when using spatial proteomics platforms. We demonstrate that IMmuneCite facilitates the identification of 32 discrete immune cell phenotypes using data from human liver samples while substantially reducing nonbiological cell clusters arising from co-localization of markers for different cell lineages. We established its versatility and ability to accommodate any antibody panel and different species by applying IMmuneCite to data from murine liver tissue. This approach enabled deep characterization of different functional states in each immune compartment, uncovering key features of the immune microenvironment in clinical liver transplantation and murine hepatocellular carcinoma. In conclusion, we demonstrated that IMmuneCite is a user-friendly, integrated computational platform that facilitates investigation of the immune microenvironment across species, while ensuring the creation of an immune focused, spatially resolved single-cell proteomic dataset to provide high fidelity, biologically relevant analyses.

Spatiotemporal delivery of BMP-2 and FGF-18 in 3D-bioprinted tri-phasic osteochondral scaffolds enhanced compartmentalized osteogenic and chondrogenic differentiation of mesenchymal stem cells isolated from rats with varied organizational morphologies

Replicating the heterogeneous structure and promoting compartmentalized osteogenesis/chondrogenesis are critical considerations in designing scaffolds for osteochondral tissue regeneration. However, desirable osteochondral regeneration cannot be achieved mainly due to the absence of effective delivery strategies for growth factors (GFs) and the insufficiency of desirable organizational morphologies for seed cells. Herein, we developed a tri-phasic osteochondral scaffold consisting of bone morphogenetic protein-2 (BMP-2)-loaded subchondral layer, fibroblast growth factor-18 (FGF-18)-loaded cartilage layer, and an interface layer that acted as a barrier to reduce the mutual interference of GFs, via cryogenic 3D bioprinting. BMP-2 could exert osteogenic effects for 14 days, and FGF-18 could exert chondrogenic effects for 21 days, demonstrating the time-controlled release function of BMP-2 and FGF-18. By further seeding discrete rat bone marrow mesenchymal stem cells (rBMSCs) and rBMSC microspheres, respectively, onto the subchondral layer and cartilage layer, the engineered cell-laden osteochondral tissue was constructed. The spatiotemporal release of BMP-2 and FGF-18 in the subchondral layer and cartilage layer promoted the osteogenic differentiation of discrete rBMSCs and chondrogenic differentiation of rBMSC microspheres in the subchondral layer and cartilage layer, respectively. In summary, by seeding rBMSCs with varied organizational morphologies in 3D-printed osteochondral scaffolds with a spatiotemporally controlled strategy, engineered osteochondral tissue with compartmentalized osteogenic/chondrogenic differentiation potent can be formed, displaying a facile and promising way to achieve desirable osteochondral tissue regeneration.

Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS.

Reproducible definition and identification of cell types is essential to enable investigations into their biological function, and understanding their relevance in the context of development, disease and evolution. Current approaches model variability in data as continuous latent factors, followed by clustering as a separate step, or immediately apply clustering on the data. We show that such approaches can suffer from qualitative mistakes in identifying cell types robustly, particularly when the number of such cell types is in the hundreds or even thousands. Here, we propose an unsupervised method, MMIDAS, which combines a generalized mixture model with a multi-armed deep neural network, to jointly infer the discrete type and continuous type-specific variability. Using four recent datasets of brain cells spanning different technologies, species, and conditions, we demonstrate that MMIDAS can identify reproducible cell types and infer cell type-dependent continuous variability in both uni-modal and multi-modal datasets.

Premixed calcium silicate-based ceramic sealers promote osteogenic/cementogenic differentiation of human periodontal ligament stem cells: A microscopy study.

To evaluate the effects of premixed calcium silicate based ceramic sealers on the viability and osteogenic/cementogenic differentiation of human periodontal ligament stem cells (hPDLSCs). The materials evaluated were TotalFill BC Sealer (TFbc), AH Plus Bioceramic Sealer (AHPbc), and Neosealer Flo (Neo). Standardized discs and 1:1, 1:2, and 1:4 eluates of the tested materials were prepared. The following in vitro experiments were carried out: ion release, cell metabolic activity 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, cell migration, immunofluorescence experiment, cell attachment, gene expression, and mineralization assay. Statistical analyses were performed using one-way ANOVA followed by Tukey's post hoc test (p < .05). Increased Ca2+ release was detected in TFbc compared to AHPbc and Neo (*p < .05). Biological assays showed a discrete cell metabolic activity and cell migration in Neo-treated cell, whereas scanning electronic microscopy assay exhibited that TFbc group had a better cell adhesion process of substrate attachment, spreading, and cytoskeleton development on the niche-like structures of the cement than AHPbc and Neo. The sealers tested were able to induce overexpression of the CEMP-1, ALP, and COL1A1 genes in the first days of exposure, particularly in the case of TFbc (***p < .001). All materials tested significantly increased the mineralization of hPDLSCs when compared to the negative control, although more pronounced calcium deposition was observed in the TFbc-treated cells (***p < .001). Our results suggested that TFbc promotes cell differentiation, both by increasing the expression of key osteo/odontogenic genes and by promoting mineralization of the extracellular matrix, whereas this phenomenon was less evident in Neo and AHPbc. RESEARCH HIGHLIGHTS: TFbc group had a better cell adhesion process of substrate attachment, spreading, and cytoskeleton development on the niche-like structures of the cement than AHPbc and Neo. The sealers tested were able to induce overexpression of the CEMP-1, ALP, and COL1A1 genes in the first days of exposure, particularly in the case of TFbc. All materials tested significantly increased the mineralization of hPDLSCs when compared to the negative control, although more pronounced calcium deposition was observed in the TFbc-treated cells.

The use of solar film elements on a neonate manikin surface to estimate the received output power of neonatal phototherapy lamp systems

The work described was undertaken to develop a means to estimate the delivered power over the exposed body surface of a neonate receiving phototherapy. Previous work of the group had involved the use of discrete photodiodes distributed over a newborn manikin surface. It was considered that improved accuracy of sensing over curved surfaces would be provided with the use of flexible solar cell elements. A group of products based on amorphous silicon was identified as potentially suitable and a range of its properties investigated. These included the wavelength sensitivity, the relative sensitivity of similar elements and the cosine response of elements. It was identified that with selection of elements of matched sensitivity, specific element types were appropriate for intended use. A total of 44 discrete solar cell elements of three separate sizes was used to cover the previously used manikin surface and a dedicated interface circuit was designed and constructed. A handheld calibrated spectroradiometer provided a means to relate incident irradiance values within specific wavelength bands to corresponding optical power over the manikin surface. Initial use of the system is described together with future potential developments in relation to clinical applications and testing standards for neonatal phototherapy devices.

Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis.

Introduction: Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord-forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Methods: Here we use high-throughput sequencing approaches to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Results and Discussion: Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, RNA-seq of sequential tissue sections (RNA-tomography) provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single cell and RNA-tomography datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.

#1976 Non-IgA mesangial proliferative glomerulonephritis in a patient with IgA deficiency, a case report

Abstract Background and Aims IgA deficiency (IgAD) is the most common primary immunoglobulin deficiency in western countries. This entity is associated with increased risk of other autoimmune diseases. Mesangial proliferative glomerulonephritis (MesPGN) is a histological pattern defined by mesangial cell proliferation and expansion of the extracellular matrix within the mesangium. The clinical presentation can vary, from nephrotic syndrome to isolated hematuria. 30-40% of MesPGN cases are associated with IgA nephropathy. Other common diagnostic entities that present with this pattern include IgM nephropathy, C1q nephropathy or lupus nephritis, as well as Hepatitis B or C virus infection; idiopathic MesPGN is poorly described in the literature. To the best of our knowledge, this is the first report of idiopathic MesPGN associated with IgAD. Results A 17-year old woman with a background of IgAD and occasional episodes of bronchitis in her childhood presented in January 2022 with nonspecific abdominal pain and macroscopic hematuria. She had been suffering these symptoms for the last few weeks, usually after physical exercise. She was normotensive and showed no fever, skin rashes or other symptoms. Laboratory tests revealed normal renal function (serum creatinine 0.65 mg/dL), urinary albumin-to-creatinine ratio of 23.9 mg/g, a 24-h protein excretion ranging from 40 to 240 mg and non-dysmorphic hematuria of up to 51-150 erythrocytes/field. Additional laboratory tests repeatedly showed only low IgA serum levels, with normal ANA, ANCA or complement levels. Renal ultrasound showed both kidneys with normal size and cortical thickness. A CT urogram observed multiple, bilateral, non-obstructive small-sized kidney stones and a persistent nephrogram. Genetic tests were negative for Alport syndrome-related mutations. Additional workup included occult blood in the stool, stool culture, rectal biopsy and colonoscopy, which were all negative. Symptoms persisted during the following 12 months. A kidney biopsy was performed, finding 40 glomeruli with normal optical appearance, none of them sclerosed. Discrete mesangial expansion and cell proliferation was observed, with capillary lumens with occasional congestion but without thrombi or fibrinoid necrosis. Tubules and interstitium showed no sign of sclerosis or fibrosis, with conserved basement membranes and brush borders. In vessels, subintimal fibrosis, hyalinosis or concentric arteriolar hyperplasia or endarteritis were ruled out. Immunofluorescence showed low-intensity, discrete granular C3 mesangial deposits and no deposition of IgA, IgG, IgM, fibrinogen, C4, C1q or albumin. A diagnosis of non-IgA MesPGN was reached. The patient stopped performing intense physical exercise on a regular basis. This translated in hematuria and abdominal pain of much lower intensity. The patient is currently receiving only supportive therapy and maintains a normal renal function, with persistence of microscopic non-dysmorphic hematuria and occasional, low-grade proteinuria as described. Conclusion MesPGN is the most diagnosed form of glomerulonephritis worldwide. However, most cases are associated with granular IgA deposition in the mesangium, which was absent in this case. Idiopathic, non-IgA MesPGN is a much rarer condition that has been considered by some authors as a form focal segmental glomerulosclerosis or minimal change disease, although others believe it to be a separate condition. IgAD has been previously associated with Crohn's disease, which could explain this patient's symptoms. Crohn's disease has also been associated with non-IgA MesPGN in a low number of patients. Nevertheless, no findings in the patient workup were suggestive of Crohn's disease. A capsule endoscopy study will be performed to clearly rule out such diagnosis.

Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation

Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.

Spatial transcriptomics in health and disease.

The ability to localize hundreds of macromolecules to discrete locations, structures and cell types in a tissue is a powerful approach to understand the cellular and spatial organization of an organ. Spatially resolved transcriptomic technologies enable mapping of transcripts at single-cell or near single-cell resolution in a multiplex manner. The rapid development of spatial transcriptomic technologies has accelerated the pace of discovery in several fields, including nephrology. Its application to preclinical models and human samples has provided spatial information about new cell types discovered by single-cell sequencing and new insights into the cell-cell interactions within neighbourhoods, and has improved our understanding of the changes that occur in response to injury. Integration of spatial transcriptomic technologies with other omics methods, such as proteomics and spatial epigenetics, will further facilitate the generation of comprehensive molecular atlases, and provide insights into the dynamic relationships of molecular components in homeostasis and disease. This Review provides an overview of current and emerging spatial transcriptomic methods, their applications and remaining challenges for the field.