Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNA in situ hybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope-a recently developed novel technology-repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation

Skeletal muscle is essential for both movement and metabolic processes, characterized by a complex and ordered structure. Despite its importance, a detailed spatial map of gene expression within muscle tissue has been challenging to achieve due to the limitations of existing technologies, which struggle to provide high-resolution views. In this study, we leverage the Seq-Scope technique, an innovative method that allows for the observation of the entire transcriptome at an unprecedented submicron spatial resolution. By applying this technique to the mouse soleus muscle, we analyze and compare the gene expression profiles in both healthy conditions and following denervation, a process that mimics aspects of muscle aging. Our approach reveals detailed characteristics of muscle fibers, other cell types present within the muscle, and specific subcellular structures such as the postsynaptic nuclei at neuromuscular junctions, hybrid muscle fibers, and areas of localized expression of genes responsive to muscle injury, along with their histological context. The findings of this research significantly enhance our understanding of the diversity within the muscle cell transcriptome and its variation in response to denervation, a key factor in the decline of muscle function with age. This breakthrough in spatial transcriptomics not only deepens our knowledge of muscle biology but also sets the stage for the development of new therapeutic strategies aimed at mitigating the effects of aging on muscle health, thereby offering a more comprehensive insight into the mechanisms of muscle maintenance and degeneration in the context of aging and disease.

Tailoring MXene Thickness and Functionalization for Enhanced Room-Temperature Trace NO2 Sensing

In this study, precise control over the thickness and termination of Ti3C2TX MXene flakes is achieved to enhance their electrical properties, environmental stability, and gas-sensing performance. Utilizing a hybrid method involving high-pressure processing, stirring, and immiscible solutions, sub-100 nm MXene flake thickness is achieved within the MXene film on the Si-wafer. Functionalization control is achieved by defunctionalizing MXene at 650 °C under vacuum and H2 gas in a CVD furnace, followed by refunctionalization with iodine and bromine vaporization from a bubbler attached to the CVD. Notably, the introduction of iodine, which has a larger atomic size, lower electronegativity, reduce shielding effect, and lower hydrophilicity (contact angle: 99°), profoundly affecting MXene. It improves the surface area (36.2 cm2 g-1), oxidation stability in aqueous/ambient environments (21 days/80 days), and film conductivity (749 S m-1). Additionally, it significantly enhances the gas-sensing performance, including the sensitivity (0.1119 Ω ppm-1), response (0.2% and 23% to 50 ppb and 200 ppm NO2), and response/recovery times (90/100 s). The reduced shielding effect of the -I-terminals and the metallic characteristics of MXene enhance the selectivity of I-MXene toward NO2. This approach paves the way for the development of stable and high-performance gas-sensing two-dimensional materials with promising prospects for future studies.

FICTURE: Scalable segmentation-free analysis of submicron resolution spatial transcriptomics

Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide gene expression analysis at submicron resolution over large areas. Analysis of high-resolution ST data relies heavily on image-based cell segmentation or gridding, which often fails in complex tissues due to diversity and irregularity of cell size and shape. Existing segmentation-free analysis methods scale only to small regions and a small number of genes, limiting their utility in high-throughput studies. Here we present FICTURE, a segmentation-free spatial factorization method that can handle transcriptome-wide data labeled with billions of submicron resolution spatial coordinates. FICTURE is orders of magnitude more efficient than existing methods and it is compatible with both sequencing- and imaging-based ST data. FICTURE reveals the microscopic ST architecture for challenging tissues, such as vascular, fibrotic, muscular, and lipid-laden areas in real data where previous methods failed. FICTURE's cross-platform generality, scalability, and precision make it a powerful tool for exploring high-resolution ST.

Wireless Inchworm-like Compact Soft Robot by Induction Heating of Magnetic Composite

Microrobots and nanorobots have been produced with various nature-inspired soft materials and operating mechanisms. However, freely operating a wirelessly miniaturized soft robot remains a challenge. In this study, a wireless crawling compact soft robot using induction heating was developed. The magnetic composite heater built into the robot was heated wirelessly via induction heating, causing a phase change in the working fluid surrounding the heater. The pressure generated from the evaporated fluid induces the bending of the robot, which is composed of elastomers. During one cycle of bending by heating and shrinking by cooling, the difference in the frictional force between the two legs of the robot causes it to move forward. This robot moved 7240 μm, representing 103% of its body length, over nine repetitions. Because the robot's surface is made of biocompatible materials, it offers new possibilities for a soft exploratory microrobot that can be used inside a living body or in a narrow pipe.

External validation of the biomarker based ABCD score in atrial fibrillation patients with a non gender CHA2DS2 VASc score 0 to 1, A Korean multicenter retrospective cohort

Background

Patients with low to intermediate risk atrial fibrillation (AF), defined as non-gender CHA2DS2-VASc score of 0–1, are still at risk of stroke. This study verified the usefulness of ABCD score (Age [≥60 years], B-type natriuretic peptide [BNP] or N-terminal pro-BNP [≥300 pg/ml], Creatinine clearance [<50 ml/min/1.73 m2], and Dimension of the left atrium [≥45 mm]) for stroke risk stratification in non-gender CHA2DS2-VASc score 0–1.

Methods

This multi-center cohort study retrospectively analyzed AF patients with non-gender CHA2DS2-VASc score 0–1. The primary endpoint was the incidence of stroke with or without anti-thrombotic treatment (ATT). An ABCD score was also validated.

Results

Overall, 2694 patients (56.3±9.5 years; female, 726 [26.9%]) were followed-up for 4.0±2.8 years. The overall stroke rate was 0.84/100 person-years (P-Y), stratified as follows: 0.46/100P-Y for an ABCD score 0; 1.02/100P-Y for an ABCD score≥1. The ABCD score was superior to the non-gender CHA2DS2-VASc score in stroke risk stratification (C-index=0.618, P=0.015; net reclassification improvement=0.576, P=0.040; integrated differential improvement=0.033, P=0.066). ATT was prescribed in 2353 patients (86.5%), and the stroke rate was significantly lower in patients receiving non-vitamin K antagonist oral anticoagulant (NOAC) therapy and an ABCD score≥1 than in those without ATT (0.44/100P-Y versus 1.55/100 P-Y; hazard ratio=0.26, 95% confidence interval 0.11–0.63, P=0.003).

Conclusion

The biomarker-based ABCD score demonstrated improved stroke risk stratification in AF patients with non-gender CHA2DS2-VASc score 0–1. Furthermore, NOAC with an ABCD score≥1 was associated with significantly lower stroke rate in AF patients with a non-gender CHA2DS2-VASc score 0–1.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Korean Disease Control and Prevention Agency

Wireless Micro Soft Actuator without Payloads Using 3D Helical Coils

To receive a greater power and to demonstrate the soft bellows-shaped actuator's wireless actuation, micro inductors were built for wireless power transfer and realized in a three-dimensional helical structure, which have previously been built in two-dimensional spiral structures. Although the three-dimensional helical inductor has the advantage of acquiring more magnetic flux linkage than the two-dimensional spiral inductor, the existing microfabrication technique produces a device on a two-dimensional plane, as it has a limit to building a complete three-dimensional structure. In this study, by using a three-dimensional printed soluble mold technique, a three-dimensional heater with helical coils, which have a larger heating area than a two-dimensional heater, was fabricated with three-dimensional receiving inductors for enhanced wireless power transfer. The three-dimensional heater connected to the three-dimensional helical inductor increased the temperature of the liquid and gas inside the bellows-shaped actuator while reaching 176.1% higher temperature than the heater connected to the two-dimensional spiral inductor. Thereby it enables a stroke of the actuator up to 522% longer than when it is connected to the spiral inductor. Therefore, three-dimensional micro coils can offer a significant approach to the development of wireless micro soft robots without incurring heavy and bulky parts such as batteries.

The first survey on patient needs for remote monitoring of cardiac implantable electronic device in South Korea

Funding Acknowledgements

Type of funding sources: None.

Background/Aims: Studies showed that remote device monitoring reduced unnecessary outpatient visits and increased patient satisfaction. As there was no local research on remote monitoring (RM) in Korea, there was a lack of evidence for policy or insurance standards due to the lack of domestic data despite high demand by domestic arrhythmia experts. In order to establish the basis for patient satisfaction, economic efficiency, and safety of wireless monitoring, a survey-based study was planned.

Methods

This was a single-university hospital survey. The satisfaction index was evaluated using a questionnaire to investigate patient satisfaction in outpatient clinics, economic efficiency (measured as home-to-clinic time, waiting time, and actual clinic time), and demand for RM in patients with implantable cardiac devices. The questionnaire was adopted and modified from the Survey on Telehealth Patient Experience by Bas-Villalobos, 2006 (modified Korean version 2.0 by You Mi Hwang, 2020).

Results

Surveys were answered by 171 patients. The mean age of these patients was 71.2 ± 12.4 years. Based on the survey, home to clinic time was usually less than one h, mean waiting time in the hospital until clinic time ranged 42.6 ± 24.5 min, and mean clinic time ranged 3.1 ± 1.7 minutes. Based on the survey, patients favored RM over hospital visits with cardiac implantable electronic device follow-up mainly because of long travel times from home to clinic.

Conclusions

Based on the survey results, there is a clear need for RM in patients who have cardiac implantable electronic devices.

Diphlorethohydroxycarmalol Attenuates Palmitate-Induced Hepatic Lipogenesis and Inflammation

Non-alcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease, encompassing a range of conditions caused by lipid deposition within liver cells, and is also associated with obesity and metabolic diseases. Here, we investigated the protective effects of diphlorethohydroxycarmalol (DPHC), which is a polyphenol isolated from an edible seaweed, Ishige okamurae, on palmitate-induced lipotoxicity in the liver. DPHC treatment repressed palmitate-induced cytotoxicity, triglyceride content, and lipid accumulation. DPHC prevented palmitate-induced mRNA and protein expression of SREBP (sterol regulatory element-binding protein) 1, C/EBP (CCAAT-enhancer-binding protein) α, ChREBP (carbohydrate-responsive element-binding protein), and FAS (fatty acid synthase). In addition, palmitate treatment reduced the expression levels of phosphorylated AMP-activated protein kinase (AMPK) and sirtuin (SIRT)1 proteins, and DPHC treatment rescued this reduction. Moreover, DPHC protected palmitate-induced liver toxicity and lipogenesis, as well as inflammation, and enhanced AMPK and SIRT1 signaling in zebrafish. These results suggest that DPHC possesses protective effects against palmitate-induced toxicity in the liver by preventing lipogenesis and inflammation. DPHC could be used as a potential therapeutic or preventive agent for fatty liver diseases.

Determination of Ethoxyquin in Feeds by Liquid Chromatography: Collaborative Study

Ethoxyquin is a chemical antioxidant used in feeds, ingredients, fats, and oils. A liquid chromatographic (LC) method for determination of ethoxyquin was developed. The method involves acetonitrile extraction of the sample and isocratic Cis reversed-phase chromatography with ammonium acetate buffer-acetonitrile as mobile phase and fluorescence detection. A collaborative study of the determination of ethoxyquin in various meals and extruded pet foods was conducted by The lams Company Research Laboratory. Eleven laboratories analyzed 16 samples (including 2 blind duplicates) consisting of 7 meat meals and 9 extruded pet foods. Sample means ranged from 0.25 to 289 ppm. Repeatability standard deviations ranged from 0.08 to 3.2 ppm, and repeatability relative standard deviations ranged from 4.5 to 32%. Reproducibility standard deviations ranged from 0.12 to 13 ppm, and reproducibility relative standard deviations ranged from 4.5 to 55%. The LC method for determination of ethoxyquin in feeds has been adopted first action by AOAC INTERNATIONAL.

Indole-4-carboxaldehyde Isolated from Seaweed, Sargassum thunbergii, Attenuates Methylglyoxal-Induced Hepatic Inflammation

Glucose degradation is aberrantly increased in hyperglycemia, which causes various harmful effects on the liver. Glyoxalase-1 (Glo-1) is a ubiquitous cellular enzyme that participates in the detoxification of methylglyoxal (MGO), a cytotoxic byproduct of glycolysis that induces protein modification (advanced glycation end-products, AGEs) and inflammation. Here, we investigated the anti-inflammatory effect of indole-4-carboxaldehyde (ST-I4C), which was isolated from the edible seaweed Sargassum thunbergii, on MGO-induced inflammation in HepG2 cells, a human hepatocyte cell line. ST-I4C attenuated the MGO-induced expression of inflammatory-related genes, such as tumor necrosis factor (TNF)-α and IFN-γ by activating nuclear factor-kappa B (NF-κB) without toxicity in HepG2 cells. In addition, ST-I4C reduced the MGO-induced AGE formation and the expression of the receptor for AGE (RAGE). Interestingly, both the mRNA and protein expression levels of Glo-1 increased following ST-I4C treatment, and the decrease in Glo-1 mRNA expression caused by MGO exposure was rescued by ST-I4C pretreatment. These results suggest that ST-I4C shows anti-inflammatory activity against MGO-induced inflammation in human hepatocytes by preventing an increase in the pro-inflammatory gene expression and AGE formation. Therefore, it represents a potential therapeutic agent for the prevention of hepatic steatosis.

Effects of Individuality, Education, and Image on Visual Attention: Analyzing Eye-tracking Data using Machine Learning

Machine learning, particularly classification algorithms, constructs mathematical models from labeled data that can predict labels for new data. Using its capability to identify distinguishing patterns among multi-dimensional data, we investigated the impact of three factors on the observation of architectural scenes: individuality, education, and image stimuli. An analysis of the eye-tracking data revealed that (1) a velocity histogram was unique to individuals, (2) students of architecture and other disciplines could be distinguished via endogenous parameters, but (3) they were more distinct in terms of seeking structural versus symbolic elements. Because of the reverse nature of the classification algorithms that automatically learn from data, we could identify relevant parameters and distinguishing eye-tracking patterns that have not been reported in previous studies.

Direct differentiation of insulin-producing cells from human urine-derived stem cells

The loss of pancreatic β-cells is a cause of diabetes. Therefore, replacement of pancreatic β-cells is a logical strategy for the treatment of diabetes, and the generation of insulin-producing cells (IPCs) from stem cells has been widely investigated as an alternative source for pancreatic β-cells. Here, we isolated stem cells from human urine and investigated their differentiation potential into IPCs. We checked the expression of surface stem cell markers and stem cell transcription factors, and found that the isolated human urine-derived stem cells (hUDSCs) expressed the stem cell markers CD44, CD90, CD105 and stage-specific embryonic antigen (SSEA)-4. In addition, these cells expressed octamer binding transcription factor (Oct)4 and vimentin. hUDSCs could differentiate into adipocytes and osteocytes, as evidenced by Oil-red O staining and Alizarin Red S-staining of differentiated cells, respectively. When we directly differentiated hUDSCs into IPCs, the differentiated cells expressed mRNA for pancreatic transcription factors such as neurogenin (Ngn)3 and pancreatic and duodenal homeobox (Pdx)1. Differentiated IPCs expressed insulin and glucagon mRNA and protein, and these IPCs also secreted insulin in response to glucose stimulation. In conclusion, we found that hUDSCs can be directly differentiated into IPCs, which secrete insulin in response to glucose.

Palmitate induces nitric oxide production and inflammatory cytokine expression in zebrafish

Inflammation markers in zebrafish embryos reflect a toxic response that is common to other animal models and humans. Free fatty acids (FFAs) are known to cause damage in various tissues by inducing inflammation. In this study, we investigated whether a FFA (palmitate) induces inflammation in zebrafish embryos. Nitrous oxide (NO) production and cyclooxygenase-2 (COX-2) mRNA expression were increased in palmitate-treated zebrafish embryos in a dose-dependent manner. mRNA expression of pro-inflammatory cytokines, interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF- α), were also increased. Additionally, the mRNA expression of p65 nuclear factor-kB and I-kB-α were significantly increased after palmitate-treatment. Increased reactive oxygen species (ROS) expression was observed in palmitate-treated zebrafish embryos as well as pericardial edema. Additionally, mRNA expression of pro-inflammatory cytokines were increased in zebrafish liver and pancreas fed with palmitate-contained diet. Taken together, these results indicated that palmitate increases pro-inflammatory mediators in zebrafish embryos, suggesting that zebrafish could be an alternative animal model for inflammatory disease including diabetes.

Evolving affinity between Coulombic reversibility and hysteretic phase transformations in nano-structured silicon-based lithium-ion batteries

Nano-structured silicon is an attractive alternative anode material to conventional graphite in lithium-ion batteries. However, the anode designs with higher silicon concentrations remain to be commercialized despite recent remarkable progress. One of the most critical issues is the fundamental understanding of the lithium-silicon Coulombic efficiency. Particularly, this is the key to resolve subtle yet accumulatively significant alterations of Coulombic efficiency by various paths of lithium-silicon processes over cycles. Here, we provide quantitative and qualitative insight into how the irreversible behaviors are altered by the processes under amorphous volume changes and hysteretic amorphous-crystalline phase transformations. Repeated latter transformations over cycles, typically featured as a degradation factor, can govern the reversibility behaviors, improving the irreversibility and eventually minimizing cumulative irreversible lithium consumption. This is clearly different from repeated amorphous volume changes with different lithiation depths. The mechanism behind the correlations is elucidated by electrochemical and structural probing.

Fabrication of truly 3D microfluidic channel using 3D-printed soluble mold

The field of complex microfluidic channels is rapidly expanding toward channels with variable cross-sections (i.e., beyond simple rounded channels with a constant diameter), as well as channels whose trajectory can be outside of a single plane. This paper introduces the use of three-dimensional (3D) printed soluble wax as cast molds for rapid fabrication of truly arbitrary microfluidic polydimethylsiloxane (PDMS) channels that are not achieved through typical soft lithography. The molds are printed directly from computer-aided design files, followed by simple dissolution using a solvent after molding PDMS, making rapid prototyping of microfluidic devices possible in hours. As part of the fabrication method, the solubility of several build materials in solvents and their effect on PDMS were investigated to remove the 3D-printed molds from inside the replicated PDMS microfluidic channels without damage. Technology limits, including surface roughness and resolution by comparing the designed channels with fabricated cylindrical channels with various diameters, are also characterized. We reproduced a 3D image of an actual human cerebral artery as cerebral artery-shaped PDMS channels with a diameter of 240 μm to prove the developed fabrication technique. It was confirmed that the fabricated vascular channels were free from any leakage by observing the fluorescence fluid fill.

Non-planar PDMS microfluidic channels and actuators: a review

This review examines the state of the art for manufacturing non-planar miniature channels and actuators from PDMS, where non-planar structures are defined here as those beyond simple extrusions of 2D designs, either with rounded or variable cross sections or with an emergence of the channel trajectory out-of-plane. The motivation for 3D PDMS structures and advances in their fabrication are described, focusing on geometries that were previously unachievable through conventional microfabrication. The motivation for non-planar microfluidic channels and actuators is first discussed and the existing literature is grouped into general fabrication themes and described. The structures are organized by their method of fabrication and evaluated based on their relevant properties, including the capability of producing structures with complex geometry, automation of the fabrication process, and minimum feature size. Additional properties are included for work in the more recently emerging field of non-planar PDMS actuators, where the feature size, actuation stroke, and actuation method are the key parameters of interest. In particular, this review considers the impact from recent advances in additive manufacturing, which now allow creation of truly arbitrary 3D structures down to ∼100 μm size scales.

Targeting EphA2 impairs cell cycle progression and growth of basal-like/triple-negative breast cancers

Basal-like/triple-negative breast cancers (TNBCs) are among the most aggressive forms of breast cancer, and disproportionally affects young premenopausal women and women of African descent. Patients with TNBC suffer a poor prognosis due in part to a lack of molecularly targeted therapies, which represents a critical barrier for effective treatment. Here, we identify EphA2 receptor tyrosine kinase as a clinically relevant target for TNBC. EphA2 expression is enriched in the basal-like molecular subtype in human breast cancers. Loss of EphA2 function in both human and genetically engineered mouse models of TNBC reduced tumor growth in culture and in vivo. Mechanistically, targeting EphA2 impaired cell cycle progression through S-phase via downregulation of c-Myc and stabilization of the cyclin-dependent kinase inhibitor p27/KIP1. A small molecule kinase inhibitor of EphA2 effectively suppressed tumor cell growth in vivo, including TNBC patient-derived xenografts. Thus, our data identify EphA2 as a novel molecular target for TNBC.

Baicalein protects rat insulinoma INS-1 cells from palmitate-induced lipotoxicity by inducing HO-1

Objective

β-Cell dysfunction plays a central role in the pathogenesis of type 2 diabetes (T2D), and the identification of novel approaches to improve β-cell function is essential to treat this disease. Baicalein, a flavonoid originally isolated from the root of Scutellaria Baicalensis, has been shown to have beneficial effects on β-cell function. Here, the authors investigated the molecular mechanism responsible for the protective effects of baicalein against palmitate (PA)-induced impaired β-cell function, and placed focus on the role of heme oxygenase (HO)-1.

Methods

Rat pancreatic β-cell line INS-1 cells or mouse pancreatic islets were cultured with PA (500 μM) to induce lipotoxicity in the presence or absence of baicalein (50 μM), and the expressions of the ER stress markers, ATF-3, CHOP and GRP78 were detected by Western blotting and/or qPCR. The involvement of HO-1 was evaluated by HO-1 siRNA transfection and using the HO-1 inhibitor ZnPP.

Results

Baicalein reduced PA-induced ER stress and inflammation and enhanced insulin secretion, and these effects were associated with the induction of HO-1. Furthermore, these protective effects were attenuated by ZnPP and by HO-1 siRNA. Pretreatment of PD98059 (an ERK inhibitor) significantly inhibited the protective effects of baicalein and blocked HO-1 induction. On the other hand, CO production by RuCO (a CO donor) ameliorated PA-induced ER stress, suggesting that CO production followed by HO-1 induction may contribute to the protective effects of baicalein against PA-induced β-cell dysfunction.

Conclusion

Baicalein protects pancreatic β-cells from PA-induced ER stress and inflammation via an ERK-HO-1 dependent pathway. The authors suggest HO-1 induction in pancreatic β-cells appears to be a promising therapeutic strategy for T2D.

Alkylmethylimidazolium tricyanomethanide based supported ion gel membranes for CO2 separation

Supported ion gel membranes with good mechanical stability for CO₂ separation were prepared using triblock copolymers in an ionic liquid.

Transcriptome sequencing of the choroid plexus in schizophrenia

The choroid plexus (CP) has a key role in maintaining brain homeostasis by producing cerebrospinal fluid (CSF), by mediating transport of nutrients and removing metabolic products from the central nervous system and by responding to peripheral inflammatory signals. Although abnormal markers of immune response and inflammation are apparent in individuals with schizophrenia, the CP of these individuals has not been characterized. We therefore sequenced mRNA from the CP from two independent collections of individuals with schizophrenia and unaffected controls. Genes related to immune function and inflammation were upregulated in both collections. In addition, a co-expression module related to immune/inflammation response that was generated by combining mRNA-Seq data from both collections was significantly associated with disease status. The immune/inflammation-related co-expression module was positively correlated with levels of C-reactive protein (CRP), cortisol and several immune modulator proteins in the serum of the same individuals and was also positively correlated with CRP, cortisol and pro-inflammatory cytokines in the frontal cortex of the same individuals. In addition, we found a substantial number of nodes (genes) that were common to our schizophrenia-associated immune/inflammation module from the pooled data and a module we generated from lippopolysaccharides-treated mouse model data. These results suggest that the CP of individuals with schizophrenia are responding to signals from the periphery by upregulating immune/inflammation-related genes to protect the brain and maintain the homeostasis but nevertheless fails to completely prevent immune/inflammation related changes in the brain.

Differential activation of immune/inflammatory response-related co-expression modules in the hippocampus across the major psychiatric disorders

The Stanley Neuropathology Consortium Integrative Database (SNCID, http://sncid.stanleyresearch.org) is a data-mining tool that includes 379 neuropathology data sets from hippocampus, as well as RNA-Seq data measured in 15 well-matched cases in each of four groups: schizophrenia, bipolar disorder (BPD), major depression (MD) and unaffected controls. We analyzed the neuropathology data from the hippocampus to identify those abnormalities that are shared between psychiatric disorders and those that are specific to each disorder. Of the 379 data sets, 20 of them showed a significant abnormality in at least one disorder as compared with unaffected controls. GABAergic markers and synaptic proteins were mainly abnormal in schizophrenia and the two mood disorders, respectively. Two immune/inflammation-related co-expression modules built from RNA-seq data from both schizophrenia and controls combined were associated with disease status, as well as negatively correlated with the GABAergic markers. The correlation between immune-related modules and schizophrenia was replicated using microarray data from an independent tissue collection. Immune/inflammation-related co-expression modules were also built from RNA-seq data from BPD cases or from MD cases but were not preserved when using data from control cases. Moreover, there was no overlap in the genes that comprise the immune/inflammation response-related modules across the different disorders. Thus, there appears to be differential activation of the immune/inflammatory response, as determined by co-expression of genes, which is associated with the major psychiatric disorders and which is also associated with the abnormal neuropathology in the disorders.