Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization.

SUMMARY: In the era where transcriptome profiling moves toward single-cell and spatial resolutions, the traditional co-expression analysis lacks the power to fully utilize such rich information to unravel spatial gene associations. Here, we present a Python package called Spatial Enrichment Analysis of Gene Associations using L-index (SEAGAL) to detect and visualize spatial gene correlations at both single-gene and gene-set levels. Our package takes spatial transcriptomics datasets with gene expression and the aligned spatial coordinates as input. It allows for analyzing and visualizing genes' spatial correlations and cell types' colocalization within the precise spatial context. The output could be visualized as volcano plots and heatmaps with a few lines of code, thus providing an easy-yet-comprehensive tool for mining spatial gene associations. AVAILABILITY AND IMPLEMENTATION: The Python package SEAGAL can be installed using pip: https://pypi.org/project/seagal/. The source code and step-by-step tutorials are available at: https://github.com/linhuawang/SEAGAL.

Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss.

BACKGROUND: Single-cell omics technology is rapidly developing to measure the epigenome, genome, and transcriptome across a range of cell types. However, it is still challenging to integrate omics data from different modalities. Here, we propose a variation of the Siamese neural network framework called MinNet, which is trained to integrate multi-omics data on the single-cell resolution by using graph-based contrastive loss. RESULTS: By training the model and testing it on several benchmark datasets, we showed its accuracy and generalizability in integrating scRNA-seq with scATAC-seq, and scRNA-seq with epitope data. Further evaluation demonstrated our model's unique ability to remove the batch effect, a common problem in actual practice. To show how the integration impacts downstream analysis, we established model-based smoothing and cis-regulatory element-inferring method and validated it with external pcHi-C evidence. Finally, we applied the framework to a COVID-19 dataset to bolster the original work with integration-based analysis, showing its necessity in single-cell multi-omics research. CONCLUSIONS: MinNet is a novel deep-learning framework for single-cell multi-omics sequencing data integration. It ranked top among other methods in benchmarking and is especially suitable for integrating datasets with batch and biological variances. With the single-cell resolution integration results, analysis of the interplay between genome and transcriptome can be done to help researchers understand their data and question.

Quantification and visualization of cis-regulatory dynamics in single-cell multi-omics data with TREASMO.

Recent advances in single-cell multi-omics technologies have provided unprecedented insights into regulatory processes. We introduce TREASMO, a versatile Python package designed to quantify and visualize transcriptional regulatory dynamics in single-cell multi-omics datasets. TREASMO has four modules, spanning data preparation, correlation quantification, downstream analysis and visualization, enabling comprehensive dataset exploration. By introducing a novel single-cell gene-peak correlation strength index, TREASMO facilitates accurate identification of regulatory changes at single-cell resolution. Validation on a hematopoietic stem and progenitor cell dataset showcases TREASMO's capacity in quantifying the gene-peak correlation strength at the single-cell level, identifying regulatory markers and discovering temporal regulatory patterns along the trajectory.

Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model.

Physical exercise represents a primary defense against age-related cognitive decline and neurodegenerative disorders like Alzheimer's disease (AD). To impartially investigate the underlying mechanisms, we conducted single-nucleus transcriptomic and chromatin accessibility analyses (snRNA-seq and ATAC-seq) on the hippocampus of mice carrying AD-linked NL-G-F mutations in the amyloid precursor protein gene (APPNL-G-F) following prolonged voluntary wheel-running exercise. Our study reveals that exercise mitigates amyloid-induced changes in both transcriptomic expression and chromatin accessibility through cell type-specific transcriptional regulatory networks. These networks converge on the activation of growth factor signaling pathways, particularly the epidermal growth factor receptor (EGFR) and insulin signaling, correlating with an increased proportion of immature dentate granule cells and oligodendrocytes. Notably, the beneficial effects of exercise on neurocognitive functions can be blocked by pharmacological inhibition of EGFR and the downstream phosphoinositide 3-kinases (PI3K). Furthermore, exercise leads to elevated levels of heparin-binding EGF (HB-EGF) in the blood, and intranasal administration of HB-EGF enhances memory function in sedentary APPNL-G-F mice. These findings offer a panoramic delineation of cell type-specific hippocampal transcriptional networks activated by exercise and suggest EGF-related growth factor signaling as a druggable contributor to exercise-induced memory enhancement, thereby suggesting therapeutic avenues for combatting AD-related cognitive decline.

AI-MARRVEL - A Knowledge-Driven AI System for Diagnosing Mendelian Disorders.

BACKGROUND: Diagnosing genetic disorders requires extensive manual curation and interpretation of candidate variants, a labor-intensive task even for trained geneticists. Although artificial intelligence (AI) shows promise in aiding these diagnoses, existing AI tools have only achieved moderate success for primary diagnosis. METHODS: AI-MARRVEL (AIM) uses a random-forest machine-learning classifier trained on over 3.5 million variants from thousands of diagnosed cases. AIM additionally incorporates expert-engineered features into training to recapitulate the intricate decision-making processes in molecular diagnosis. The online version of AIM is available at https://ai.marrvel.org. To evaluate AIM, we benchmarked it with diagnosed patients from three independent cohorts. RESULTS: AIM improved the rate of accurate genetic diagnosis, doubling the number of solved cases as compared with benchmarked methods, across three distinct real-world cohorts. To better identify diagnosable cases from the unsolved pools accumulated over time, we designed a confidence metric on which AIM achieved a precision rate of 98% and identified 57% of diagnosable cases out of a collection of 871 cases. Furthermore, AIM's performance improved after being fine-tuned for targeted settings including recessive disorders and trio analysis. Finally, AIM demonstrated potential for novel disease gene discovery by correctly predicting two newly reported disease genes from the Undiagnosed Diseases Network. CONCLUSIONS: AIM achieved superior accuracy compared with existing methods for genetic diagnosis. We anticipate that this tool may aid in primary diagnosis, reanalysis of unsolved cases, and the discovery of novel disease genes. (Funded by the NIH Common Fund and others.).

scGREAT: Graph-based regulatory element analysis tool for single-cell multi-omics data.

Motivation: With the development in single-cell multi-omics sequencing technology and data integration algorithms, we have entered the single-cell multi-omics era. Current multi-omics analysis algorithms failed to systematically dissect the heterogeneity within the datasets when inferring cis-regulatory events. Thus, there is a need for cis-regulatory element inferring algorithms that considers the cellular heterogeneity. Results: Here, we propose scGREAT, a single-cell multi-omics regulatory state analysis Python package with a rapid graph-based correlation measurement L. The graph-based correlation method assigns each cell a local L index, pinpointing specific cell groups of certain regulatory states. Such single-cell resolved regulatory state information enables the heterogeneity analysis equipped in the package. Applying scGREAT to the 10X Multiome PBMC dataset, we demonstrated how it could help subcluster cell types, infer regulation-based pseudo-time trajectory, discover feature modules, and find cluster-specific regulatory gene-peak pairs. Besides, we showed that global L index, which is the average of all local L values, is a better replacement for Pearson's r in ruling out confounding regulatory relationships that are not of research interests. Availability: https://github.com/ChaozhongLiu/scGREAT.

Unraveling Spatial Gene Associations with SEAGAL: a Python Package for Spatial Transcriptomics Data Analysis and Visualization.

Summary: In the era where transcriptome profiling moves towards single-cell and spatial resolutions, the traditional co-expression analysis lacks the power to fully utilize such rich information to unravel spatial gene associations. Here we present a Python package called Spatial Enrichment Analysis of Gene Associations using L-index (SEAGAL) to detect and visualize spatial gene correlations at both single-gene and gene-set levels. Our package takes spatial transcriptomics data sets with gene expression and the aligned spatial coordinates as input. It allows for analyzing and visualizing spatial correlations at both single-gene and gene-set levels. The output could be visualized as volcano plots and heatmaps with a few lines of code, thus providing an easy-yet-comprehensive tool for mining spatial gene associations. Availability and Implementation: The Python package SEAGAL can be installed using pip: https://pypi.org/project/seagal/ . The source code and step-by-step tutorials are available at: https://github.com/linhuawang/SEAGAL . Contact: linhuaw@bcm.edu.

The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells.

Estrogen receptor-positive (ER+) breast cancer exhibits a strong bone tropism in metastasis. How the bone microenvironment (BME) impacts ER signaling and endocrine therapy remains poorly understood. Here, we discover that the osteogenic niche transiently and reversibly reduces ER expression and activities specifically in bone micrometastases (BMMs), leading to endocrine resistance. As BMMs progress, the ER reduction and endocrine resistance may partially recover in cancer cells away from the osteogenic niche, creating phenotypic heterogeneity in macrometastases. Using multiple approaches, including an evolving barcoding strategy, we demonstrated that this process is independent of clonal selection, and represents an EZH2-mediated epigenomic reprogramming. EZH2 drives ER+ BMMs toward a basal and stem-like state. EZH2 inhibition reverses endocrine resistance. These data exemplify how epigenomic adaptation to BME promotes phenotypic plasticity of metastatic seeds, fosters intra-metastatic heterogeneity, and alters therapeutic responses. Our study provides insights into the clinical enigma of ER+ metastatic recurrences despite endocrine therapies.

[Brain natriuretic peptide and left ventricular remodeling after emergency percutaneous coronary intervention in acute myocardial infarction patients].

OBJECTIVE: To investigate the effect of emergency percutaneous coronary interventional (PCI) treatment on plasma brain natriuretic peptide (BNP) levels and left ventricular remodeling in patients with acute myocardial infarction (AMI). METHODS: This study included 118 patients with AMI and 20 healthy volunteers (their results were regarded as normal reference). Fifty-two patients who underwent successful emergency PCI 6-12 hours after onset were named as PCI group, and 66 patients rejected or in whom emergency PCI failed served as the control group. Plasma BNP levels were determined with Triage rapid assay at admission,at 12, 24, 48, 72 hours and 7, 14, 28 days after admission for both groups. Left ventricular ejection function (LVEF) was assessed by echocardiography with the modified Simpson's equation on 3-5 days and 28 days. Same assay was performed for 20 healthy volunteers. RESULTS: Plasma BNP levels of both groups were significantly higher at admission than those of volunteers. There was significant difference in BNP levels between two groups at corresponding time points (all P<0.01). In PCI group, BNP level peaked during 12-24 hours after admission, whereas two peaks of elevation of BNP levels were detected in control group, the first peak appeared during 12-24 hours and the second peak on 7 days after admission. Plasma BNP levels in PCI group were significantly lower than those of control group at corresponding time points (all P<0.01). There was no difference in LVEF level between two groups on 3-5 days after admission. LVEF level after emergency PCI was significantly higher than that of control group on 28 days after admission (P<0.01). CONCLUSION: Emergency PCI lowers plasma BNP level and improve LVEF level in patients with AMI, and it may reverse ventricular remodeling.

Cell-material interactions in tendon tissue engineering.

The interplay between cells and materials is a fundamental topic in biomaterial-based tissue regeneration. One of the principles for biomaterial development in tendon regeneration is to stimulate tenogenic differentiation of stem cells. To this end, efforts have been made to optimize the physicochemical and bio-mechanical properties of biomaterials for tendon tissue engineering. However, recent progress indicated that innate immune cells, especially macrophages, can also respond to the material cues and undergo phenotypical changes, which will either facilitate or hinder tissue regeneration. This process has been, to some extent, neglected by traditional strategies and may partially explain the unsatisfactory outcomes of previous studies; thus, more researchers have turned their focus on developing and designing immunoregenerative biomaterials to enhance tendon regeneration. In this review, we will first summarize the effects of material cues on tenogenic differentiation and paracrine secretion of stem cells. A brief introduction will also be made on how material cues can be manipulated for the regeneration of tendon-to-bone interface. Then, we will discuss the characteristics and influences of macrophages on the repair process of tendon healing and how they respond to different materials cues. These principles may benefit the development of novel biomaterials provided with combinative bioactive cues to activate tenogenic differentiation of stem cells and pro-resolving macrophage phenotype. STATEMENT OF SIGNIFICANCE: The progress achieved with the rapid development of biomaterial-based strategies for tendon regeneration has not yielded broad benefits to clinical patients. In addition to the interplay between stem cells and biomaterials, the innate immune response to biomaterials also plays a determinant role in tissue regeneration. Here, we propose that fine-tuning of stem cell behaviors and alternative activation of macrophages through material cues may lead to effective tendon/ligament regeneration. We first review the characteristics of key material cues that have been manipulated to promote tenogenic differentiation and paracrine secretion of stem cells in tendon regeneration. Then, we discuss the potentiality of corresponding material cues in activating macrophages toward a pro-resolving phenotype to promote tissue repair.

Aberrant intrinsic functional connectivity in thalamo-cortical networks in major depressive disorder.

OBJECTIVE: Growing evidence has implicated dysfunction of the thalamus and its projection cortical targets in depression. However, the anatomical specificity of thalamo-cortical connectivity in major depressive disorder (MDD) remains unknown due to the regional heterogeneity of the thalamus and limited methods to examine this. METHODS: Resting-state fMRI was collected on 70 MDD patients and 70 healthy controls. The thalamus was parcellated based on connectivity with six predefined cortical regions of interest (ROIs). The segmented thalamic nuclei were used as seeds to map connectivity with the rest of the whole brain. The cortical-to-thalamus connectivity values and thalamus-based connectivity maps were compared between groups. RESULTS: The cortical ROIs demonstrated correlations with spatially distinct zones within the thalamus. We found a trend toward reduced parietal ROI-to-thalamus connectivity in MDD. Importantly, MDD patients demonstrated reduced connectivity between prefrontal and parietal thalamus ROIs and bilateral middle frontal gyrus (MFG) and the right posterior default mode network (DMN) and between the prefrontal and motor thalamus ROIs and lateral temporal regions. Conversely, increased connectivity emerged between the motor thalamus ROI and right MFG and right medial frontal gyrus/anterior cingulate; between motor/somatosensory thalamus ROIs and right posterior DMN; between prefrontal/somatosensory thalamus ROIs and cerebellum; and between the parietal thalamus ROI and left insula. CONCLUSIONS: This study is the first to examine the anatomical specificity of thalamo-cortical connectivity disturbances in MDD. Subjects with MDD demonstrated altered thalamo-cortical connectivity characterized by a complex pattern of region-dependent hypo- or hyperconnectivity. We therefore speculate that selectively modulating the connectivity of thalamo-cortical circuitry may be a potential novel therapeutic mechanism for MDD.

Surface Phosphatidylserine Is Responsible for the Internalization on Microvesicles Derived from Hypoxia-Induced Human Bone Marrow Mesenchymal Stem Cells into Human Endothelial Cells.

BACKGROUND: Previous data have proven that microvesicles derived from hypoxia-induced mesenchymal stem cells (MSC-MVs) can be internalized into endothelial cells, enhancing their proliferation and vessel structure formation and promoting in vivo angiogenesis. However, there is a paucity of information about how the MSC-MVs are up-taken by endothelial cells. METHODS: MVs were prepared from the supernatants of human bone marrow MSCs that had been exposed to a hypoxic and/or serum-deprivation condition. The incorporation of hypoxia-induced MSC-MVs into human umbilical cord endothelial cells (HUVECs) was observed by flow cytometry and confocal microscopy in the presence or absence of recombinant human Annexin-V (Anx-V) and antibodies against human CD29 and CD44. Further, small interfering RNA (siRNA) targeted at Anx-V and PSR was delivered into HUVECs, or HUVECs were treated with a monoclonal antibody against phosphatidylserine receptor (PSR) and the cellular internalization of MVs was re-assessed. RESULTS: The addition of exogenous Anx-V could inhibit the uptake of MVs isolated from hypoxia-induced stem cells by HUVECs in a dose- and time-dependent manner, while the anti-CD29 and CD44 antibodies had no effect on the internalization process. The suppression was neither observed in Anx-V siRNA-transfected HUVECs, however, addition of anti-PSR antibody and PSR siRNA-transfected HUVECs greatly blocked the incorporation of MVs isolated from hypoxia-induced stem cells into HUVECs. CONCLUSION: PS on the MVs isolated from hypoxia-induced stem cells is the critical molecule in the uptake by HUVECs.

Mild coronary artery stenosis has no impact on cardiac and vascular parameters in miniature swine exposed to positive acceleration stress.

BACKGROUND: Exposure of pilots' heart to acceleration-associated stress (+Gz stress) is an adverse effect of high-performance aviation. The occurrence of coronary heart diseases is one of the most frequent medical causes leading to cessation of flying. AIM: To assess the effects of +Gz stress on coronary artery stenosis (CAS) in a minimally invasive miniature swine model with a fast recovery. METHODS: The proximal left anterior descending branch was ligated in 20 swine using silk suture. CAS degree (mild, moderate, severe) was analyzed by quantitative computerized angiography. Five swine underwent a sham operation. +Gz stress exposure was performed and venous blood was collected before/after exposure. Plasma C-reactive protein (CRP), endothelin (ET)-1, angiotensin (Ang) II and urotensin 2 (U2) levels were measured. RESULTS: CAS models were successful in 18 animals. Two swine exhibited ventricular fibrillation during the procedure and died. Plasma CRP, ET-1, Ang II and U2 changed significantly after maximal tolerated +Gz stress exposure (all P < 0.05). After maximal tolerated +Gz stress exposure, plasma CRP, ET-1, Ang II and U2 levels increased in the moderate and severe stenosis groups, compared with the sham group (all P < 0.05), but there was no significant difference between the mild stenosis group and the sham group (all P > 0.05). CONCLUSION: The fully endoscopic operation method successfully generated animal models of different degrees of CAS. Plasma CRP, ET-1, Ang II and U2 levels increased after +Gz stress exposure with increasing CAS severity. Animals with mild stenosis showed no ill effect under +Gz stress, suggesting that pilots with mild stenosis might be allowed to continue flying, but it must be confirmed in humans.

Endoplasmic Reticulum Is Involved in Myocardial Injury in a Miniature Swine Model of Coronary Artery Stenosis Exposed to Acceleration-Associated Stress.

This study aimed to investigate the effects of myocardial injury in a minimally-invasive miniature swine model with different levels of coronary artery stenosis (CAS) and exposed to maximal tolerated +Gz. Proximal left anterior descending branch was ligated in 20 swine. Five swine underwent a sham operation. A trapezoid acceleration curve was used for +Gz stress. Pathological changes of myocardial tissue were detected by H&E staining. Apoptotic cardiomyocytes were detected by TUNEL. GRP78 and CHOP were investigated by immunohistochemistry and western blot. CAS models were successful in 18 animals.Compared with the sham-operated group (+8.00±0.71 Gz), the maximal tolerated +Gz values of the moderate stenosis (+6.00±0.89 Gz, P<0.05) and severe stenosis groups (+5.20±0.84 Gz, P<0.05) were decreased.Compared with sham animals (12.16±1.25%), after exposure to maximum +Gz, apoptotic cells of the moderate (43.53±8.42%, P<0.05) and severe stenosis group (60.50±9.35%, P<0.05) were increased, MDA content was increased (1.89 and 4.91 folds, respectively, P<0.05), and SOD activity was reduced (-13.66% and -21.71%, respectively). After exposure to maximum +Gz, GRP78 protein expression was low in the sham-operated (0.29±0.05) and mild stenosis groups (0.35±0.04), while expression was high in the moderate (0.72±0.04, P<0.05) and severe stenosis groups (0.65±0.07, P<0.05). CHOP protein expression was not observed in the sham-operated group, while expression was high in the moderate and severe stenosis groups. These results indicated that Under maximum exposure to +Gz stress, different levels of CAS led to different levels of myocardial injury. Endoplasmic reticulum response is involved in the apoptosis of cardiomyocytes after +Gz stress.

[Silymarin Protects Umbilical Cord-Derived Mesenchymal Stem Cells against Apoptosis Induced by Serum-Deprivation].

OBJECTIVE: To investigate the protection of silymarin against the human mesenchymal stem cell (MSC) apoptosis induced by serum deprivation and its underlying mechanism. METHODS: Human umbilical cord MSCs were cultured in the absence of serum, and the silymain of different concentration (1-10 µg/ml) was added into the medium. MTT test was performed to observe the cell proliferation status. After being cultured for 72 hours, the cells were collected, and flow cytometry with Annexin-V-PI double-staining was used to detect the apoptotic cells from the control and silymarin-treated groups. Furthermore, the intracellular contents of BAX and BCL-2 were detected by Western blot for exploring the potential mechanism. RESULTS: The silymarin promoted the proliferation of human UC-MSCs in a dose-dependent manner, reaching its maximal at a dose of 5 µg/ml. Moreover, silymarin could inhibit the serum deprivation-induced apoptosis of MSCs and, the inhibitory rate reached up to 30% when it was added at a concentration of 5 µg/ml. The content of intracellular BAX was obviously elevated after serum-deprivation treatment, and this increase could be blunted by the addition of silymarin. Meanwhile, the content of BCL-2 was not obviously changed. CONCLUSION: The silymarin can stimulate MSC growth and inhibit the apoptosis of MSCs probably by the mitochondria pathway.

[Investigation on the internalization pathway of microparticles into human umbilical cord endothelial cells].

OBJECTIVE: To investigate the mechanisms underlying the incorporation of microparticles(MP) derived from human bone marrow mesenchymal stem cells (MSCs) into human umbilical cord endothelial cells (HUVECs). METHODS: MPs were isolated from the supernatants of MSCs which had exposed to a hypoxia/serum-deprivation condition. Electron microscope was used to identify the MPs. The surface molecule profile was evaluated with the bead-based flow cytometry technique. The expression level of the phosphatidylserine receptor (PSR) was detected by immunofluorescence cytochemistry. MPs were co-cultured with HUVECs in the presence or absence PSR-antibody, and the internalization of MPs was observed with laser scanning microscopy. RESULTS: The MPs derived from MSCs expressed highly PS, while PSR expressed on the surface of HUVECs. The confocal result revealed that MPs could quickly be uptaken by the endothelial cells, and mainly distributed in the cytoplasm surrounding of the nuclei. The internalization of MPs reduced significantly after PSR specific blockage. CONCLUSION: The reaction between PS on the MP and the PSR of HUVECs plays an important role in the internalization of MSC-MPs.

Modification of atrioventricular node in a special condition treating paroxysmal supraventricular tachycardia.

Modification of atrioventricular node is a usual and necessary operation to cure atrioventricular nodal reentrant tachycardia (AVNRT). In this operation, atrioventricular block is the most severe complication and its prevention is of our great concern. This complication always occurs under some special circumstances with potential risk. So, it is very important to realize such conditions, as in this paper. A patient with paroxysmal palpitation for 10 years, aggravating to shortness of breath with chest distress for 1 year; cardiac electrophysiological examination found slow conduction in both antegrade and retrograde paths of reentrant loop, and typical AVNRT could be induced. During effective ablation there was no junctional rhythm. In some special cases, modification of atrioventricular node should not only rely on the junctional rhythm to determine the ablation effect, but also on the time of cardiac electrophysiological examination, as such to avoid the severe complication of atrioventricular block caused by excessive ablation.