Cell-specific Expression Patterns Research Articles

Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy.

Cardiac allograft vasculopathy (CAV), a diffuse thickening of the intima of the coronary arteries and microvasculature, is the leading cause of late graft failure and mortality after heart transplantation (HT). Diagnosis involves invasive coronary angiography, which carries substantial risk, and minimally-invasive approaches to CAV diagnosis are urgently needed. Using single-cell RNA-sequencing in peripheral blood mononuclear cells (PBMCs), we sought to identify cell-specific gene expression profiles in CAV. Whole blood was collected from 22 HT recipients with angiographically-confirmed CAV and 18 HT recipients without CAV. PBMCs were isolated and subjected to single-cell RNA-sequencing using a 10X Genomics microfluidic platform. Downstream analyses focused on differential expression of genes, cell compositional changes, and T cell receptor repertoire analyses. Across 40 PBMC samples, we isolated 134,984 cells spanning 8 major clusters and 31 subclusters of cell types. Compositional analyses showed subtle, but significant increases in CD4+ T central memory cells, and CD14+ and CD16+ monocytes in high-grade CAV (CAV-2 and CAV-3) as compared to low-grade or absent CAV. After adjusting for age, gender, and prednisone use, 745 genes were differentially expressed in a cell-specific manner in high-grade CAV. Weighted gene co-expression network analyses showed enrichment for putative pathways involved in inflammation and angiogenesis. There were no significant differences in T cell clonality or diversity with increasing CAV severity. Unbiased whole transcriptomic analyses at single-cell resolution identify unique, cell-specific gene expression patterns in CAV, suggesting the potential utility of peripheral gene expression biomarkers in diagnosing CAV.

Fish arginase constrains excessive production of nitric oxide and limits mitochondrial damage during Aeromonas hydrophila infection

Bacteria-enhanced inducible nitric oxide synthase (iNOS) overproduces nitric oxide (NO) leading to mitochondrial and cellular damage. In mammals, arginase (ARG), the enzyme consuming the same substrate l-arginine with iNOS, was believed to inhibit iNOS activity by competing the substrate. But in fish, this conception has been widely challenged. In this study, the gene expression using real-time quantitative PCR (RT-qPCR) technology showed that when stimulated by Aeromonas hydrophila (A. hydrophila), grass carp (gc) iNOS was up-regulated in head kidney monocytes/macrophages (M0/MФ), and its changes were not detected in the whole tissue of liver or spleen, showing a high degree of cell-specific expression pattern. At the same time, gcARG2 had a high basal expression in tissues and was up-regulated by A. hydrophila stimulation. Next, phthalaldehyde-primaquine reaction was first used in the determination of intracellular urea in fish cells. It was found that the induced gcARG2 led to an increase in the intracellular urea content. Moreover, urea and NO production in M0/MФ were increased in a substrate dose-dependent manner from 30 to 100 μM of l-arginine and reached the highest yield at 300 and 3000 μM of l-arginine, respectively. Furthermore, head kidney M0/MФ was cultured in RPMI1640 medium containing physiological concentration (500 μM) of l-arginine to evaluate the effect of ARG. Under A. hydrophila stimulation, treatment with the arginase inhibitor S-(2-boronoethyl)-l-cysteine (BEC) showed that inhibition of arginase could further enhance the NO production stimulated by A. hydrophila. This in turn led to a cumulation in peroxynitrite (ONOO-) content and an injury of the mitochondrial membrane potential. Our study showed for the first time that fish ARG in head kidney M0/MФ can limit excessive production of NO and harmful products by iNOS to maintain mitochondrial and cellular homeostasis.

P119 Single-cell RNA sequencing in Inflammatory Bowel Disease in patients with Primary Sclerosing Cholangitis: a distinct form of colitis

Abstract Background Primary sclerosing cholangitis (PSC) is an inflammatory disorder of the bile ducts, in which Inflammatory bowel disease (IBD) concomitantly occurs (PSC-IBD). Substantial differences in clinical presentation are observed between PSC-IBD and ulcerative colitis (UC). In this study we aim to find distinct pathomechanisms for PSC-IBD using single-cell RNA sequencing. Methods Forty-seven colonic samples of PSC-IBD (n=24), UC (n=18) and non-IBD subjects (n=5) were collected. Whole biopsies were dissociated into single cells using collagenase digestion. Library preparation was done with 10x Genomics and sequencing was performed on an MGI2000 sequencer. Then, differential abundance, differential expression, and cell-cell interaction analyses were performed. Stainings for DUOX2 and HLA-DR were performed on paraffin embedded colon mucosal slides. Results In total, 71,798 high quality cells identified 54 distinct cell types, including a new type of epithelial cells: DUOX2+ enterocytes. DUOX2+ enterocytes are almost exclusively present in diseased inflamed colon and can act as antigen presenting cells through the expression of MHC2 on its surface. A general shift in cell type composition upon inflammation was observed, comparable between PSC and UC samples. However, an increased abundance was seen for stem cells in non-inflamed (NI) PSC, and not in UC-NI, compared to healthy controls. Additionally, we found distinct gene expression patterns between PSC and UC inflammation: while activation of inflammatory monocytes was observed in PSC inflammation, several types of fibroblasts were activated upon UC inflammation. Conclusion We describe DUOX2+ enterocytes, which may play a role in both PSC and UC colitis through antigen presentation. Furthermore, we show that intestinal inflammation in PSC-IBD, as compared to UC, is characterized by distinct mucosal cell composition and cell-specific gene expression patterns. PSC colitis, and not UC colitis, is driven by activation of inflammatory monocytes, with antigen presentation through HLA-DRB1, and activation of CD4+ T cells. Additionally, an increased abundance of stem cells in PSC-NI could be related with the increased colorectal cancer risk in PSC-IBD.

RBPome identification in egg-cell like callus of Arabidopsis.

RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.

Insulin signaling promotes neurogenesis in the brain of adult zebrafish.

Insulin is a peptide hormone that plays a central role in the regulation of circulating blood glucose in vertebrates, including zebrafish. Increasing evidence has demonstrated the important role of insulin in many brain functions. In zebrafish, two insulin receptor genes (insra and insrb) have been identified. However, their biodistribution in the adult brain as well as their cell-specific expression pattern has not been well described. Using gene expression analysis, in situ hybridization and transgenic fish, we confirmed the expression of insra, insrb, and irs1 (insulin receptor substrate 1, the downstream effector of insulin receptor) in the brain of adult zebrafish and characterized their specific expression in neurons and neural stem cells (radial glia). After demonstrating that intracerebroventricular (ICV) injection resulted in the diffusion of the injected solution within the ventricular system, we analyzed the effect of insulin ICV injection on neurogenesis. We showed that insulin promotes ventricular cell proliferation 24h postinjection. This neurogenic effect appeared to be independent of neuroinflammatory processes. Also, after a mechanical telencephalic stab-wound injury, we highlighted the overexpression of irs1 gene 5 days postlesion notably in the ventricular zone where radial glial cells (RGCs) are localized, suggesting key roles of insulin signaling in regenerative processes. Finally, our results reinforced the expression of insulin-related proteins in the brain of adult zebrafish, highlighting the potential role of insulin signaling on neurogenesis.

Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution.

In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.

The RLR intrinsic antiviral system is expressed in neural retina and restricts lentiviral transduction of human Mueller cells

The retinoic acid-inducible gene I (RIG)-I-like receptor (RLR) family of RNA sensor proteins plays a key role in the innate immune response to viral nucleic acids, including viral gene delivery vectors, but little is known about the expression of RLR proteins in the retina. The purpose of this study was to characterize cell-specific expression patterns of RLR proteins in non-human primate (NHP) neural retina tissue and to examine if RLR pathway signaling restricts viral gene delivery transduction. Since RLR protein signaling converges at the mitochondrial antiviral signaling protein (MAVS), experiments were performed to determine if knockdown of MAVS affected FIVGFP transduction efficiency in the human Mueller cell line MIO-M1. Immunoblotting confirmed expression of RIG-I, melanoma differentiation-associated protein 5 (MDA5), laboratory of genetics and physiology 2 (LGP2), and MAVS proteins in MIO-M1 cells and NHP retina tissue. Double label immunofluorescence (IF) studies revealed RIG-I, LGP2, and MAVS were expressed in Mueller microglial cells in the NHP retina. In addition, LGP2 and MDA5 proteins were detected in cone and retinal ganglion cells (RGC). MDA5 was also present in a subset of calretinin positive amacrine cells, and in nuclei within the inner nuclear layer (INL). Knockdown of MAVS significantly increased the transduction efficiency of the lentiviral vector FIVGFP in MIO-M1 cells, compared to control cells. FIVGFP or AAVGFP challenge did not alter expression of the LGP2, MAVS, MDA5 or RIG-I genes in MIO-M1 cells or NHP retina tissue compared to media treated controls. Our data demonstrate that innate immune response proteins involved in viral RNA sensing, including MDA5, RIG-I, LGP2, and MAVS, are expressed in several cell types within the NHP neural retina. In addition, the MAVS protein restricts non-human lentiviral transduction efficiency in MIO-M1 cells.

Pharmacological HDAC inhibition impairs pancreatic β-cell function through an epigenome-wide reprogramming

Histone deacetylases enzymes (HDACs) are chromatin modifiers that regulate gene expression through deacetylation of lysine residues within specific histone and non-histone proteins. A cell-specific gene expression pattern defines the identity of insulin-producing pancreatic β cells, yet molecular networks driving this transcriptional specificity are not fully understood. Here, we investigated the HDAC-dependent molecular mechanisms controlling pancreatic β-cell identity and function using the pan-HDAC inhibitor trichostatin A through chromatin immunoprecipitation assays and RNA sequencing experiments. We observed that TSA alters insulin secretion associated with β-cell specific transcriptome programming in both mouse and human β-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative β-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. Our data indicate that HDAC activity could be required to protect against loss of β-cell identity with unsuitable expression of genes associated with alternative cell fates.

Identification of Spatial Proteomic Signatures of Colon Tumor Metastasis: A Digital Spatial Profiling Approach

Over 150,000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually >50,000 individuals are estimated to die of CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. CRC tumors are removed en bloc with surrounding vasculature and lymphatics. Examination of regional lymph nodes at the time of surgical resection is essential for prognostication. Developing alternative approaches to indirectly assess recurrence risk would have utility in cases where lymph node yield is incomplete or inadequate. Spatially dependent, immune cell-specific (eg, tumor-infiltrating lymphocytes), proteomic, and transcriptomic expression patterns inside and around the tumor-the tumor immune microenvironment-can predict nodal/distant metastasis and probe the coordinated immune response from the primary tumor site. The comprehensive characterization of tumor-infiltrating lymphocytes and other immune infiltrates is possible using highly multiplexed spatial omics technologies, such as the GeoMX Digital Spatial Profiler. In this study, machine learning and differential co-expression analyses helped identify biomarkers from Digital Spatial Profiler-assayed protein expression patterns inside, at the invasive margin, and away from the tumor, associated with extracellular matrix remodeling (eg, granzyme B and fibronectin), immune suppression (eg, forkhead box P3), exhaustion and cytotoxicity (eg, CD8), Programmed death ligand 1-expressing dendritic cells, and neutrophil proliferation, among other concomitant alterations. Further investigation of these biomarkers may reveal independent risk factors of CRC metastasis that can be formulated into low-cost, widely available assays.

Long non‐coding RNA‐regulated alternative splicing modulates key cancer pathway in lung adenocarcinoma

Long non‐coding RNA‐regulated alternative splicing modulates key cancer pathway in lung adenocarcinoma

EMP1 as a Potential Biomarker in Liver Fibrosis: A Bioinformatics Analysis.

Liver fibrosis is a wound-healing response to chronic injury, which may result in cirrhosis and liver failure. Studies have been carried on the mechanisms and pathogenesis of liver fibrosis. However, the potential cell-specific expressed marker genes involved in fibrotic processes remain unknown. In this study, we combined a publicly accessible single-cell transcriptome of human liver with microarray datasets to evaluate the cell-specific expression patterns of differentially expressed genes in the liver. We noticed that EMP1 (epithelial membrane protein 1) is significantly active not only in CCl4 (carbon tetrachloride)-treated mouse liver fibrosis but also in BDL (bile duct ligation)-induced liver fibrosis and even in human fibrotic liver tissues such as alcoholic hepatitis, NASH (nonalcoholic steatohepatitis), and advanced stage liver fibrosis. Furthermore, we demonstrated that EMP1 is a specific fibrotic gene expressed in HSCs (hepatic stellate cells) and endothelial cells using the Protein Atlas single-cell transcriptome RNA-sequencing clustering. Its expression was significantly elevated in fibrotic HSCs or CCl4 and NASH-induced fibroblasts. Previous research revealed that EMP1 plays a role in proliferation, migration, metastasis, and tumorigeneses in different cancers via a variety of mechanisms. Because HSC activation and proliferation are two important steps following liver injury, it would be interesting to investigate the role of EMP1 in these processes. All of this information suggested that EMP1 could be used as a novel fibrotic liver marker and a possible target in the future.

The Fifth Bioelectronic Medicine Summit Hosted by the Feinstein Institutes for Medical Research (Manhasset, NY) and Columbia Engineering (NY, NY) at The Garden City Hotel, Garden City, NY 11530 on October 11-12th, 2022- Bioelectronic Medicine: Today’s Tools, Tomorrow’s Therapies

The Fifth Bioelectronic Medicine Summit Hosted by the Feinstein Institutes for Medical Research (Manhasset, NY) and Columbia Engineering (NY, NY) at The Garden City Hotel, Garden City, NY 11530 on October 11-12th, 2022- Bioelectronic Medicine: Today’s Tools, Tomorrow’s Therapies

Exploring the potential mechanisms of impairment on genitourinary system associated with coronavirus disease 2019 infection: Bioinformatics and molecular simulation analyses

ObjectiveThe novel coronavirus (severe acute respiratory syndrome coronavirus 2) has been spreading worldwide since December 2019, posing a serious danger to human health and socioeconomic development. A large number of clinical trials have revealed that coronavirus disease 2019 (COVID-19) results in multi-organ damage including the urogenital system. This study aimed to explore the potential mechanisms of genitourinary damage associated with COVID-19 infection through bioinformatics and molecular simulation analysis. MethodsWe used multiple publicly available databases to explore the expression patterns of angiotensin-converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2), and CD147 in major organs in the healthy and disease-specific populations, particularly the genitourinary organs. Single-cell RNA sequencing was used to analyze the cell-specific expression patterns of ACE2, TMPRSS2, CD147, cytokine receptors, and cytokine interacting proteins in genitourinary organs, such as the bladder, kidney, prostate, and testis. Additionally, gene set enrichment analysis was used to investigate the relationship between testosterone levels and COVID-19 vulnerability in patients with prostate cancer. ResultsThe results revealed that ACE2, TMPRSS2, and CD147 were highly expressed in normal urogenital organs. Then, they were also highly expressed in multiple tumors and chronic kidney diseases. Additionally, ACE2, TMPRSS2, and CD147 were significantly expressed in a range of cells in urogenital organs according to single-cell RNA sequencing. Cytokine receptors and cytokine interacting proteins, especially CCL2, JUN, and TIMP1, were commonly highly expressed in urogenital organs. Finally, gene set enrichment analysis results showed that high testosterone levels in prostate cancer patients were significantly related to the JAK-STAT signaling pathway and the Toll-like receptor signaling pathway which were associated with COVID-19. ConclusionOur study provides new insights into the potential mechanisms of severe acute respiratory syndrome coronavirus 2 damage to urogenital organs from multiple perspectives, which may draw the attention of urologists to COVID-19 and contribute to the development of targeted drugs.

Lipid-induced transcriptomic changes in blood link to lipid metabolism and allergic response

Immune cell function can be altered by lipids in circulation, a process potentially relevant to lipid-associated inflammatory diseases including atherosclerosis and rheumatoid arthritis. To gain further insight in the molecular changes involved, we here perform a transcriptome-wide association analysis of blood triglycerides, HDL cholesterol, and LDL cholesterol in 3229 individuals, followed by a systematic bidirectional Mendelian randomization analysis to assess the direction of effects and control for pleiotropy. Triglycerides are found to induce transcriptional changes in 55 genes and HDL cholesterol in 5 genes. The function and cell-specific expression pattern of these genes implies that triglycerides downregulate both cellular lipid metabolism and, unexpectedly, allergic response. Indeed, a Mendelian randomization approach based on GWAS summary statistics indicates that several of these genes, including interleukin-4 (IL4) and IgE receptors (FCER1A, MS4A2), affect the incidence of allergic diseases. Our findings highlight the interplay between triglycerides and immune cells in allergic disease.

Testicular Expression of Antioxidant Enzymes and Changes in Response to a Slow-Release Deslorelin Implant (Suprelorin® 4.7 mg) in the Dog.

Simple SummaryWe investigated the expression of the testicular antioxidant enzyme system, i.e., superoxide dismutase (SOD1 and 2), catalase (CAT), glutathione peroxidase (GPx1), and glutathione disulfide reductase (GSR), in healthy adult and prepubertal dogs and after slow-release GnRH superagonist deslorelin (Suprelorin® 4.7 mg subcutaneous implant, Virbac, France) treatment in adult dogs. qPCR and immunohistochemistry were used to detect gene expression and protein expression and localization, respectively. These antioxidant enzymes were variably expressed within cellular compartments in the seminiferous epithelium and the interstitium. SOD1, CAT, and GSR protein expression were also dependent on the stage of the seminiferous epithelium cycle in normal adult dogs. Deslorelin treatment and prepubertal status affected the expression and localization of the investigated antioxidant enzymes. Our results confirmed the presence of a functional antioxidant enzyme system in the canine testis, which was also observed during deslorelin-induced spermatogenic and steroidogenic arrest, as well as in prepubertal dogs. These results improve our current understanding of the local antioxidant protective mechanisms within the testis in the dog. Spermatogenesis takes place in a hypoxic environment, and antioxidant enzymes protect germ and somatic cells from free radical-mediated damage. Expression of the antioxidant enzyme system in the canine testis has not yet been investigated. We hypothesized that the slow-release GnRH superagonist deslorelin 4.7 mg implant, which induces temporary reversible suppression of endocrine and germinative testicular function, would affect the testicular expression of antioxidant enzymes compared to untreated adult and prepubertal dogs. The goal of this study was to investigate and compare gene (by qPCR, in whole-tissue homogenates) and protein expression (by immunohistochemistry) of superoxide dismutase (SOD1, SOD2), catalase (CAT), glutathione peroxidase (GPx1), and glutathione disulfide reductase (GSR) in the testes of untreated adult (CON, n = 7), prepubertal (PRE, n = 8), and deslorelin-treated (DES, n = 5, 16 weeks after implantation) dogs. We found that in DES dogs, the gene expression of SOD1 was significantly (p < 0.05) lower and GPx1 was higher than in CON, and SOD2 was higher than in PRE. Expression of all, except for the SOD2 mRNA, differed between the CON and PRE dogs. Immunohistochemistry showed distinct cell-specific localization and expression patterns for the antioxidant enzymes in each experimental group. Additionally, in the CON animals, cell-specific SOD1, CAT, and GSR expression was dependent on the stage of the seminiferous epithelium cycle. These findings confirm that members of the antioxidant enzyme system are present in normal adult and prepubertal testis as well as in the deslorelin-treated downregulated adult canine testis, and that this local antioxidant system protects developing germ cells and somatic cells from oxidative damage. Different expression patterns of antioxidant enzymes in various germ cell populations and stages of the seminiferous epithelium cycle may indicate differences in their susceptibility to oxidative stress depending on their developmental and maturation stage. The continued presence of the antioxidant enzymes in the testis of DES dogs offers protection to spermatogonia as well as Sertoli and Leydig cells from oxidative stress during temporary infertility, potentially contributing to ensure the reversibility of suppression and the return of normal spermatogenesis and steroidogenesis after the end of deslorelin treatment.

Comprehensive analysis of shared genetic loci between hippocampal volume and schizophrenia

Schizophrenia and hippocampal volume exhibit a genetic correlation, but the underlying genetic mechanisms remain unclear. Here, we investigated the shared genetic variants in schizophrenia and hippocampal volume using the largest genome-wide association studies (GWASs) data. We identified three genetic loci associated with both schizophrenia and hippocampal volume. Functional annotation analysis suggested that shared genetic variants play a major role via the regulatory effect on gene expression. Expression pattern analyses showed that candidate genes have a spatiotemporal and cell-specific expression pattern across human brain development. These findings provided deeper insights into the genetic mechanisms underlying hippocampus and schizophrenia risk.

P747: LR-MDS IS CHARACTERIZED BY DIFFERENTIAL EXPRESSION OF INFLAMMASOME-RELATED GENES IN SPECIFIC CELL POPULATIONS

Background: Myelodysplastic Syndromes (MDS) are a group of hematopoietic neoplasms characterized by clonal expansion of hematopoietic stem and progenitor cells (HSPC) and peripheral blood cytopenia. MDS can develop from clonal hematopoiesis of indeterminate potential (CHIP) and progress through low-risk (LR) to high-risk (HR)-MDS and further to acute myeloid leukemia (AML). Recent findings emphasize the role of sterile inflammation in the bone marrow (BM) as a driver of neoplastic progression. Our previous analysis of whole BM mononuclear cells (BM-MNC) has revealed distinct expression patterns of inflammasome-related genes, including IL1B and IL18, to be associated with LR-MDS subgroups and clinical features. This raises the prospect of interrupting disease evolution at an early stage by targeted, personalized anti-inflammatory therapy. The development and stratification of such therapies will ultimately require more detailed knowledge of the variety and consequences of inflammation networks in MDS bone marrow. Aims: Our objective was to assess inflammasome-related gene expression levels in individual cell types in the BM of CHIP, LR-MDS and HR-MDS individuals as well as non-CHIP controls in order to determine a) which cell types contribute to the expression of inflammasome-related genes and b) whether specific disease states are associated with consistent patterns of cell-specific gene expression. Methods: Cryopreserved BM-MNC from 3 non-CHIP controls, 3 CHIP individuals, 14 LR-MDS and 5 HR-MDS patients were obtained from the MDS registry and the BoHemE Study (NCT02867085) at the University Hospitals in Dresden and Leipzig. Hematopoietic stem and progenitor cells (HSPC), monocytes, monocytic myeloid-derived suppressor cells (M-MDSC), polymorphonuclear MDSC (PMN-MDSC), B lymphocytes, T lymphocytes and CD45- cells (control) were sorted from thawed BM-MNC on a BD FACS Jazz. RNA was isolated and the gene expression of IL1B, IL18, S100A9, IRAK4, NLRP3, PYCARD, CASP1 and NLRC4 was assessed by RT-qPCR. Results: The majority of the inflammasome-related genes, including IL1B, NLRP3, NLRC4 and S100A9 were expressed in all disease states predominantly by monocytes and M-MDSC (p<0.001). However, IL18 was expressed at the highest level in HSPC. Consistent to our previous analysis of whole BM-MNC, we found an association between cell-specific gene expression and LR-MDS genetics, with HSPC-derived IL18 mRNA being highest in SF3B1-mutated LR-MDS, while monocytic IL1B mRNA was highest in del(5q) LR-MDS. Furthermore, an apparent progression in expression from non-CHIP through to LR-MDS was detected, with mRNA levels of IL1B and NLRP3 in monocytic cells and PYCARD and CASP1 in HSPC increasing from non-CHIP to CHIP between 1.5- and 7.9-fold. From CHIP to LR-MDS, mRNA levels of CASP1 and NLRC4 in monocytic cells and PYCARD both in HPSC and in monocytic cells increased by 1.8- to 2.1-fold. Summary/Conclusion: We identify features of inflammasome-related gene expression in individual cell populations and disease states reflecting the progression from non-CHIP through CHIP to MDS. Our analysis suggests strongly that high resolution studies of gene expression in specific populations or single cells will resolve a spectrum of MDS-related inflammation states relevant to prognosis and personalized therapy. Therefore, we are currently performing RNA-Seq from sorted cell populations in order to extend our analysis beyond the core inflammasome reported here.

Maintaining Transcriptional Specificity Through Mitosis.

Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.

Comprehensive Characterization of Circular RNAs in Ovary and Testis From Nile Tilapia.

Circular RNA (circRNA) is an endogenous biomolecule in eukaryotes. It has tissue- and cell-specific expression patterns and can act as a microRNA sponge or competitive endogenous RNA. Although circRNA has been found in several species in recent years, the expression profiles in fish gonad are still not fully understood. We detected the expression of circRNA in the ovary, testis, and sex-changed gonad of tilapia by high-throughput deep sequencing, and circRNA-specific computing tools. A total of 20,607 circRNAs were obtained, of which 141 were differentially expressed in the testis and ovary. Among these circRNAs, 135 circRNAs were upregulated and 6 circRNAs were downregulated in female fish. In addition, GO annotation and KEGG pathway analysis of the host genes of circRNAs indicated that these host genes were mainly involved in adherens junction, androgen production, and reproductive development, such as ZP3, PLC, delta 4a, ARHGEF10, and HSD17b3. It is worth noting that we found that circRNAs in tilapia gonads have abundant miRNA-binding sites. Among them, 935 circRNAs have a regulatory effect on miR-212, 856 circRNAs have a regulatory effect on miR-200b-3p, and 529 circRNAs have a regulatory effect on miR-200b-5p. Thus, our findings provide a new evidence for circRNA–miRNA networks in the gonads in tilapia.

Biological network topology features predict gene dependencies in cancer cell-lines.

Protein-protein interaction (PPI) networks have been shown to successfully predict essential proteins. However, such networks are derived generically from experiments on many thousands of different cells. Consequently, conventional PPI networks cannot capture the variation of genetic dependencies that exists across different cell types, let alone those that emerge as a result of the massive cell restructuring that occurs during carcinogenesis. Predicting cell-specific dependencies is of considerable therapeutic benefit, facilitating the use of drugs to inhibit those proteins on which the cancer cells have become specifically dependent. In order to go beyond the limitations of the generic PPI, we have attempted to personalise PPI networks to reflect cell-specific patterns of gene expression and mutation. By using 12 topological features of the resulting PPIs, together with matched gene dependency data from DepMap, we trained random-forest classifiers (DependANT) to predict novel gene dependencies. We found that DependANT improves the power of the baseline generic PPI models in predicting common gene dependencies, by up to 10.8% and is more sensitive than the baseline generic model when predicting genes on which only a small number of cell types are dependent. Software available at https://bitbucket.org/bioinformatics_lab_sussex/dependant2. Supplementary data are available at Bioinformatics Advances online.