CBIO-14. SINGLE CELL RNA SEQUENCING ANALYSIS OF HUMAN GLIOBLASTOMA STEM-LIKE CELL CULTURES AND XENOGRAFT TUMORS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi30-vi30
Author(s):  
Sonali Arora ◽  
Anca Mihalas ◽  
John Bassett ◽  
Anoop Patel ◽  
Patrick Paddison
Keyword(s):  
Single Cell ◽  
Developmental Trajectories ◽  
Expression Patterns ◽  
Experimental Models ◽  
Tumor Formation ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Human Glioblastoma

Abstract Single cell RNA-seq (scRNA-seq) studies for glioma have yielded critical insight into intratumoral heterogeneity and developmental gene expression patterns for primary gliomas. One key conclusion from these studies is that each tumor represents a complex, yet maligned, neuro-developmental ecosystem, harboring diverse cell types, which presumably contribute to tumor growth and homeostasis in specific ways (e.g., vascular mimicry, immune evasion, recreating NSC niches, neural injury responses, etc.). Here, to better understand experimental models of human glioblastoma (GB), we performed single cell RNA-seq analysis of human GB stem-like cells (GSCs) of distinct tumor subtypes (mesenchymal and proneural) during their in vitro culture in serum-free conditions and also during tumor formation in immunocompromised mice. This analysis revealed surprising differences between in vitro and in vivo grown GSCs. Among our results, we find that in vivo mesenchymal GSCs are capable of transitioning to proneural-like states, while proneural GSCs are capable of transitioning to mesenchymal states. We characterize cycling cells based on expression of and G2/M and S phase makers, estimate RNA velocity, and examine different developmental trajectories arising in vitro and in vivo. We also compare and discuss different analysis pipelines for scRNA-seq data.

scholarly journals xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

2018 ◽  
Author(s):  
Avi Z. Rosenberg ◽  
Carrie Wright ◽  
Karen Fox-Talbot ◽  
Anandita Rajpurohit ◽  
Courtney Williams ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Small Rna ◽  
Mirna Expression ◽  
Low Cost ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

scholarly journals Single cell RNA sequencing of calvarial and long bone endocortical cells

2019 ◽  
Author(s):  
Ugur M. Ayturk ◽  
Joseph P. Scollan ◽  
Alexander Vesprey ◽  
Christina M. Jacobsen ◽  
Paola Divieti Pajevic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cultured Cells ◽  
Neutralizing Antibody ◽  
Long Bone ◽  
Appendicular Skeleton ◽  
Rna Seq ◽  
Isolated Cells

ABSTRACTSingle cell RNA-seq (scRNA-seq) is emerging as a powerful technology to examine transcriptomes of individual cells. We determined whether scRNA-seq could be used to detect the effect of environmental and pharmacologic perturbations on osteoblasts. We began with a commonly used in vitro system in which freshly isolated neonatal mouse calvarial cells are expanded and induced to produce a mineralized matrix. We used scRNA-seq to compare the relative cell type abundances and the transcriptomes of freshly isolated cells to those that had been cultured for 12 days in vitro. We observed that the percentage of macrophage-like cells increased from 6% in freshly isolated calvarial cells to 34% in cultured cells. We also found that Bglap transcripts were abundant in freshly isolated osteoblasts but nearly undetectable in the cultured calvarial cells. Thus, scRNA-seq revealed significant differences between heterogeneity of cells in vivo and in vitro. We next performed scRNA-seq on freshly recovered long bone endocortical cells from mice that received either vehicle or Sclerostin-neutralizing antibody for 1 week. Bone anabolism-associated transcripts were also not significantly increased in immature and mature osteoblasts recovered from Sclerostin-neutralizing antibody treated mice; this is likely a consequence of being underpowered to detect modest changes in gene expression, since only 7% of the sequenced endocortical cells were osteoblasts, and a limited portion of their transcriptomes were sampled. We conclude that scRNA-seq can detect changes in cell abundance, identity, and gene expression in skeletally derived cells. In order to detect modest changes in osteoblast gene expression at the single cell level in the appendicular skeleton, larger numbers of osteoblasts from endocortical bone are required.

68 GENE EXPRESSION COMPARISONS BETWEEN BOVINE IN VIVO AND CLONED EMBRYOS PRODUCED BY THREE DIFFERENT METHODS

2006 ◽  
Vol 18 (2) ◽  
pp. 142
Author(s):  
N. Ruddock ◽  
K. Wilson ◽  
M. Cooney ◽  
R. Tecirlioglu ◽  
V. Hall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Nuclear Transfer ◽  
Expression Patterns ◽  
Experimental Models ◽  
Gene Expression Patterns ◽  
Imprinted Genes ◽  
Mammalian Embryo

Developmental pathways in the mammalian embryo are profoundly influenced by the epigenetic interaction of the environment and the genome. Loss of epigenetic control has been implicated in aberrant gene expression and altered imprinting patterns with consequence to the physiology and viability of the conceptus. Bovine somatic cell nuclear transfer (SCNT) is contingent on in vitro culture, and both SCNT and culture conditions are known to induce changes in embryonic gene expression patterns. Using these experimental models, this study compared gene expression of Day 7 cloned blastocysts created from three different SCNT protocols using the same cell line, with Day 7 in vivo blastocysts to elucidate mechanisms responsible for variations in phenotypic outcomes. SCNT methods included: (1) traditional SCNT by subzonal injection (SI); (2) handmade cloning (HMC); and (3) modified serial nuclear transfer (SNT), developed within the group. Four imprinted genes (Grb10, Ndn, Nnat, and Ube3a), four chromatin remodeling genes (Cbx1, Cbx3, Smarca4, and Smarcb1) and two genes implicated in polycystic liver disease (Prkcsh and Sec63) were analyzed in single blastocysts from each treatment (n = 5). All blastocysts expressed Actin, Oct-4 and Ifn-tau. All genes were sequence verified. Several genes were expressed ubiquitously across all groups, including Ndn, Ube3a, Cbx1, Cbx3, and Smarcb1. Interestingly, Grb10 was not expressed in two HMCs and one SNT blastocyst. Nnat was weakly expressed in one in vivo blastocyst and in the majority of cloned blastocysts in all groups. Prkcsh and Sec63 were expressed in all but one HMC blastocyst. While gene expression patterns were mostly maintained following SCNT, the imprinted genes Nnat and Grb10 showed instances of differential or abnormal expression in SCNT embryos. The chromatin remodeling genes were maintained in all SCNT treatments. Prkcsh and Sec63 were both absent in one HMC blastocyst, with implications for liver dysfunction, a condition previously reported in abnormal cloned offspring. The variable mRNA expression following SCNT provides an insight into genetic and environmental factors controlling implantation, placentation, organ formation, and fetal growth.

EBV-Encoded Mirnas Facilitate Inflammation and Tumor Formation Through Both Intra- and Inter-Cellular Regulation In Vivo Mouse Model

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3735-3735
Author(s):  
Natsuko Yamakawa ◽  
Jun Ogata ◽  
Takashi Yahata ◽  
Jun Lu ◽  
Kazuaki Yokoyama ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Tumor Cells ◽  
Small Rnas ◽  
Conflicts Of Interest ◽  
Functional Characterization ◽  
Tumor Formation ◽  
Sequencing Analysis ◽  
Immunodeficient Mice

Abstract Introduction EB virus (EBV) is associated with heterogeneous lymphomas. Hodgkin's lymphoma (HL) cells are embedded in non-neoplastic bystanders: B, T cells, and macrophages. Without these bystander cells, the lymphoma cells are incapable of being engrafted in immunodeficient mice. In this context, the bystanders are tumor-supportive “inflammatory niche”. Recently, EBV-infected cells produce exosomes that contain EBV specifically encoded miRNAs (EBV-miRNAs). The miRNAs are transferred to cells, and involved in tumor metastasis. However, the detailed mechanism is unknown. Accordingly, we hypothesized that exosomal EBV-miRNAs might redirect tumor surrounding immune cells from tumor reactive into tumor-supportive “inflammatory niche”. Methods We evaluated the expression of EBV-miRNAs in EBV+HL clinical specimens by in situ hybridization, their functional characterization in vitro, and their effects on persistent infection and tumor development in vivo humanized NOG mice model. Moreover, in order to clarify its sorting mechanism, trans factor and cis factor which determined secreted and non-secreted miRNAs was analyzed by use of mass-spectrograhy and next-generation sequencing. Results and Discussion The EBV-miRNAs effects were potent on monocyte/macrophage Mo/Mf in inducing CD69, IL-10, and TNF, suggesting that EBV-miRNAs might polarize Mo/Mf into tumor associated Mf (TAM). EBV-miRNAs suppress tumor cell proliferation in vitro, implying that it works as tumor-suppressor in the tumor cells, while they are required to develop LPD in vivo, which seems contradict to the result in vitro. These results suggest that EBV-miRNAs intra-cellularly regulate the tumor cells to adjust to the surrounding circumstances, for example, to escape from immune surveillance, and inter-cellularly regulate Mo/Mf to support the tumor survival or development. Most importantly, exosomal EBV-miRNAs derived from the tumor cells were transferred to Mf in human EBV+ HL samples. Interestingly, one EBV coded miRNA was not secreted at all, though it abundantly expresses in the cells. The miRNA has been reported to strongly promote cell proliferation in EBV infected tumor cells. It made us hypothesized that the sorting system of secretary and non-secretary miRNAs is critical in the formation of “inflammatory niche”. In order to clarify the mechanism of the sorting, the chimeric miRNA was constructed then, we determined the sequence, which regulates secretion and non-secretion, and purified the protein complex, which specifically bound to the sequence. Mass spectrography and successive knockdown assay, the trans factor which inhibits secretion was identified. Moreover, the next sequencing analysis for the small RNAs revealed that abundant EBV-coded small RNAs occupied RNA-induced silencing complex (RISC), and that non-secreted EBV-miRNA was specifically modified. It is now under investigation whether the modification is involved in the sort mechanism between secretary and non-secretary miRNAs. Taken together, EBV-miRNAs have critical roles in intra- and inter-cellular manner. Especially, the functions as an inter-cellular communicator might be important in the tumor formation and the mechanism needs further investigation. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Single Cell RNA-Seq Characterises Pre-Leukemic Transformation Driven By CEBPA N321D in the Hoxb8-FL Cell Line

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3887-3887
Author(s):  
Moosa Qureshi ◽  
Fernando Calero-Nieto ◽  
Iwo Kucinski ◽  
Sarah Kinston ◽  
George Giotopoulos ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Single Cell ◽  
Cell Line ◽  
Single Cells ◽  
Mutant Form ◽  
Rna Seq ◽  
Wild Type ◽  
Leukemic Transformation

Abstract The C/EBPα transcription factor plays a pivotal role in myeloid differentiation and E2F-mediated cell cycle regulation. Although CEBPA mutations are common in acute myeloid leukaemia (AML), little is known regarding pre-leukemic alterations caused by mutated CEBPA. Here, we investigated early events involved in pre-leukemic transformation driven by CEBPA N321D in the LMPP-like cell line Hoxb8-FL (Redecke et al., Nat Methods 2013), which can be maintained in vitro as a self-renewing LMPP population using Flt3L and estradiol, as well as differentiated both in vitro and in vivo into myeloid and lymphoid cell types. Hoxb8-FL cells were retrovirally transduced with Empty Vector (EV), wild-type CEBPA (CEBPA WT) or its N321D mutant form (CEBPA N321D). CEBPA WT-transduced cells showed increased expression of cd11b and SIRPα and downregulation of c-kit, suggesting that wild-type CEBPA was sufficient to promote differentiation even under LMPP growth conditions. Interestingly, we did not observe the same phenotype in CEBPA N321D-transduced cells. Upon withdrawal of estradiol, both EV and CEBPA WT-transduced cells differentiated rapidly into a conventional dendritic cell (cDC) phenotype by day 7 and died within 12 days. By contrast, CEBPA N321D-transduced cells continued to grow for in excess of 56 days, with an initial cDC phenotype but by day 30 demonstrating a plasmacytoid dendritic cell precursor phenotype. CEBPA N321D-transduced cells were morphologically distinct from EV-transduced cells. To test leukemogenic potential in vivo, we performed transplantation experiments in lethally irradiated mice. Serial monitoring of peripheral blood demonstrated that Hoxb8-FL derived cells had disappeared by 4 weeks, and did not reappear. However, at 6 months CEBPA N321D-transduced cells could still be detected in bone marrow in contrast to EV-transduced cells but without any leukemic phenotype. To identify early events involved in pre-leukemic transformation, the differentiation profiles of EV, CEBPA WT and CEBPA N321D-transduced cells were examined with single cell RNA-seq (scRNA-seq). 576 single cells were taken from 3 biological replicates at days 0 and 5 post-differentiation, and analysed using the Automated Single-Cell Analysis Pipeline (Gardeux et al., Bioinformatics 2017). Visualisation by t-SNE (Fig 1) demonstrated: (i) CEBPA WT-transduced cells formed a distinct cluster at day 0 before withdrawal of estradiol; (ii) CEBPA N321D-transduced cells separated from EV and CEBPA WT-transduced cells after 5 days of differentiation, (iii) two subpopulations could be identified within the CEBPA N321D-transduced cells at day 5, with a cluster of five CEBPA N321D-transduced single cells distributed amongst or very close to the day 0 non-differentiated cells. Differential expression analysis identified 224 genes upregulated and 633 genes downregulated specifically in the CEBPA N321D-transduced cells when compared to EV cells after 5 days of differentiation. This gene expression signature revealed that CEBPA N321D-transduced cells switched on a HSC/MEP/CMP transcriptional program and switched off a myeloid dendritic cell program. Finally, in order to further dissect the effect of the N321D mutation, the binding profile of endogenous and CEBPA N321D was compared by ChIP-seq before and after 5 days of differentiation. Integration with scRNA-seq data identified 160 genes specifically downregulated in CEBPA N321D-transduced cells which were associated with the binding of the mutant protein. This list of genes included genes previously implicated in dendritic cell differentiation (such as NOTCH2, JAK2), as well as a number of genes not previously implicated in the evolution of AML, representing potentially novel therapeutic targets. Disclosures No relevant conflicts of interest to declare.

scholarly journals A systematic dissection of human primary osteoblasts in vivo at single-cell resolution

2020 ◽  
Author(s):  
Yun Gong ◽  
Junxiao Yang ◽  
Xiaohua Li ◽  
Cui Zhou ◽  
Yu Chen ◽  
...  
Keyword(s):  
Bone Formation ◽  
Single Cell ◽  
Bone Cells ◽  
Expression Patterns ◽  
Cellular Heterogeneity ◽  
Human Osteoblasts ◽  
Primary Osteoblasts ◽  
Human Primary Osteoblasts

AbstractOsteoblasts are multifunctional bone cells, which play essential roles in bone formation, angiogenesis regulation, as well as maintenance of hematopoiesis. Although both in vivo and in vitro studies on mice have identified several potential osteoblast subtypes based on their different transition stages or biological responses to external stimuli, the categorization of primary osteoblast subtypes in vivo in humans has not yet been achieved. Here, we used single-cell RNA sequencing (scRNA-seq) to perform a systematic cellular taxonomy dissection of freshly isolated human osteoblasts. Based on the gene expression patterns and cell lineage reconstruction, we identified three distinct cell clusters including preosteoblasts, mature osteoblasts, and an undetermined rare osteoblast subpopulation. This novel subtype was mainly characterized by the nuclear receptor subfamily 4 group A member 1 and 2 (NR4A1 and NR4A2), and its existence was confirmed by immunofluorescence staining. Trajectory inference analysis suggested that the undetermined cluster, together with the preosteoblasts, are involved in the regulation of osteoblastogenesis and also give rise to mature osteoblasts. Investigation of the biological processes and signaling pathways enriched in each subpopulation revealed that in addition to bone formation, preosteoblasts and undetermined osteoblasts may also regulate both angiogenesis and hemopoiesis. Finally, we demonstrated that there are systematic differences between the transcriptional profiles of human osteoblasts in vivo and mouse osteoblasts both in vivo and in vitro, highlighting the necessity for studying bone physiological processes in humans rather than solely relying on mouse models. Our findings provide novel insights into the cellular heterogeneity and potential biological functions of human primary osteoblasts at the single-cell level, which is an important and necessary step to further dissect the biological roles of osteoblasts in bone metabolism under various (patho-) physiological conditions.

248 Immunotherapy persister cells uncovered by dynamic single-cell RNA-sequencing

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A268-A269
Author(s):  
Kartik Sehgal ◽  
Andrew Portell ◽  
Elena Ivanova ◽  
Patrick Lizotte ◽  
Navin Mahadevan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Single Cell ◽  
Rna Sequencing ◽  
Ex Vivo ◽  
Interferon Γ ◽  
Rna Seq ◽  
Persister Cells ◽  
Pre Treatment

BackgroundTo understand fundamental mechanisms of immune escape, we leveraged our functional ex vivo platform of murine derived organotypic tumor spheroids (DOTS)1 to determine if drug-tolerant persister cells analogous to oncogene targeted therapies limit efficacy of programmed death (PD)-1 blockade, and to identify therapeutic vulnerabilities to overcome anti-PD-1 (αPD-1) resistance.MethodsMurine syngeneic cancer models with well-characterized response to αPD-1 therapy were chosen: MC38 (sensitive) and CT26 (partially resistant). Bulk and single-cell (sc) RNA-sequencing (RNA-seq) were performed on αPD-1 treated DOTS. In vitro culture studies were conducted with or without cytokines (100 ng/ml) or drugs (500 nM). In vivo studies in mice bearing MC38 or CT26 tumors evaluated the combinatorial strategy with PD-1 blockade. We further evaluated our findings in scRNA-seq of an αPD-1 refractory colorectal cancer (CRC) patient tumor.2ResultsBulk RNA-seq of αPD-1 treated DOTS revealed a mesenchymal resistant phenotype with upregulated TNF-α/NFκB signaling (figure 1). scRNA-seq further identified a discrete sub-population of immunotherapy persister cells (IPCs). These cells expressed a stem-like phenotype including downregulation of E2F targets indicative of quiescence, suppression of interferon-γ response genes, induction of hybrid epithelial-to-mesenchymal state, and active IL-6 signaling (figure 1). Ly6a/stem cell antigen-1 (Sca-1) and Snai1 were found to be differentially upregulated in IPCs resistant to PD-1 blockade (not shown). Sca-1 positivity was confirmed in pre-existing tumor populations in vitro (figure 2). When enriched via sorting, these cells remained more persistently Sca-1+ at 96 hours in culture of CT26 compared to MC38 cells, related to increased autocrine IL-6 production by CT26 Sca-1+ cells. Indeed, IL-6 supplementation was capable of expanding Sca-1+ cells in culture (figure 2). Sca-1+ cells expressing ovalbumin peptide were refractory to OT-1 T cell mediated killing and failed to upregulate MHC class-1 antigen presentation (H-2Kb) in response to IL-6, in contrast to interferon-γ (not shown). Analysis of RNA-seq data further identified Birc2/3 as potential targets limiting TNF-mediated apoptosis of these cells (not shown). Notably, Birc2/3 antagonism depleted Sca-1+ IPCs in vitro and significantly potentiated the impact of PD-1 blockade in vivo in MC38, and less robustly in CT26 (figure 3). Evaluation in a microsatellite-instability high CRC patient identified a pre-existent IPC subpopulation within the αPD-1 refractory pre-treatment tumor, with high SNAI1 expression compared to CRC samples in TCGA (figure 4).Abstract 248 Figure 1Bulk and single-cell (sc) RNA-sequencing (RNA-seq) of MDOTS identifies an anti-PD-1 (αPD-1) resistant subpopulation of persister cells. IgG= isotype controlAbstract 248 Figure 2Pre-existent population of stem cell antigen-1 (Sca-1)+ cells expands in response to interleukin-6 (IL-6), as characterized by flow cytometry evaluation in murine syngeneic cancer models at baseline and after purification by fluorescence-activated cell sorting (FACS). H = hoursAbstract 248 Figure 3Combination of anti-PD-1 therapy with Birc2/3 antagonism increases tumor responses and improves survival. CR = complete responseAbstract 248 Figure 4Single-cell RNA-sequencing (scRNA-seq) of a pre-treatment microsatellite-instability (MSI-H) colorectal cancer (CRC) patient tumor, refractory to anti-PD-1 (αPD-1) therapy, reveals presence of SNAI1-high immunotherapy persister cellsConclusionsHigh-resolution functional ex vivo profiling identified Sca-1+/Snai1high stem-like ‘immunotherapy persister cells‘ and uncovered their anti-apoptotic dependencies targetable with Birc2/3 antagonism to augment αPD-1 efficacy.Ethics ApprovalThis study was approved by the Dana-Farber Animal Care and Use Committee and Novartis Institutional Animal Care and Use Committee. Informed written consent to participate in Dana-Farber/Harvard Cancer Center institutional review board (IRB)-approved research protocols was obtained from the human subject. A copy of the written consent is available for review by the Editor of this journal. The study was conducted per the WMA Declaration of Helsinki and IRB-approved protocols.ReferencesJenkins RW, Aref AR, Lizotte PH, Ivanova E, Stinson S, Zhou CW, et al. Ex Vivo Profiling of PD-1 Blockade using organotypic tumor spheroids. Cancer Discov. 2018;8(2):196–668 215.Gurjao C, Liu D, Hofree M, AlDubayan SH, Wakiro I, Su MJ, et al. intrinsic resistance to immune checkpoint blockade in a mismatch repair-deficient colorectal cancer. Cancer Immunol Res 2019;7(8):1230–6.

scholarly journals Single-cell RNA-seq revealed the role of Alkbh5 in reproduction

2021 ◽  
Author(s):  
Xiaozhong Shen ◽  
Gangcai Xie
Keyword(s):  
Single Cell ◽  
Messenger Rna ◽  
Single Cells ◽  
Rna Seq ◽  
Single Cell Sequencing ◽  
Differential Gene ◽  
Higher Eukaryotes

AbstractN(6)-methyladenosine (m(6)a) is the most common internal modification of messenger RNA (mRNA) in higher eukaryotes. According to previous literature reports, alkbh5, as another demethylase in mammals, can reverse the expression of m(6)a gene in vivo and in vitro. In order to reveal the effect of Alkbh5 deletion on the level of single cells in the testis during spermatogenesis in mice, the data were compared using single-cell sequencing. In this article, we discussed the transcription profile and cell type identification of mouse testis, the expression of mitochondrial and ribosomal genes in mice, the analysis of differential gene expression, and the effects of Alkbh5 deletion, and try to explain the role and influence of Alkbh5 on reproduction at the level of single-cell sequencing.

144 DOSAGE COMPENSATION AND X-LINKED GENE EXPRESSION IN BOVINE IN VIVO AND IN VITRO EMBRYOS

2016 ◽  
Vol 28 (2) ◽  
pp. 202 ◽  
Author(s):  
J. E. Duan ◽  
N. K. Jue ◽  
Z. Jiang ◽  
R. O'Neill ◽  
E. Wolf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Dosage Compensation ◽  
Expression Patterns ◽  
Autosomal Gene ◽  
Rna Seq ◽  
X Gene ◽  
Diploid Cells

In human and mouse diploid cells and gametes, expression levels of X-linked genes are hypothesised to balance with those of autosomal genes (Ohno’s “dosage compensation”). Such a phenomenon, however, has not been systematically studied in cattle or compared between in vivo and in vitro embryos. Using RNA-seq data, we compared dosage compensation and expression differences of X-linked genes in bovine in vitro and in vivo oocytes and embryos. RNA-seq datasets GSE59186 and GSE52415 were non-uniquely (paralogs included) mapped to the bovine reference genome assembly UMD3.1 using tophat2. Cufflinks v1.0.3 was used to estimate fragments per kb of exon per million fragments (FPKM), which were then log2-transformed. In order to assess overall patterns of chromosomal gene expression without bias, statistical outliers were removed. A total of 12 928 X-linked transcripts were used to calculate the relative X to autosomal gene (A) expression (RXE): log2 (X expression) – log2 (A expression) for dosage compensation. Values ≥0 indicate dosage compensation (or X : A ratio ≥ 1); values <0 indicate incomplete dosage compensation; value = –1 indicates no dosage compensation (or X : A ratio = 0.5). Cuffdiff was used to identify differentially expressed genes between stages and the 2 datasets. Cuffnorm normalized FPKM for expression patterns, which were further clustered and graphed in R. Expression pattern distributions across regions on X were calculated by merging Cuffnorm output genes.attr_table to the expression pattern lists. The RXE values were higher than –1 in all embryonic stages studied, with in vitro embryos having higher RXE, suggesting some but incomplete dosage compensation and in vitro embryos exhibiting higher levels of X-gene expression. In vitro-produced immature oocytes and 4-cell embryos had RXE of 0, suggesting that both may be completely compensated. Additionally, embryos of the 2 sources exhibited significant differences in levels of X-gene expression at 4-cell to 8-cell and 16-cell to blastocyst stages. All expressed X-linked genes fell in 5 groups (patterns 1–5): increased, decreased, increased and then decreased, constant, decreased and then increased. Patterns 1 to 4 were seen in both datasets, whereas pattern 5 was only present in vitro, which may be why in vitro embryos had higher dosage of X. We further found that these expression patterns correlated with the genes’ proximity to the X inactivation centre (Xic: ~82 Mb): the highly dynamic patterns 3 and 5 were associated with proximity to Xic, supporting the notion that the Xist RNA spreads along the X through the Xic. In vivo and in vitro bovine oocytes and embryos have undergone some degree but incomplete dosage compensation. Expression of X-linked genes is correlated with their proximity to Xic. Globally, in vivo and in vitro embryos exhibit major differences in levels of X-gene expression.

scholarly journals Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic Hearts

2020 ◽  
Vol 7 ◽  
Author(s):  
Lingfang Zhuang ◽  
Lin Lu ◽  
Ruiyan Zhang ◽  
Kang Chen ◽  
Xiaoxiang Yan
Keyword(s):  
Myocardial Infarction ◽  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Developmental Trajectories ◽  
Transcriptional Profiling ◽  
Sequencing Data ◽  
Signature Genes

Advances in single-cell RNA sequencing (scRNA-seq) technology have recently shed light on the molecular mechanisms of the spatial and temporal changes of thousands of cells simultaneously under homeostatic and ischemic conditions. The aim of this study is to investigate whether it is possible to integrate multiple similar scRNA-seq datasets for a more comprehensive understanding of diseases. In this study, we integrated three representative scRNA-seq datasets of 27,349 non-cardiomyocytes isolated at 3 and 7 days after myocardial infarction or sham surgery. In total, seven lineages, including macrophages, fibroblasts, endothelia, and lymphocytes, were identified in this analysis with distinct dynamic and functional properties in healthy and nonhealthy hearts. Myofibroblasts and endothelia were recognized as the central hubs of cellular communication via ligand-receptor interactions. Additionally, we showed that macrophages from different origins exhibited divergent transcriptional signatures, pathways, developmental trajectories, and transcriptional regulons. It was found that myofibroblasts predominantly expand at 7 days after myocardial infarction with pro-reparative characteristics. We identified signature genes of myofibroblasts, such as Postn, Cthrc1, and Ddah1, among which Ddah1 was exclusively expressed on activated fibroblasts and exhibited concordant upregulation in bulk RNA sequencing data and in vivo and in vitro experiments. Collectively, this compendium of scRNA-seq data provides a valuable entry point for understanding the transcriptional and dynamic changes of non-cardiomyocytes in healthy and nonhealthy hearts by integrating multiple datasets.

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