title: Illumina Infinium MethylationEPIC BeadChip (850k) data of Peripheral blood mononuclear cells from psoriatic patients with blood heat syndrome and blood stasis syndrome, as well as healthy controls

first: Bin

last: Li

address: 1200 Cailun Road, Pudong New Area

institute: Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine

summary: Traditional Chinese medicine emphasizes treatment based on syndrome differentiation. This study aimed to clarify the characteristics of DNA methylation expression profiles in peripheral blood mononuclear cells in patients with psoriasis and analyze the differences in these profiles among different traditional Chinese medicine syndromes of psoriasis in order to provide a material basis for the diversity of these syndromes. Blood samples were collected from 32 participants, including 13 patients with psoriatic blood heat syndrome, 13 patients with psoriatic blood stasis syndrome, and 6 healthy controls. Peripheral blood mononuclear cells were extracted and subjected to DNA quality inspection. An Illumina Human Methylation 850k chip was used to sequence each group of samples. After screening out differentially methylated sites, the distribution of the corresponding differentially methylated genes on the chromatin was determined. According to gene annotation classification and CpG island annotation classification, the differentially methylated regions between sample groups were screened, and Gene Ontology and KEGG pathway analyses were used to perform functional analysis of differentially methylated genes. Finally, the differentially methylated genes closely correlating with psoriasis severity were screened using Spearman’s correlation analysis.

first: Luo

last: Ying

first: Kuai

last: Le

first: Ru

last: Yi

first: Ding

last: Xiaojie

first: Song

last: Jiankun

first: Yang

last: Chunmei

first: Li

last: Xin

last: Bin


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [ChIP-seq]

status: Public on Oct 05 2022

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Room LC6115

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.

overall_design: ChIP-seq binding data to evaluate the effect of ETV6 loss in Ewing sarcoma were determined from paired-end sequencting of ChIP-seq samples in A673 and EW8 cell lines. A673 and EW8 Ewing sarcoma cells engineered to express FKBP12F36V-HA-ETV6 were treated with either DMSO control or dTAGV-1 for 6 or 72 hours to induce ETV6 degradation. Duplicates were used for paired-end ChIP-seq experiments used to evaluate differental binding with ETV6 loss. Base line ChIP-seq binding was also evaluated in parental Ewing sarcoma cell lines with single replicates.  All ChIP-seq samples have matching input DNA reference sample from the same batch and treatment condition.

first: Diana

last: Lu

first: Kimberly

last: Stegmaier


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [ATAC-seq]

overall_design: ATAC-seq was used to evaluate changes in chromatin accessibility with ETV6 loss. ATAC-seq was performed using triplicate samples of A673 ETV6-dTAG cells seeded and treated separately with DMSO or 1 µM dTAGV-1 for 72 hours.


title: RNA-seq of HRasV12-induced senescence with WSTF overexpression

first: Zhixun

last: Dou

address: 185 Cambridge Street, CPZN 4-234

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: We discovered that WSTF is downregulated in senescent cells by autophagy degradation. Forced expression of WSTF inhibits senescence-associated secretory phenotype, via inhibition of chromatin accesibility over inflammatory genes.

overall_design: Primary IMR90 cells were stably expressing vector control or WSTF. The cells were then infected by HRasV12 retrovirus to induce senescence. Three replicates each were included in each conditon for RNA-seq analyses.

first: Murat

last: Cetinbas

first: Ruslan

middle: I

last: Sadreyev


title: Metabolic control of histone acetylation for precise and timely regulation of minor ZGA in early mammalian embryos

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

country: China

institute: College of Life Science,Northeast Agricultural University

summary: We report that oxidized nicotinamide adenine dinucleotide (NAD+) is indispensable for mouse pre-implantation development. NAD+ could avoids excessive minor zygotic gene activation (ZGA) by cooperating with SIRT1 to remove zygotic H3K27ac. In human, NAD+ supplement can promote the removal of zygotic H3K27ac and benefit pre-implantation development. Our findings demonstrate that precise and timely regulation of minor ZGA is controlled by metabolic dynamics, and enhance our understanding of the metabolism of mammalian early embryos.

overall_design:
Examination of H3K27ac in mouse pre-implantation embryos.
Examination of RNA-seq in mouse pre-implantation embryos.

first: Jingyu

first: Jiaming

last: Zhang

first: Weibo

last: Hou

first: Shaorong

last: Gao

first: Guoning

last: Huang

first: Qingran

last: Kong


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [RNA-seq]

overall_design: Gene expression values to evaluate the effect of ETV6 loss in Ewing sarcoma were determined from paired-end sequencting of RNA-seq samles in A673 and EW8 cell lines. A673 and EW8 Ewing sarcoma cells engineered to express FKBP12F36V-HA-ETV6 were treated with either DMSO control or dTAGV-1 for 6, 24, or 72 hours to induce ETV6 degradation. Triplicates for all groups were used for paired-end RNA-sequencing. RNA-seq samples of CRISPR KO of ETV6 in A673 were also obtained to validate the dTAG results (4 control vs. 6 ETV6 KO samples).


title: Fourteen commensals restore immunocompetence in adult germfree mice via maturation of the intestinal vascular system

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary:
The intestinal microbiota influences the development of a normal intestinal physiology, education and functioning of the mucosal immune system. The goal of this study is to analyze how the transcriptional profile of the colonic endothelial cells is influence by colonization of gnotobiotic mice with specific bacterial strains .
The goal of this study is to analyze how the transcriptional profile of the colonic endothelial cells is influence by colonization of gnotobiotic mice with specific bacterial strains .

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent-074809 SurePrint G3 Mouse GE v2 8x60K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied. We analyzed endothelial cells from OMM12 and OMM12+MC2 mice.

first: Rossana

last: Romero

first: Ulrich

last: Steinhoff


title: Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: Lowance Center for Human Immunology

institute: Emory University School of Medicine

summary: Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissue and disease contexts. Still, deeper biological understanding requires comprehensive integration of multiple single-cell -omics (transcriptomic, proteomic, and cell receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in our datasets, we developed SuPERR-seq, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery and characterization of previously hidden cell subsets. We show that by incorporating information from cell-surface proteins and immunoglobulin transcript counts, we accurately remove cell doublets, and prevent widespread cell-type misclassification. This approach uniquely improves identification of heterogenous cell types in the human immune system, including a novel subset of antibody-secreting cells in the bone marrow.

overall_design:
scRNA-seq of the gene expression profile, surface-protein expression profile and the V(D)J profile of 3 Peripheral blood mononuclear cell (PBMC) and 2 Bone marrow (BM) from healthy donors.
Please note that processed data was generated from all GEX, ADT and V(D)J raw data and is linked to the corresponding *[GEX] sample records.

first: Congmin

last: Xu

first: Junkai

last: Yang

first: Astrid

last: Kosters

first: Benjamin

last: Babcock

first: Peng

last: Qiu

middle: E


title: SOX4 facilitates PGR protein stability and FOXO1 expression conducive for human endometrial decidualization

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the direct target genes of SOX4 in differentiated human endometrial stromal cells(hEnSC), differentiated hEnSC cells at the presence of MPA, E2 and cAMP are collected and subjected to ChIP-Seq. After aligned to human Hg38 by STAR, peaks are called by MACS2. Our results show that SOX4 is the key regulator for decidualization by regulating FOXO1, STAT3, PRL and FOSL2. This specific enrichment is confirmed by ChIP-qPCR. Additionally, there are also some other direct genes of SOX4, indicating the essential role of SOX4 in decidualization. This ChIP-Seq data provides fundamental information for our further physiological study of SOX4.

overall_design: ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 hEnSC cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.


title: Transcriptome analysis the iPSC-RPE cells and their derivatives

city: Shanghai

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

summary: We aim to explore the types and expression of RNA in the iPSC-RPE cells and their drivatives.

overall_design: Two iPSC-RPE cells, three dedifferentiatd iPSC-RPE cells (De-iPSC-RPE), three induced iPSC-RPE cells (iRPE), two 4TFs minus crx (4TFs−crx), two 4TFs minus mitf-a (4TFs−mitf-a), two 4TFs minus nr2e1 (4TFs−nr2e1), and two 4TFs minus c-myc (4TFs−c-myc) samples were analysed with RNA sequencing.

first: Xiaoman

last: Zhu

first: Zhiyang

last: Chen


title: Chip-seq analysis the Irpe cells

summary: We aim to explore the target genes regulated by CRX, MITF-A, NE2E1, and C-MYC in iRPE cells

overall_design: Sampes of FLAG-CRX-iRPE cells, FLAG-MITF-A-iRPE cells, FLAG-NR2E1-iRPE cells, FLAG-C-MYC-iRPE cells were used for ChIP-seq analysis


title: Transcriptome and chromatin accessiblity analysis of Gli1+ and Amhr2+ mesenchymes in the fetal murine reproductive tracts

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Precursors for the male and female reproductive tracts (also known as the Wolffian duct and the Müllerian duct) co-exist in a mammalian embryo before sexual differentiation. The Wolffian duct and Müllerian duct are surrounded by their own mesenchymes in the mesonephros, which can be distinguished by their specific expression of Gli1 and Amhr2, respectively. In the XX embryo, during sexual differentiation, the Wolffian duct degenerates. In this study, by tracking the fate of the Gli1+ Wolffian duct mesenchyme in the tamoxifen inducible genetic lineage tracing model Gli1-CreER; Rosa-Tomato, we demonstrate that the Wolffian duct mesenchyme does not regress along with the Wolffian duct epithelium in the XX embryo. Instead, the Wolffian duct mesenchyme is repurposed and becomes a unique mesenchymal population in the female reproductive tract. Profiling the transcriptomes and chromatin accessibilities of the Gli1+ Wolffian duct mesenchyme in XX and XY during sexual differentiation (E14.5 and E16.5) shows signaling pathways and transcriptional factors that potentially involves the female and male fate differentiation of the Gli1+ Wolffian duct mesenchyme. Comparing the transcriptomes between the Gli1+ Wolffian duct mesenchyme and the Amhr2+ Müllerian duct mesenchyme from the neonatal uterus reveals similarities and differences between the two mesenchymal populations in the female reproductive tract. Ex vivo ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract. In summary, our discovery of the contribution of the Wolffian duct mesenchyme to the female reproductive tract provides new insights into our understanding of sexual differentiation of reproductive tracts.

overall_design: RNA-seq and ATAC-seq on sorted Gli1+ mesenchymal cells from XX and XY mesonpehroi on E14.5 and E16.5; and RNA-seq of sorted Gli1+ and Amhr2+ mesenchymes on neontal uteri

first: Fei

last: Zhao

middle: H


title: CAR Density Influences Antitumoral Efficacy of BCMA CAR T Cells and Correlates with Clinical Outcome [ATAC-seq]

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

summary: In this work, we address the impact of CAR density on the in vitro and in vivo functionality of BCMA-CAR T cells. Phenotypic, functional, transcriptomic and epigenomic studies at bulk and single cell level revealed different profiles between CAR T cells with high and low expression of the CAR molecule (CARHigh and CARLow T cells). We analyzed the phenotype of CARHigh and CARLow T cell populations before and after stimulation with tumor cells. Sorted CD4+ and CD8+ CARHigh and CARLow T cell populations from six different CAR T cell productions were profiled using high-throughput RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin (ATAC-seq). To better understand the heterogeneity of CAR T cells and the influence of CAR level on their transcriptomic profile, we performed single cell transcriptomic analysis on 43,981 CAR T cells from three independent productions.

overall_design: We have carried out a comprehensive study of the influence of CAR density in CAR T cell function. We have performed ATAC-seq of CAR T cells.

first: Juan

middle: R

first: Paula

last: Rodriguez-Marquez

first: Felipe

last: Prosper-Cardoso

first: Mikel

last: Hernaez


title: Altered transcriptional profile of Smad4-deficient CTLs during infection with Listeria

status: Public on Oct 04 2022

city: Farmington

first: Linda

middle: S

last: Cauley

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: TGFb is a pleiotropic cytokine which can exert its regulatory effects on differentiation of cytotoxic T lymphocytes (CTLs) and alter their cell fate. Canonical TGFb signaling inhibits the formation of KLRG1+ effector cells and circulating memory cells while inducing the formation of resident memory cells. However, SMAD4 functions contradictory to TGFb where it is required for the formation of KLRG1+ effector cells and circulating memroy cells and actively inhibit the formation of resident memory cells. Using, RNA-Sequencing we identified that Smad4 alters the gene expression profile of pathogen-specific CTLs after intranasal infection with Listeria monocytogenes expressing chicken ovalbumin.

overall_design: mRNA expressiong analysis of 2 samples: WT and Smad4 deficient early effector CD8 T cells (KLRG1lo, CD127lo, CD103lo). D8 Listeria monocytogenes infection

first: Karthik

last: Chandiran


title: Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process

city: Bonn

first: Dan

last: Ehninger

state: NRW

address: Venusberg-Campus 1/99

department: AG Ehninger

institute: DZNE

summary: We employed large-scale phenotyping to analyze not only a few, but hundreds of phenotypes and thousands of molecular markers across tissues and organ systems in a single study in aging C57BL/6J mice. For each phenotype, we established lifetime profiles to determine at which age age-dependent phenotypic change is first detectable relative to the young adult baseline.

overall_design: The study includes young treated groups of animals, subjected to putative anti-aging interventions prior to the onset of age-dependent phenotypic change. In parallel, we assessed genetic variants for their effects on age-sensitive phenotypes in humans.

first: Enzo

last: Scifo

first: Kan

last: Xie

first: Brandon

middle: L

last: Pearson


title: Downstream genes and pathways of ASH1-miR-375-YWHAZ axis in hepatocellular carcinoma

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To explore the mechanism and downstream pathways of  ASH1-miR-375-YWHAZ axis  in hepatocellular carcinoma (HCC). We performed microarray assay to identify the downstream genes of YWHAZ. As a result, we obtained 507 (245 upregulation and 262 downregulation) differentially expressed genes significantly affected by YWHAZ knockdown. Function enrichment analysis showed that these genes were enriched in the “Regulation of actin cytoskeleton” pathway which is related with cell migration and tumor metastasis. We also find that most of the autophagy-associated genes, such as ATG3, ATG5 and ATG7 and EMT related gene E-cadherin were highly correlated with YWHAZ and changed by silencing YWHAZ. Real-time quantitative RT-PCR was performed to verify the microarray results. In conclusion,  the expression profile of many genes were significantly affected by YWHAZ knockdown, which helps to further explore the mechanism of the effects of ASH1-miR-375-YWHAZ axis  in HCC.

overall_design: SMMC-7721 cells transfected with si-YWHAZ_1 or siRNA-NC were used to synthesize double-stranded complementary DNA (cDNA), which was labeled and hybridized on the SurePrint G3 Human Gene Expression Microarray 8×60K v2 (Agilent Technologies, Santa Clara, CA, USA). Processed slides were scanned with the Agilent G2565CA Microarray Scanner (Agilent Technologies) after hybridization and washing. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed lncRNAs and mRNAs between two samples were identified through Fold Change filtering and Student’s t-test. The normalized intensity for each lncRNA and mRNA was presented as a log2-transformed pattern, fold changes >2 and p-values <0.05 were selected as significantly differentially expressed.

first: Juan-Feng

first: Qiu

first: Hui

last: Hu

first: An-Yuan

last: Guo


title: Genes regulated by Hfq (PAR-CLIP)

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

summary: RNAs that cross-link to proteins were isolated and sequenced from FLAG-tagged Hfq or wild-type strains

overall_design: Cells were treated with 4-thiouridine, cross-linked with long wavelength UV light and proteins were purified by using anti-FLAG beads

first: Sandeep

last: Ojha


title: DNA methylation profile from three pairs of melanoma cell lines (WM115/W226-4 ; M4Be/M4BeS2 ; M4Be/TW12)

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

type: Methylation profiling by genome tiling array

summary: DNA methylation profile from three pairs of cell lines (WM115/W226-4 ; M4Be/M4BeS2 ; M4Be/TW12) with common genetic background (human) and derived in tree different organisms (human-rat-mouse) were analysed by Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). The WM-115 cell line was derived from a human primary melanoma in early stage of vertical growth phase (VGP). The WM-266-4 cell line was derived from a cutaneous metastatic site of a malignant melanoma. The M4Be melanoma cell line was established from a human metastatic lymph node. The TW12 cell line is an aggressive variant of the parental M4Be cell line that was obtained in vivo after two serial transplantations (subcutaneous xenografts in new-born immuno-deprived rats). A subclone (TW12) was selected after limit dilutions for its high ability to form lung metastasis. Briefly, M4Be cells were xenografted intravenously in nude mice. Lung metastases were collected, shortly grown in vitro and used for a second cycle of intravenous injection. Lung metastases were collected and established in vitro as the M4BeS2 cell line.

overall_design: DNA methylation analysis on genomic DNA extracted from three pairs of melanoma cell lines, showing different aggressiveness

first: Arnaud

last: Carrier

first: Cécile

last: Desjobert

first: Antoine

last: Daunay

first: Florence

last: Busato

first: Jörg

first: Chantal

last: Etievant

first: Joëlle

last: Riond

first: Paola

middle: B

last: Arimondo


title: Oncogenic role of the non-canonical base-pairing between miRNAs/mRNAs in uveal melanoma.

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Chromosome 3p monosomy is associated with a poor clinical outcome of patients with uveal melanoma. Since a copy of the tumor suppressor miR-16 gene is lost for these patients, we postulated that a 3p loss may reduce the miR-16 amount and activity, promoting RNA derepression and tumor burden (loss of brake effect) as observed in chronic lymphocytic leukemia. Unexpectedly, we found that miR-16 expression level is not decreased despite the 3p monosomy. In contrast, our results suggested that miR-16 activity is impaired in uveal melanoma. Here, we investigated the molecular mechanism explaining the sequestration of miR-16 by RNAs. By defining the miR-16 interactome, two genes sets have been highlighted, suggesting two divergent miR-16 functions. In addition to the canonical miR-16 targets such as CCND3 and CDC25A, we identified another set of miR-16-interacting RNAs called thereafter miR-16 sponges. miR-16 binds to these RNAs sponge without inducing their decay. Mechanistically, the miR-16/RNA non-canonical base-pairing promoted stability of mRNAs involved in cancer cell proliferation. The biological relevance has been challenged in uveal melanoma. We showed that patients with poor overall survival expressed higher levels of miR-16 sponges and canonical miR-16 targets. These results strongly suggested that miR-16 is no longer able to repress its targets and, in contrast, promotes RNA stability and protein expression of oncogenes. miR-16 activity assessment using our Sponge-signature discriminates the patient’s overall survival as efficiently as the current method based on copy number variations and driver mutations detection. To conclude, miRNA loss of function due miRNA sequestration seems to promote cancer burden by two combined events – “loss of brake and an acceleration”. Our results highlight the oncogenic role of the non-canonical base-pairing between miRNAs/mRNAs in uveal melanoma.

overall_design: MP41 cells were transfected with synthetic  miRNA-16 vs miRNA-Control (66nM) (Dharmacon). Cells were harvested before transfection (0h) and then at 6h, 12h, 24h and 48h. RNA was extracted and the RIN was evaluated to ensure the good quality of RNA.

first: Anais

last: Quemener

first: Mari

last: Bernard

first: David

last: Gilot


title: Human umbilical cord mesenchymal stem cells-derived exosomes for treating traumatic pancreatitis in rats

city: chengdu

first: Ruiwu

last: Dai

state: Sichuan

address: No.270 Rongdu Rd, Jinniu District

institute: General Hospital of Western Theater

summary: Background: The therapeutic and protective efects of human umbilical cord mesenchymal stem cells-exosomes (hucMSC-Exs) on traumatic pancreatitis (TP) remain unknown. Here, we established a rat model of TP and evaluated and compared the therapeutic efects of hucMSC-Exs.  Methods: HucMSC-Exs were obtained by ultracentrifugation and identifed using transmission electron microscopy and western blot analysis. TP rats were treated by tail vein injection of hUC-MSCs and hucMSC-Exs. Their homing in rats was observed by performing fuorescence microscopy. Rat pancreatic tissue was subjected to high-throughput sequence to determine transcriptome expression levels. The degree of pancreatic tissue damage was assessed by HE staining, the expression levels of amylase, lipase, and infammatory cytokines were detected by ELISA, apoptosis was detected by TUNEL assay, and the expression levels of various apoptosis-related proteins were detected by western-blot. The expression levels of apoptosis-related molecular markers were detected by RT-qPCR.  Results: The colonization of exosomes was observed in pancreatic tissue. Compared to TP group, the histopathological score of pancreas was signifcantly decreased in the TP+hucMSC-Exs group (P<0.05). Compared to TP group, the activity of serum amylase and lipase was signifcantly decreased (P<0.05). The expression levels of IL-6 and TNF-α were signifcantly decreased, while those of IL-10 and TGF-β were signifcantly increased (P<0.05). The apoptosis index of the TP group was signifcantly increased (P<0.05), whereas that of the TP+hucMSC-Exs groups was signifcantly decreased (P<0.05). Compared to TP group, the expression levels of Bax, Bcl-2, and Caspase-3 were signifcantly decreased in the TP+hUC-MSCs group and TP+hucMSC-Exs group (P<0.05).  Conclusion: HucMSC-Exs can colonize injured pancreatic tissue, inhibit the apoptosis of acinar cells, and control the systemic infammatory response to facilitate the repair of pancreatic tissue.

overall_design: Six SD rats were randomly divided into three groups, namely the control group (Control group), TP group, and human umbilical cord mesenchymal stem cells-Exosomes group (TP+hucMSC-Exs group). In the control group, rats were fxed after anesthesia and laparotomy was performed. The pancreas was gently turned over several times with sterile cotton swabs and then closed. Approximately 1 ml normal saline was injected via the tail veins of rats. In the TP group, rats were anesthetized and fxed as mentioned above and pancreatic tissues were gently isolated. An animal model of TP was established via controlling the injury area using a self-developed multifunctional impactor. Pancreatic tissue was percussed and squeezed at extrusion parameters of 3 cm2/10 kg. Similarly, approximately 1 ml normal saline was injected via the tail veins of rats in the TP+hUC-MSCs group, and a TP model was established for this group. hUC-MSCs (1× 10^5/100  g) were injected via the tail veins of rats in the TP+hUCMSCs group, and a TP model was established for this group. hucMSC-Exs (10 μg/100 g) were injected via the tail veins of rats in the TP+hucMSC-Exs group (Fig. 1). All rats were sacrificed after 24 h of modeling, and pancreatic tissue were retained for subsequent experiments. The multifunctional animal impact equipment has been authorized patent (self-developed, patent number: ZL 2016 1 0347341.5). hUC-MSCs were provided by the Chengdu KangErmei Biological Cell Preparation Center (Number: G01210001).

first: Zhirong

last: Zhao

first: Hongyin

last: Liang

first: Li

last: Han


title: Gene expression-based, individualized outcome prediction for SAbR treated patients with primary RCC

city: Dallas

first: Sangeetha

last: Reddy

state: Texas

address: 2280 Inwood Road

institute: UT Southwestern Medical Center

summary: Transcriptomic GSEA of the pre- and at 1-year post-radiation tumor cells shows changes in the apoptosis and cell senescence pathways

overall_design: In the study presented here, 3 patients out of a cohort of 16 RCC cases, followed up for 1-year post-RT, was used to acquire expression profiles of a total of ~ 19 K unique genes

first: Hannan

last: Raquibul

first: Zhu

last: James


title: Epigenetic regulation of microRNAs in a hepatocellular carcinoma cell line

first: Xing-Xing

last: He

summary: Emerging evidence indicates that microRNAs (miRNAs) are often deregulated in hepatocellular carcinoma (HCC) and that some specific miRNAs are associated with the initiation and progression of HCC. Although miRNAs plays important roles in HCC tumor formation, little is known about the mechanisms that control miRNA expression in HCC. To test if miRNA genes are targeted by epigenetic modifications, miRNA expression profiling was performed in the HCC cell line SK-HEP-1 treated or untreated with 5-AzaC (DNA hypomethylating agent). The results showed that the expression of 33 miRNAs was regulated by the epigenetic drugs. Considering the functional importance of miRNAs in tumorigenesis, it is clear that additional layers of control by miRNA function linked to the epigenetic regulators may exist during cancer development.

overall_design: A genome-wide miRNA microarray was used to identify differentially expressed miRNAs between 5μM 5-azacytidine-treated SK-HEP-1 (SK-2) cells and untreated SK-HEP-1 cells.

first: Qiong-Hui

last: Xie

first: Ju-sheng

last: Lin

first: Ying

last: Chang


title: Transcriptomic analyses of normal-appearing CNS white matter from multiple sclerosis donors reveal subtype-specific molecular signatures of disease

city: Broadway

first: Alessandro

last: Castorina

state: NSW

address: PO box 123

country: Australia

institute: University of Technology Sydney

summary: The transcriptome of normal-appearing white matter for relapse-remitting multiple sclerosis (MS), primary progressive MS and secondary progressive MS was determined using total RNA-sequencing. We then performed a differential gene analysis comparing the normal-appearing white matter for each clinical subtype of MS with non-MS control tissue

overall_design: Comparative analysis of the transcriptional profiles of normal-appearing white matter obtained from non-MS and MS donors diagnosed with different clinical subtypes of disease (RRMS, SPMS, PPMS)

first: Margo

last: Jansen


title: 3’ RNA-seq of whole organisms is superior to standard in cases of sparse data but inferior with respect to identified functions

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary:
Purpose: The goal of this study was to compare 3’ RNA-seq data to standard sequencing in samples collected from zebrafish exposed to control conditions or an elevated level of perfluorobutane sulfonamide (FBSA).
Methods: Dechorionated embryonic zebrafish were statically exposed at 8 hours post fertilization (hpf) to either vehicle control (0.5% methanol) or to 47 µM perfluorobutane sulfonamide (FBSA) in 96-well plate format. Zebrafish embryos were sampled at 48 hpf, before morphological effects were observable but with samples phenotypically anchored to abnormal morphology at 120 hpf. At 48 hpf, 10 embryos were pooled per replicate (n = 3), euthanized via ice bath, and total RNA extracted using a Zymo Research Direct-zol RNA MiniPrep kit. For the standard RNA-seq, library preparation and sequencing was performed by Beijing Genomics Institute (BGI) on their BGISEQ-500 platform (raw data files previously submitted to GEO; GSE186576). For the 3' RNA-seq, library preparation and sequencing was performed by the Center for Quantitative Life Sciences (CQLS) at Oregon State University using the Lexogen QuantSeq 3' FWD library preparation kit and a HiSeq 3000. Both datasets were analyzed using the same RNA-seq analysis pipeline.
Results: We found that 3’ RNA-seq and standard showed specific alignment advantages when focusing on annotated or unannotated regions of the genome, with 3’ RNA-seq showing better alignment to annotated regions. We also found that 3’ RNA-seq was far better at detecting DEGs under conditions of sparse data (fewer reads) but that DEGs identified by standard RNA-seq led to a greater number of statistically enriched biological functions.

overall_design: Comparing 3' RNA-seq data to standard RNA-seq data in samples collected from zebrafish (3 replicates of 10 pooled 48 hpf embryos) developmentally exposed to either control colditions or elevated levels (47 uM) of perfluorobutane sulfonamide (FBSA).

first: Ryan

last: McClure

first: Yvonne

last: Rericha

first: Katrina

middle: M

last: Waters

first: Robyn

last: Tanguay


title: Plants grown in Kennedy Fixation Tubes (KFT)

city: Gainesville

first: Robert

last: Ferl

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

summary: A simulated human-tended flight experiment was conducted by growing Arabidopsis thaliana plants on a phytagel matrix-encased coupon which was inserted into a Kennedy Fixation Tube (KFT) preloaded with RNAlater. RNAseq analysis conducted on these plants showed the ability to capture gravitational responses with high reproducibility. To mimick a suborbital flight profile, plants in KFTs were subjected to clinorotation and its transcriptome was compared to various quiescent controls.

overall_design: Arabidopsis thaliana (Col-0) was grown in Kennedy Fixation Tubes

first: Natasha

middle: J

last: Haveman

first: Mingqi

last: Zhou

first: Jordan

last: Callaham

first: Hunter

middle: F

last: Strickland

first: Anna-Lisa

last: Paul


title: Single-cell transcriptome profiling of primary tumors and paired organoids of pancreatic cancer

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

summary: Pancreatic cancer (PC) is the most lethal common gastrointestinal malignancy with an overall 5-year survival rate of 11%. Recently, a variety of patient-derived models, including patient-derived xenograft (PDX) and cancer organoid models, have paved a way for identifying common responders to chemotherapy. However, the utility of PC organoid for recapitulating hallmarks of corresponding primary tumor at transcriptome level remains to be investigated. We conducted single-cell RNA sequencing (scRNA-seq) for three paired primary tumors and organoids using the 10x Genomics platform to identify common and different phenotypes between them.

overall_design:
All fresh resection specimens and cultured organoids were enzymatically digested to generate single-cell suspensions for scRNA-seq.
-----------------------------------------
Authors state "The corresponding raw data will be submitted to SRA."


title: Distinct responses of newly identified monocyte subsets to advanced gastrointestinal cancer and COVID-19

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: Monocytes are critical cells of the immune system but their role as effectors is relatively poor understood, as they have long been considered only as precursors of tissue macrophages or dendritic cells. Moreover, it is known that this cell type is heterogeneous, but our understanding of this aspect is limited to the broad classification in classical/intermediate/non-classical monocytes, commonly based on their expression of only two markers, i.e. CD14 and CD16. We deeply dissected the heterogeneity of human circulating monocytes in healthy donors by transcriptomic analysis at single-cell level and identified 9 distinct monocyte populations characterized each by a profile suggestive of specialized functions. The classical monocyte subset in fact included five distinct populations, each enriched for transcriptomic sets related to either inflammatory, neutrophil-like, interferon-related, and platelet-related pathways. Non-classical monocytes included two distinct populations, one of which marked specifically by elevated expression levels of complement components. Intermediate monocytes were not further divided in our analysis and were characterized by high levels of HLA genes. Finally, we identified one cluster included in both classical and non-classical monocytes, characterized by a strong cytotoxic signature. These findings provided the rationale to exploit the relevance of newly identified monocyte populations in disease evolution. Collectively, this study unravels an unexpected complexity among human circulating monocytes.

overall_design: Human circulating CD45pos/HLA-DRpos/lineageneg (CD3, CD19, CD56) cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Alessandra

last: Rigamonti

last: Castagna

first: Marika

last: Viatore

first: Federico

last: Colombo

first: Clelia

last: Peano

first: Federica

last: Marchesi

first: Massimo

last: Locati


title: Trib3 modulates PPARg-mediated growth inhibition by interfering with the MLL complex in breast cancer cells

city: Utrecht

first: Miguel

last: Hernandez-Quiles

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

summary: To study the role of Trib3 in breast cancer, we performed RNAseq in Trib3-knockdown MCF7 cells compared to control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of MCF7 cells with blunted expression of Trib3 and control.

first: Aldo

last: Jongejan

first: Eric

last: Kalkhoven


title: Deciphering the transcriptional landscape of human pluripotent stem cell-derived GnRH neurons: the role of Wnt signaling in patterning the neural fate

city: Helsinki

first: Yafei

last: Wang

state: Finland

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Hypothalamic gonadotropin-releasing hormone (GnRH) neurons lays the foundation for human development and reproduction, however, the critical cell populations and the entangled mechanisms underlying the development of human GnRH neurons remain poorly understood. Here, by utilizing our established human pluripotent stem cells-derived GnRH neuron model, we decoded the cellular heterogeneity and differentiation trajectories at the single-cell level. We found that a glutamatergic neuron population, which generated together with GnRH neurons, showed similar transcriptomic properties with olfactory sensory neuron and provided the migratory path for GnRH neurons. Through trajectory analysis, we identified a specific gene module activated along the GnRH neuron differentiation lineage, and we examined one of the transcription factors, DLX5, expression in human fetal GnRH neurons. Furthermore, we found that Wnt inhibition could increase DLX5 expression, and improve the GnRH neuron differentiation efficiency through promoting neurogenesis and switching the differentiation fates of neural progenitors into glutamatergic neurons/GnRH neurons. Our research comprehensively reveals the dynamic cell population transition and gene regulatory network during GnRH neuron differentiation.

overall_design: Single Cell RNA-seq data for human pluripotent stem cells and the cells collected along GnRH neuron differentiation.

first: Taneli

last: Raivio


title: DNA Methylation Profiling in Rare Sellar Esthesioneuroblastoma

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

summary: Histologic diagnosis of sellar masses can be challenging, particularly in rare neoplasms and tumors without definitive biomarkers. DNA methylation has recently emerged as a useful diagnostic tool. To illustrate the clinical utility of machine-learning-based DNA methylation classifiers, we report a rare case of primary sellar esthesioneuroblastoma diagnosed by DNA methylation classificiation but histologically mimicking a nonfunctioning pituitary adenoma.

overall_design: This is a case report in which DNA methylation data was obtained using illumina arrays on a single tissue sample obtained from a mass of the sella turcica.

first: Kyla

last: Wright

first: Kristyn

last: Galbraith

first: Matija

last: Snuderl

first: Nidhi

last: Agrawal


title: SARS-CoV-2 infection of human pluripotent stem cell-derived liver organoids reveals potential mechanisms of liver pathology

city: Cambridge

first: Rudolf

last: Jaenisch

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: SARS-CoV-2 infection of human pluripotent stem cell-derived liver organoids reveals potential mechanisms of liver pathology (scRNA-Seq)

summary: Symptoms of liver damage are observed in nearly half of patients that succumb to severe SARS-CoV-2 infection. Here we use human induced pluripotent stem cell-derived liver organoids (HLOs) to recapitulate and characterize liver pathology following virus exposure. Utilizing single-cell sequencing technology, we identified robust transcriptomic changes that occur in SARS-CoV-2 infected liver cells as well as uninfected bystander cells.  Our results show a significant induction of many inflammatory pathways, including IFN-α, INF-γ and IL-6 signaling. Our results further identify IL-6 signaling as a potential mechanism for liver-mediated activation of circulating macrophages.

overall_design: Human liver organoids were differentiated from human pluripotent stem cells (hPSCs) and  infected with live SARS-CoV-2 virus. The transcriptional changes observed were compared with hPSC derived liver organoids infected with either heat-inactivated SARS-CoV-2 virus or mock infected.

first: Alexsia

last: Richards

first: Max

last: Friesen

first: M

last: Barrasa


title: FBP1 acts as a protein phosphatase to dephosphorylate histone H3

city: hangzhou

first: zhimin

last: lu

address: 258kaixuan rd

institute: zhejiang university

summary:
We report nuclear FBP1 interacts with PPARa and binds to the promoter regions of PPARa-mediated b-oxidation genes. S170-phosphorylated FBP1 with an altered catalytic domain structure functions as a protein phosphatase that dephosphorylates histone H3 at T11 and suppresses PPARa-mediated gene expression.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FBP1 and PPARa with glucose deprivation in L02 cells.

overall_design: Examine of FBP1 and PPARa regulated genes under glucose deprivation in L02 cells.

first: ZHENG

first: MIN

last: Li


title: SARS-CoV-2 infection of human pluripotent stem cell-derived liver organoids reveals potential mechanisms of liver pathology (Bulk RNA-Seq)

overall_design: Human liver organoids were differentiated from human pluripotent stem cells (hPSCs) and infected with live SARS-CoV-2 virus. Some of the samples were exposed to macrophages and treated with tocilizumab. The transcriptional changes observed were compared with hPSC derived liver organoids infected with either heat-inactivated SARS-CoV-2 virus or mock infected, either exposed or not exposed to macrophages.


title: TGF-beta-upregulated Lnc-Nr6a1 acts as a reservoir of miR-181 and mediates assembly of a glycolytic complex [RNA-seq]

city: Seville

first: Jose

middle: Antonio

last: Guerrero-Martinez

state: Seville

address: Av. Americo Vespucio, N 24

department: Genome Biology

institute: CABIMER

summary: Long noncoding RNAs (lncRNAs) have emerged as key regulators in a wide range of biological processes. The involvement of lncRNAs in epithelial-to-mesenchymal transition (EMT) has been well stablished; however, the role as immediate-early regulators is still unclear. Here, we identified a mouse miRNA-host gene lncRNA (lnc-Nr6a1) early upregulated during EMT. We show that this lncRNA is processed giving rise to abundant polyadenylated isoforms, lnc-Nr6a1 and lnc-Nr6a1-2, and a longer non-polyadenylated microprocessor-driven lnc-pri-miRNAS containing clustered pre-miRNA-181a2 and pre-miRNA-181b2 hairpins. Ectopic expression of lnc-Nr6a1-1/2 isoforms enhance cell migration and invasive capacity of the cells, whereas the expression of isoforms and miR-181a2/b2 confers anoikis resistance. Lnc-Nr6a1 gene deletion results in cells with lower adhesion capacity and reduced glycolytic metabolism which are restored by lnc-Nr6a1-1 isoform expression. We perform identification of direct RNA interacting proteins (iDRIP) to identify proteins interacting directly with lnc-Nr6a1-1 isoform. We define a network of interacting proteins, including glycolytic enzymes, desmosome proteins and chaperone proteins and we demonstrated that lnc-Nr6a1-1 isoform directly binds and acts as a scaffold molecule for the assembly of ENO1, ALDOA, GAPDH, PKM glycolytic enzymes along with LDHA, supporting substrate canneling for efficient glycolysis. Our results unveil a role of lnc-Nr6a1 as a multifunctional lncRNA acting as a backbone for multiprotein complexes formation and as a primary microRNAs reservoir.

overall_design: Transcriptome profiles of NMuMG mouse glandular epithelial cells treated with TGFβ1 at 2h and control cells were generated by deep sequencing, in duplicates, using Illumina NextSeq 500 Mid Output.

first: José

middle: A

last: Pintor-Toro

first: Salvador

last: Polo Generelo

first: Belén

last: Torres

last: Guerrero-Martínez

middle: C

last: Reyes

first: Jesús

last: Vázquez


title: TGF-beta-upregulated Lnc-Nr6a1 acts as a reservoir of miR-181 and mediates assembly of a glycolytic complex [ChIP-seq]

overall_design: Binding profiles of Lamin A/C from NMuMG mouse glandular epithelial cells (control and KO cells) were generated by deep sequencing.


title: Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta

city: Farmington

first: Stefan

last: Pinter

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health


title: Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [Infinium methylEPIC]

summary: Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants of these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development.  Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely-used model for the human syncytiotrophoblast. While these isogenic panels trigger a GATA2/3 and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes, and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene co-expression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition and function, and that the compound haploinsufficiency of the pseudoautosomal region likely plays a key role in these changes.

overall_design: Bisulfite converted DNA from the 2 samples were hybridised to the Illumina Infinium methylEPIC (850K) Human Methylation Beadchip

first: Darcy

middle: T

last: Ahern

first: Prakhar

last: Bansal

first: Maria

middle: K

last: Armillei

first: Isaac

middle: V

last: Faustino

first: Yuvabharath

last: Kondaveeti

first: Heather

last: Glatt-Deeley

first: Erin

last: Banda


title: Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [RNA-seq]

summary:
Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants of these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development.
Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely-used model for the human syncytiotrophoblast. While these isogenic panels trigger a GATA2/3 and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes, and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene co-expression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition and function, and that the compound haploinsufficiency of the pseudoautosomal region likely plays a key role in these changes.

overall_design: 3'mRNA from the hiPSCs was sequenced on a NextSeq500 in 75bp single-end reads.


title: Murine models of pancreatic cancer: KPC

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

summary: We harvested and sequenced the spontaneous pancreatic tumor generated by a 6-month-old KPC mouse (KrasLSL-G12D; Trp53LSL-R172H; Ptf1a-Cre).

overall_design: This 10X Genomics single-cell RNA sequencing repository includes raw and processed data files from a pancreatic KPC tumor. Single-cell cDNA libraries were prepared and sequenced at the University of Michigan Advanced Genomics Core using the 10x Genomics platform. The sample was run using paired-end 50 cycle reads on NovaSeq 6000 (Illumina) to a depth of 100,000 reads. Alignment was performed by the University of Michigan Advanced Genomics Core. Parameters include Cell Ranger version 3.1.0 (default settings), initial expected cell count of 10,000.

first: Katelyn

last: Donahue

first: Nina

last: Steele


title: TGF-beta-upregulated Lnc-Nr6a1 acts as a reservoir of miR-181 and mediates assembly of a glycolytic complex

last: Guerrero-Martinez


title: Determination of transcriptomic changes associated with progressive drought stress in ethanol treated vs non-treated control Arabidopsis plants

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

summary: We report the gene expression profiles of Arabidopsis seedlings treated with or without ethanol under drought conditions.

overall_design: Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 10 days. Seedlings were then transferred to ceramics granular soil (SAKATA SEED CORPORATION, Japan) and grown for 5 days. Ethanol pretreatment was performed by immersing the pots in trays containing 10 mM Ethanol for 3 days. Drought treatment was then started by removing excess water from the trays and stopping subsequent watering. Shoots were harvested at 0, 1, 3, 5, and 7 days after the onset of drought treatment.

first: Zarnab

last: Ahmad

first: Daisuke

last: Todaka

first: Kuhrram

last: Bashir

first: Satoshi

last: Takahashi

first: Maho

last: Tanaka

first: Atsushi

last: Nagano

first: Motoaki

last: Seki


title: Transcriptomic analysis of ethanol-pretreated Arabidopsis WT shoots under drought conditions

summary: We report the differentially expressed  genes between water-pretreated and ethanol-pretreated plants under drought conditions.

overall_design: Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Seedlings were then transferred to ceramics granular soil (SAKATA SEED CORPORATION, Japan) and grown for 5 days. Ethanol pretreatment was performed by immersing the pots in trays containing 10 mM Ethanol for 3 days. Drought treatment was then started by removing excess water from the trays and stopping subsequent watering. Shoots were harvested at 0, 3, 10 and 13 days after the onset of drought treatment.


title: Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [CytoSNP-850k]

first: Stefan

last: Pinter

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

overall_design: Genomic DNA was isolated from the hiPSCs and analyzed by CytoSNP-850k Infinium bead array (Illumina)

first: Darcy

last: Ahern

first: Prakhar

last: Bansal

last: Armillei


title: Ethanol Treatment Enhances Drought Stress Tolerance in Plants

summary: Gene expression profiles of ethanol treated drought-stressed roots and shoots was performed at 3, 24, and 72 h after ethanol treatment and 1, 3, and 5 days after drought stress were analyzed using the custom microarray Agilent-034592.

overall_design: Seeds of Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Plantlets were then transferred to ceramics granular soil (size 2.5L, Sakatanotane, Japan) and grown for 8 days at 22°C. The drought treatment was then commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately at 0, 1, 3, 5, 7 and 9 days after the onset of drought treatment.

first: Khurram

first: Sultana

last: Rasheed

first: Akihiro

last: Matsui


title: Tumor-produced and aging-associated oncometabolite, methylmalonic acid, promotes cancer-associated fibroblast activation to drive metastatic progression

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: The systemic metabolic shifts that occur during aging and the local metabolic alterations of a tumor, its stroma and their communication cooperate to establish a unique tumor microenvironment (TME) that fosters cancer progression. Here, we show that methylmalonic acid (MMA), an aging-increased oncometabolite that is also produced by aggressive cancer cells, activates fibroblasts in the TME and stimulates the release of extracellular vesicles (EVs) that drive cancer progression, drug resistance and metastasis. The cancer-associated fibroblast (CAF)-released EV cargo is modified as a result of reactive oxygen species (ROS) generation and activation of the canonical and noncanonical TGFβ signaling pathways in CAFs. EV-associated IL-6 functions as a stroma-tumor messenger that activates the JAK/STAT3 and TGFβ signaling pathways in tumor cells and promote an epithelial-to-mesenchymal transition (EMT) and drug resistance in vitro, and metastatic progression in vivo. Our findings reveal the role of MMA in the activation of CAFs to drive metastatic reprogramming, unveiling multiple potential therapeutic avenues to target MMA at the nexus of aging, the tumor microenvironment and metastasis.

overall_design: MRC5 lung fibroblasts were treated with 1mM MMA for 5days

first: Zhongchi

last: Li

first: Vivien

last: Low

first: John

last: Blenis


title: Activation of WNT signaling in CD4+ T cells promotes immune suppression in pancreatic cancer

first: Marina

last: Pasca di Magliano

institute: University of Michigan

summary: We utilized the inducible conditional knockout Tcf7 mouse model to specifically deplete Tcf7 in CD4+ T cells by providing mice with tamoxifen, and then orthotopically inject KPC cells into the pancreas to develop tumor. Single cell RNA sequencing revealed that CD4+ T cells are reprogrammed after Tcf7 depletion to shape the immune microenvironment during pancreatic tumorigenesis.

overall_design: This 10X Genomics single cell RNA sequencing repository includes raw and processed data files from orthotopic tumors in Cd4-CreERT2;Tcf7fl/fl  or Cd4-CreERT2;Tcf7+l+ mice treated with tamoxifen. Single cell cDNA libraries were prepared and sequenced at the University of Michigan Advanced Genomics Core using the 10x Genomics platform. The sample was run using paired-end 50 cycle reads on NovaSeq 6000 (Illumina) to a depth of 100,000 reads. Alignment was performed by the University of Michigan Advanced Genomics Core. Parameters include Cell Ranger version 4.0.0 (default settings), initial expected cell count of 20,000.

first: Wenting

last: Du

first: Katelyn

last: Donahue


title: MCL-1 is a Master Regulator of Cancer Dependency on Fatty Acid Oxidation

city: Boston

first: Michelle

last: Prew

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: MCL-1 is an anti-apoptotic BCL-2 family protein essential for survival of diverse cell types and is a major driver of cancer and chemoresistance. The mechanistic basis for the oncogenic supremacy of MCL-1 among its anti-apoptotic homologs is unclear and implicates physiologic roles of MCL-1 beyond apoptotic suppression. Here we find that MCL-1-dependent hematologic cancer cells specifically rely on fatty acid oxidation (FAO) as a fuel source because of metabolic wiring enforced by MCL-1 itself. We demonstrate that FAO regulation by MCL-1 is independent of its anti-apoptotic activity, based on metabolomic, proteomic, and genomic profiling of MCL-1-dependent leukemia cells lacking an intact apoptotic pathway. Genetic deletion of Mcl-1 results in transcriptional downregulation of FAO pathway proteins such that glucose withdrawal triggers cell death despite apoptotic blockade. Our data reveal that MCL-1 is a master regulator of FAO, rendering MCL-1-driven cancer cells uniquely susceptible to treatment with FAO inhibitors.

overall_design: RNA-seq data for DKO (Bax-/-,Bak-/-) and TKO (Bax-/-,Bak-/-,Mcl-1-/-) B-ALL cells cultured in regular (Reg) or low glucose (LG) media for 24 hours

first: Utsarga

last: Adhikary

first: Joseph

last: Opferman

first: Loren

middle: D

last: Walensky


title: A non-synonymous SNP in SIRT6 predicts neurological severity in Friedreich ataxia

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: Friedreich ataxia (FRDA) is a recessive neurodegenerative disease characterized by progressive ataxia, dyscoordination, and loss of vision. The variable length of the pathogenic GAA triplet repeat expansion in the FXN gene in part explains Inter-individual variability in severity of disease. The GAA repeat expansion leads to epigenetic silencing of FXN; therefore, variability in properties of epigenetic effector proteins could also regulate the severity of FRDA. In an exploratory analysis, DNA from 88 FRDA patients was analyzed to determine if any of 5 non-synonymous SNPs in HDACs/ SIRTs predicted FRDA disease severity. Results suggested the need for a full analysis  (569 FRDA patients) at the rs352493 locus in SIRT6 (S46N SNP). Disease features were compared between patients with the common N46 SIRT6 variant and the less common S46 variant. Biochemical properties of SIRT6 were compared between S46 and N46. Linear regression of the exploratory cohort suggested a SNP (rs352493) in SIRT6 predicted neurologic severity. In follow up analysis, the genotype of SIRT6 at the locus rs352493 predicted disease features of FRDA. Patients with the S46 SIRT6 variant performed better on measures of neurological and visual function over time when compared to the more common N46 SIRT6 variant. S46 SIRT6 did not alter expression or enzymatic activity of SIRT6 or FXN however, S46 patients showed whole transcriptome differences compared to N46 patients, indicative of compensatory mechanisms against whole transcriptome changes seen in FRDA.

overall_design: rnaseq and chipseq assay for 4 Friedreich Ataxia patients, 2 of which have the N46 genotype, the other two have the S46 genotype

first: Liz

last: Soragni

first: Joel

last: Gottesfeld


title: Chronic cortisol differentially impacts Major Depression-patient stem cell derived astrocytes in vitro

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Major Depression (MDD) is a prevalent psychiatric disorder and exposure to stress is robust risk factor for MDD. Clinical data and rodent models have indicated the negative impact of chronic stress induced hormones like cortisol on brain volume, memory, and cell metabolism. However, the cellular and transcriptomic changes that occur in the brain after prolonged exposure to cortisol are less understood. Furthermore, astrocyte-specific contribution to cortisol-induced neuropathology remains understudied. Here, we have developed an in vitro model of “chronic stress” using human induced pluripotent stem cell-derived astrocytes treated with cortisol for 7 days. Whole transcriptome sequencing reveals differentially expressed genes (DEGs) uniquely regulated in chronic cortisol compared to acute cortisol treatment. Utilizing this paradigm, we examined the stress response transcriptome of astrocytes generated from MDD patient iPSCs. MDD-specific DEGs related to GPCR ligand binding, synaptic signaling, and ion homeostasis. Together, these data highlight the unique role astrocytes play in the central nervous system and present interesting genes for future study into the relationship between chronic stress and MDD.

overall_design: RNA-Seq on patient-derived astrocytes under various stimulation and disease states.

first: Kelly

last: Heard

first: Maxim

middle: N

last: Shokhirev

first: Fred

last: Gage

first: Krishna

last: Vadodaria


title: CSF1R mediates effects of miR-34a loss during intestinal tumorigenesis in ApcMin mice (tumor organoid)

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: To address the in vivo relevance of CSF1R regulation by miR-34a during intestinal tumor formation, we generated ApcMin/+ mice with intestinal-epithelial cell (IEC)-specific deletions of the Mir34a and/or Csf1r genes. The mRNA expression profiles of tumor organoids derived ffrom intestinal adenomas with and without functional miR-34a and/or Csf1r were compared.

overall_design: Mice were sacrificed at 18-20 weeks of age. Tumor organoids were grown for 3-4 passages. 3 tumor organoid RNA samples were obtained for each genotype; each tumor organoid RNA sample represented a pool of 3-5 tumors isolated from the same mouse.

first: Fangteng

last: Liu

first: Heiko

last: Hermeking


title: Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [RNA-seq TBL]

first: Stefan

last: Pinter

state: CT

overall_design: mRNA from the trophoblast-like (TBL) samples was sequenced on a NovaSeq (Illumina) in 100bp paired-end reads.

first: Darcy

last: Ahern

first: Prakhar

last: Bansal

first: Maria

last: Armillei

first: Isaac

last: Faustino

first: Yuvabharath

last: Kondaveeti

first: Heather

middle: R

last: Glatt-Deeley

first: Erin

last: Banda


title: A novel oncogenic enhancer of estrogen receptor positive breast cancer

first: Wanliang

last: Lu

address: No.38 Xueyuan Road, Haidian District

institute: Peking University

summary: To understand  the regulatory landscape of oncogene c-Myc in breast cancer, two epigenetic hallmarks of open chromatin, consisting of H3K4me1 and H3K27ac, were investigated by ChIP-seq in distinct types of human breast cancer cells (estrogen receptor positive MCF-7 and triple-negative MDA-MB-231), respectively. By visualizing the ChIP-seq at c-Myc locus,  we noticed that the H3K4me1 and H3K27ac signals were enriched remarkably upstream ~65 kb of c-Myc in MCF-7 cells but not in MDA-MB-231 cells. The results indicated that c-Myc may be regulted by an enhancer located upstream ~65 kb.

overall_design: ChIP-Seq data from MCF-7 and MDA-MB-231 cells

first: Chunjie

last: Bao

first: Jialun

last: Duan

first: Ying

last: Xie


title: Inter-organellar and systemic survival responses to impaired mitochondrial matrix protein import in skeletal muscle

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

department: Research Program for Molecular Neurology

summary: Mitochondrial functions are largely performed by proteins imported from cytosol. Impaired protein import in mitochondria affects the maintenance of intra-mitochondrial anabolic and energy metabolic pathways. It leads to cytosolic accumulation of mistargeted proteins and activation of cellular stress responses. To explore the communication between these mechanism in mammalian system, we targeted the co-chaperone of mitochondrial Hsp70, a GrpE Like protein 1 (Grpel1), in mice. We show that loss of protein import into mitochondrial matrix results in mitochondrial dysfunction, which triggers stress responses. The total shut down of mtHSP70 function by overall knockout of Grpel1 resulted in early embryonic lethality, and tamoxifen-induced skeletal muscle-specific knockout of Grpel1 caused rapid muscular atrophy. We show here, with transcriptomics analysis, that protein-import failure in mitochondria increased cellular proteotoxic stress due to mitochondrial dysfunction. As a control mechanism, it triggered adaptive stress responses, including unfolded protein responses and integrated stress responses. Metabolic profiling of skeletal muscle-specific knockout mice revealed amino acid and TCA cycle intermediates shuttle between serum and muscle.

overall_design: RNA-seq analysis of Grpel1 KO vs WT

first: Nirajan

last: Neupane

first: Jayasimman

last: Rajendran

first: Sandra

last: Harjuhaahto

first: Bowen

last: Hu

first: Veijo

last: Kinnunen

first: Yang

last: Yang

first: Anni

middle: I

last: Nieminen

first: Henna

last: Tyynismaa


title: Simple and Accurate Transcriptional Start Site Identification Using Smar2C2

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: We present Smart-Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2) for the identification and quantification of transcription start sites. Smar2C2 allows for the identification of upwards of 70 million unique transcription start sites from a single sample with as little as 40 pg of RNA input.

sample_organism:
Glycine max
Oryza sativa
Sorghum bicolor
Triticum aestivum
Zea mays

overall_design: Examination of transcriptoinal start sites using a novel technique across several plant species

first: Andrew

last: Murray

first: Pablo

last: Mendieta

first: Chris

last: Vollmers


title: Genome-wide mapping of ZNF148 binding sites in MDA-MB-231 cell line

city: Austin

first: Mijeong

last: Kim

address: 2500 Speedway

institute: The University of Texas at Austin

summary: ChIP-Seq was carried out to map the genome-wide chromatin occupancy of ZNF148 in a basal subtype triple negative breast cancer cell-line, MDA-MB-231.

overall_design: MDA-MB-231 cells stably expressing the bacterial biotin ligase Bir A were stably transfected with recombinant forms of ZNF148 (Bio-ZNF148), containing an amino terminal BirA recognition/biotin acceptor motif. Clones that expressed the recombinant proteins at close to the same levels as the endogenous proteins were selected. The parental MDA-MB-231 cells expressing BirA alone were included as controls.  The BirA and Bio-ZNF148 expressing MDA-MB-231 cells were then subjected to streptavidin-based ChIP-sequencing.

last: Woo


title: Intergrative Multi-Omics of Asian Pregnant Mother

city: Singapore

first: Neerja

last: Karnani

address: 30 Medical drive

country: Singapore

institute: Singapore Institute for Clinical Sciences, A*STAR

summary: As Asians are underrepresented across many omics databases limiting the potential of precision medicine of the global population. It is thus important for multi-omics derived quantitative trait loci (QTLs) to fill the knowledge gap of complex traits in the Asian ancestry. Integrating omics data from genomics and epigenomics (including DNA methylation and RNA-seq from blood), we developed iMOMdb, an open-acesss database to enhance disease prediction models and precision medicine outcomes in Asian pregnant women.

overall_design: GUSTO (Growing Up In Singapore Towards healthy Outcome) is a prospective pregnancy and birth cohort study with follow up from prenatal stage through infancy up to 10 years of age. Whole transcriptome was used to explore gene expression changes in maternal whole blood during mid pregnancy (26 -28 weeks of gestation) on 238 mothers of Chinese, Malay and Indian ethnicities. RNA-seq was profiled on maternal whole blood samples using Illumina hiSeq 4000 platform. These data are reported in separate series.

first: Hong

last: Pan

first: Pei

last: Tan

first: Lim

middle: Y

last: Ives


title: Exogenous Oncostatin M Induces Cardiac Dysfunction, Muscluloskeletal Atrophy and Fibrosis

city: Portland

first: Teresa

last: Zimmers

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: Musculoskeletal diseases such as muscular dystrophy, cachexia, osteoarthritis, and rheumatoid arthritis impair overall physical health. Patients suffer from increased pain and death rate, decreased productivity and function. Inflammation and fibrosis are commonly observed in musculoskeletal disorders either at the bone, muscle, or joint. The Interleukin-6 Family of Cytokines primarily Interleukin-6 (IL-6) are implicated in the context of musculoskeletal disorders. In this study, we utilized adeno-associated virus expressing murine Oncostatin M or an empty vector at 10^11 viral particles to observe effects in muscle and bone of mice in the presence and absence of Interleukin-6. We performed echocardiography, microCT, quantitative polymerase chain reaction, histology, and RNA-sequencing to characterize the functional effects on muscle and bone. The echocardiography results demonstrated cardiac dysfunction as shown by reduced ejection fraction (%) and fractional shortening (%) with AAV-Osm compared to AAV-Null. RNA-sequencing results on cardiac muscle showed increased cardiac inflammation and fibrosis genes with AAV-Osm. Skeletal muscle weights and histology revealed muscle atrophy and fibrosis in the gastrocnemius, tibialis anterior, and quadriceps of the local limbs injected with AAV-Osm, but not observed in the non-injected side. MicroCT results revealed local and distant trabecular bone loss with AAV-Osm as shown by reduced bone volume, number, thickness, and increased trabeculae separation. Our findings show that Oncostatin M induces cardiac dysfunction, muscle, and bone atrophy independent of Interleukin-6.

overall_design: 10-week old wildtype mice were infected with an intramuscular injection of 10^11 viral particles of AAV-Osm and 10-week old wildtype mice were infected with an intramuscular injection of 10^11 viral particals of AAV-Null. After 12 weeks, the mice were euthanized and the cardiac muscle was isolated. The apex of the heart was used for RNA isolation and five samples from each group (AAV-Null or AAV-Osm) were submitted to the core facility. A total of nine samples were used from data analysis.

first: Daenique

middle: H

last: Jengelley

first: Ashok

last: Narasimhan


title: CSF1R mediates effects of miR-34a loss during intestinal tumorigenesis in ApcMin mice (adenoma)

first: Markus

last: Kaller

summary: To address the in vivo relevance of CSF1R regulation by miR-34a during intestinal tumor formation, we generated ApcMin/+ mice with intestinal-epithelial cell (IEC)-specific deletions of the Mir34a and/or Csf1r genes. The mRNA expression profiles of intestinal adenomas with and without functional miR-34a and/or Csf1r were compared.

overall_design: Mice were sacrificed at 18 weeks of age. 3 tumor RNA samples were obtained for each genotype; each tumor RNA sample represented a pool of 3-5 tumors isolated from the same mouse.

first: Fangteng

last: Liu

first: Heiko

last: Hermeking


title: Genome-wide ATAC-seq maps in human Treg subsets and CD4+ T effector cells

city: Oxford

first: David

last: Flores Santa Cruz

state: Oxfordshire

address: Roosevelt Drive

department: Diabetes and Inflammation Laboratory

country: United Kingdom

institute: Wellcome Centre for Human Genetics

summary: We report the application of ATAC-seq to flow sorted Foxp3+Helios+ memory and naïve regulatory T cell subsets and memory CD4+ T effector cells in both resting condition and after in vitro stimulation (4 hours) with PMA/Ionomycin.

overall_design: CD4+ T cells were isolated from whole blood by negative selection using the RosetteSep human CD4+ T cell enrichment kit.  CD4+ T cells (1–2 × 10^6 CD4s/well) were cultured in a 24-well flat-bottom cell culture plate at 37 °C + 5% CO2 resuspended in X-VIVO-15 (Lonza) + 5% heat-inactivated, filtered human AB serum  in the presence or absence of phorbol myristate acetate (PMA), ionomycin, and protein transport inhibitors (brefeldin A and monensin). After 4 hours of culture, cells were harvested and stained with a panel of fluorochrome-conjugated antibodies against surface markers, fixed and permeabilised and stained with fluorochrome-conjugated antibodies against intracellular markers and the following CD4+ CD3+ve viable and single cell gated T cell subsets were sorted;  HELIOS+FOXP3+CD25h iCD127lo CD45RA- (DP mTreg), HELIOS+FOXP3+CD25hiCD127lo CD45RA+ (nTreg) and CD25int CD127hiCD45RA- (mTeff).

first: J

last: Todd

first: R

last: Ferreira

first: A

last: Cutler


title: Arabidopsis requires a stearoyl-ACP desaturase for proper interaction with beneficial rhizobacteria

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Unlike pathogens that trigger plant defense responses, beneficial microbes are compatible with plants. One possible reason for the compatibility is that the microbial factors from beneficial microbes are inert in that they do not trigger plant defense responses. Little is known about the mechanisms underlying this seemingly inert relation. Here we report that Arabidopsis lacking the gene Growth-Promotion 1 (GP1) becomes defensive to microbial volatiles from Bacillus amyloliqueficiens strain GB03, a beneficial rhizobacterium. The gp1 mutant was isolated in a forward genetic screen for mutants that show defectiveness in GB03-triggered plant inducible vigor. GP1 encodes a stearoyl-ACP desaturase that catalyzes the desaturation of stearic acid (18:0) to oleic acid (18:1). Consistently, plant inducible vigor was also impaired by chemical enhancement of 18:1 catabolism, while genetic disruption of 18:1 catabolism largely restored the inducible vigor in gp1. When exposed to GB03-emitted microbial volatiles (GMVs), wild type plants showed transcriptional up-regulation of growth-promoting processes and down-regulation of defense responses; in contrast, the gp1 transcriptome displayed elevated defense responses when treated with GMVs. Meanwhile disruption of salicylic acid-mediated defense partially restored plant inducible vigor in gp1. Microbiota profiling revealed that GP1 dysfunction alters the assemblage of plant-associated rhizobacteria communities, including a reduction in the Bacillaceae family that is known to contain many beneficial rhizobacteria species. Consistently, gp1 mutants showed severely impaired root colonization of GB03. Our findings suggest that GP1 prevents the plant defense system from being mistakenly activated by non-pathogenic microbial factors, thereby allowing mutualistic association between the plant and beneficial microbes.

overall_design: RNA seq for 4 samples: Col-0 C (control), Col-0 T (treated), gp1-2 C, gp1-2 T; each sample has 3 biological replicates.

first: Yu

last: Yang

first: Shenglan

last: Chen

first: Li

last: Peng

first: Xiaomin


title: CSF1R mediates effects of miR-34a loss during intestinal tumorigenesis in ApcMin mice

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Aortic Cellular Diversity and Quantitative GWAS Trait Prioritization through Single Nuclear RNA Sequencing (snRNA-Seq) of the Aneurysmal Human Aorta

status: Public on Oct 03 2022

first: Mark

last: Chaffin

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

summary: In current models of ascending aortic disease, mural cells undergo phenotypic changes that promote extracellular matrix destruction and structural weakening. To explore the intersection of this biology with quantitative trait GWAS loci we analyzed the genetic features of thoracic aortic aneurysm tissue. Single nuclear RNA sequencing was performed on 13 samples from human donors, 6 with thoracic aortic aneurysm and 7 without aneurysm. Individual transcriptomes were then clustered based on transcriptional profiles. Clusters were used for between-disease differential gene expression analyses, subcluster analysis, and analyzed for intersection with genetic aortic trait data. In total, we sequenced 71,689 nuclei from human thoracic aortas without aneurysm, and with sporadic aneurysm. We identified 14 clusters, aligning with 11 cell types, predominantly VSMCs, consistent with existing histologic data, but contrary to the majority of human aortic single cell studies to-date. With unbiased methodology, we found 7 VSMC and 6 fibroblast subclusters. Differentially expressed genes (DEGs) analysis revealed a VSMC group accounting for the majority of differential gene expression. Fibroblast populations in aneurysm exhibit distinct behavior with almost complete disappearance of quiescent fibroblasts. DEGs were used to prioritize genes at aortic diameter and distensibility GWAS loci highlighting the genes JUN, LTBP4, and IL34 in fibroblasts, ENTPD1, PDLIM5, ACTN4, and GLRX in VSMCs, as well as LRP1 in macrophage populations. In conclusion, using nuclear RNA sequencing we describe the cellular diversity of healthy and aneurysmal human ascending aorta. Sporadic aortic aneurysm is characterized by differential gene expression within known cellular classes rather than by the appearance of novel cellular forms. Single nuclear RNA sequencing of aortic tissue can be used to prioritize genes at aortic trait loci.

overall_design: We performed snRNA-Seq on 13 samples from human donors, 6 with thoracic aortic aneurysm and 7 without aneurysm. For patients without aneurysm, adult human ascending aortic samples were collected from deceased organ donors by MAGNet (the Myocardial Applied Genetics Network) and the MGH rapid autopsy study. These patients had tricuspid valves, no clinical diagnosis or radiographic evidence of aortic aneurysm, or family history of aneurysm disease. For patients with aneurysm, tissue collection was performed on patients who underwent open aortic reconstruction for sporadic ascending aortic aneurysm. Patients were excluded if they had bicuspid valves, aortic dissection or heritable aortopathy.

first: Elizabeth

middle: L

last: Chou

first: Bridget

last: Simonson

first: Patrick

last: Ellinor

middle: E

last: Lindsay


title: Effects of Different Doses of rAAV 5-mCherry on Transcriptome of Hippocampal Pyramidal Neurons in Male Mouse

city: GUANGZHOU

first: YISI

last: LIU

address: SHATAI ROAD

institute: SOUTH MEDICAL UNIVERSITY

summary:
Purpose: Here, we evaluated the effects of three different doses of rAAV5 vectors, which are widely used for functional studies in the brain, on hippocampal pyramidal neurons transcription in male mice.
Results: There was a strong correlation between rAAV dose and toxicity. As dose increased, rAAV5-DIO-mCherry upregulated genes related to the immune and inflammation response and neuron death and downregulated genes associated with the synapse and axon compartments, mitochondrial potein complex suggesting that higher dose rAAV 5-DIO-mCherry may induce pyramidal neuronal fragility and impair synaptic transmission and structure.
Conclusions:the dose should be taken into consideration when rAAV vectors are used for gene transduction studies.

overall_design: nine samples were analyzed. there three groups,and three biological replication for each group

first: Yisi

first: Yihua

first: Zelin

last: Li

first: Hao

last: chen

first: Nengyuan

last: Hu

first: Jianming

first: Tianming

last: Gao


title: White Matter Tractography and Neurohistopathology after Chronic, Low-Level Exposure to Domoic Acid in a Nonhuman Primate Model

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Domoic acid (DA), a potent glutamate agonist, is produced by marine algae and can bioconcentrate in finfish and shellfish. Current regulatory limits constrain environmental exposures to this toxin to 20 ppm in shellfish tissue (~0.075-0.1 mg/kg), but changing environmental conditions are leading to more frequent and longer lasting DA algal blooms. Further, recent studies suggest that chronic DA exposure, at levels below this limit, is associated with deficits in memory in adults. To understand how low-level, chronic exposure to this toxin impacts the limbic system of the brain, the present study used magnetic resonance imaging (MRI) and histopathology to assess changes in the hippocampus, thalamus, fornix, fimbria, and internal capsule in a nonhuman primate model. Twenty-eight adult, female Macaca fascicularis were orally exposed to 0.075 and 0.15 mg/kg/day for up to two years. A subset of these females (n=12) underwent a single, sedated MRI scan in vivo, to assess volumetric and tractography changes in the hippocampus, thalamus, and connecting white matter tracts, and all animals were necropsied to evaluate the cellularity and morphology of the neurons, astrocytes, and microglia in these regions. MRI and histopathology evaluations did not suggest signs of overt neuropathology, but revealed that some animals, especially in the 0.15 mg/kg/day DA exposure group, expressed focal microglia reactions within both white and gray matter structures of the limbic system. These results suggest that chronic exposure to levels of DA near the human regulatory limit does not lead to acute neuropathic effects but may induce microglial responses and promote neuroinflammatory pathways in a nonhuman primate model of contemporary human exposure to DA.

overall_design: Observers were experimentally blinded to the exposure conditions of the macaques and employed positive reinforcement techniques to train animals to drink out of a syringe to allow for controlled dosing of DA or vehicle control. Following training, animals underwent a baseline period of assessment designed to asses clinical signs of toxicity prior to starting daily oral exposure of 0 (n=10), 0.075 (n=11), or 0.15 (n=11) mg/kg of DA (BioVectra, Charlottetown, PE, Canada) in 5% sucrose water. Animals continued to be assessed 3-5x per week throughout a 2-month pre-breeding period, a 1-8-month breeding period, a 6-month pregnancy, and a 2-12-month postpartum period. For all but 2 animals (A15234 and A15244), dosing continued until necropsy. Animals A15234 and A15244 had wash-out periods of 221 and 231 days, respectively, prior to necropsy. In all animals, behavioral assessment continued at least 3x/week until necropsy.

first: R

last: Petroff

first: G

middle: J

last: Harry

first: T

last: Bammler

first: K

middle: S

last: Grant

first: B

last: Crouthamel

first: N

last: McKain

first: S

last: Shum

first: J

last: Jing

last: Isoherranen

middle: M

last: Burbacher


title: Proteotoxic stress-induced apoptosis in cancer cells: understanding the susceptibility and enhancing the potency

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

institute: university of Udine

summary: Leiomyosarcoma (LMS) is an aggressive cancer with few therapeutic options. LMS cells are more sensitive to proteotoxic stress compared to normal smooth muscle cells. We used small compound 2c to induce proteotoxic stress and compare the transcriptomic adaptations of immortalized human uterine smooth muscle cells (HUtSMC) and LMS cells SK-UT-1. We found that the expression of the heat shock proteins (HSP) gene family is upregulated with higher efficiency in normal cells. In contrast, upregulation of BH3-only proteins is higher in LMS cells. HSF1, the master regulator of HSP transcription, is sequestered into transcriptionally incompetent nuclear foci only in LMS cells, which explains the lower HSP upregulation. We also found that several compounds can enhance the cell death response to proteotoxic stress. Specifically, when low doses were used, an inhibitor of salt-inducible kinases (SIKs) and the inhibitor of IRE1, a key element of the unfolded protein response (UPR), support proteotoxic-induced cell death with strength in LMS cells and without effects on the survival of normal cells. Overall, our data provide an explanation for the higher susceptibility of LMS cells to proteotoxic stress and suggest a potential option for co-treatment strategies.

overall_design: Examination of the transcriptome of SK-UT-1 leiomyosarcoma cells and immortalized human uterine smooth muscle cells (HUtSMC) in response to proteotoxic stress induction as elicited by the small compound 2c

first: Luca

last: Iuliano

first: Emiliano

last: Dalla

first: Raffaella

last: Picco

first: Showmeya

last: Mallarapu

first: Martina

last: Minisini

first: Claudio

last: Brancolini


title: Analysis of the α-1,3 fucosyltransferase gene funtion in diatom Phaeodactylum tricornutum

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

summary: Anylasis of the α-1,3 fucosyltransferase gene function in diatom Phaeodactylum tricornutum

overall_design: 4 days and examined cell density, Fv/Fm, sugar and protein content

first: Jichen

last: Chen

first: Zidong

last: Liu

first: Xiaojuan

first: Hua

last: Du


title: Knockdown of Znf148 by shRNA in MDA-MB-231 breast cancer cells.

city: Nedlands

first: Andrew

middle: Jonghan

last: Woo

address: 6 Verdun Street

department: UWA Centre for Medical Research

institute: University of Western Australia

summary: RNA-Sequencing of basal subtype triple negative breast cancer cells, MDA-MB-231.  MDA-MB-231 cells were lentivirally transduced with pLKO short-hairpin (sh) luciferase control or shZnf148 in triplicates.  Differentially expressed genes by the shRNA compared to the control were determined.

overall_design: 6 samples


title: RNA sequencing data from STS-109 human undifferentiated pleomorphic sarcoma (UPS) cells deficient in DNMT3A or DNMT3B expression

city: Philadelphia

first: T. S.

middle: Karin

last: Eisinger-Mathason

state: PA

address: 421 Curie Blvd, Rooom 414

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania Perelman School of Medicine

summary: DNA methylation is frequently disrupted in sarcoma but little is known about the specific roles of DNA methyltransferases (DNMTs) in this process. Using an shRNA lentivirus-mediated genetic depletion approach, we found that reduction of DNMT3A or DNMT3B expression potently reduced UPS cell proliferation. Therefore, we performed RNA sequencing to identify global gene expression changes in DNMT3A- or DNMT3B-depleted cells.

overall_design: STS-109 cells recently derived from a human UPS tumor were infected with one of two independent shRNAs targeting either DNMT3A (shDNMT3A) or DNMT3B (shDNMT3B), or a scrambled control shRNA (shSCR). Cells were selected with 3 µg/mL of puromycin 48 hours after infection, and harvested for RNA isolation 96 hours after infection. All cells were harvested at 50% confluency.

first: Ashley

last: Fuller

first: T

middle: K


title: Colocalization of GWAS and molecular QTL signals in human vascular smooth muscle cells predict candidate causal genes for coronary artery disease and vascular disorders

city: Charlottesville

first: Mete

last: Civelek

state: VA

address: 21 Hospital Drive, Old Medical School Room 3836

department: Center for Public Health Genomics

institute: University of Virginia

summary: Coronary artery disease (CAD) is the leading cause of death worldwide. A recent meta-analysis of genome-wide association studies (GWAS) identified 175 loci associated with CAD. The majority of these loci are in non-coding regions and are predicted to regulate gene expression. We hypothesized that a subset of the CAD GWAS loci was associated with the regulation of transcription in vascular smooth muscle cells (SMCs), which play critical roles in the development of CAD. We measured gene expression in SMCs isolated from the ascending aortas of 151 ethnically diverse heart transplant donors in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single nucleotide polymorphism (SNP) markers across the genome. We identified 4,910 expression and 4,412 splice quantitative trait loci (sQTL) that represent regions of the genome associated with transcript abundance and splicing. 3,660 of the expression quantitative trait loci (eQTL) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 of the eQTLs were SMC- and sex-specific, respectively. To identify the effector transcripts regulated by the CAD GWAS loci, we used four distinct colocalization approaches and identified 84 eQTL and 164 sQTLs that colocalized with CAD loci, suggesting a more significant role for the genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. Two of the CAD loci colocolized with SMC eQTL showed sex-specific (AL160313.1 and TERF2IP) and one of the loci colocalized with SMC-specific eQTLs (ALKBH8). 27% and 37% of the sQTLs were unique to quiescent or proliferative SMCs, respectively. The most significantly associated CAD locus, 9p21, was an sQTL for the long non-coding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. Collectively, these results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in vascular smooth muscle cells.'

overall_design: ATAC sequencing data across proliferative and quiescent smooth muscle cells (SMCs) in 5 donors

first: Noah

last: Perry

first: Redouane

last: Aherrahrou


title: A transcriptomic analysis of the effects of macrophage polarization and endotoxin tolerance on the response to Salmonella

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

summary: Salmonella is an intracellular pathogen causing significant morbidity and mortality. Its ability to grow inside macrophages is important to virulence, and is dependent on the activation state of the macrophages. Classically activated M1 macrophages are non-permissive for Salmonella growth, while alternatively activated M2 macrophages are permissive for Salmonella growth. Here we showed that endotoxin-primed macrophages (MEP), such as those associated with sepsis, showed similar levels of Salmonella resistance to M1 macrophages after 2 hr of intracellular infection, but at the 4 hr and 24 hr time points were susceptible like M2 macrophages. To understand this mechanistically, transcriptome sequencing, RNA-Seq, was performed. This showed that M1 and MEP macrophages that had not been exposed to Salmonella, demonstrated a process termed here as primed activation, in expressing relatively higher levels of particular anti-infective genes and pathways, including the JAK-STAT pathway. In contrast, in M2 macrophages these genes and pathways were largely expressed only in response to infection. Conversely, in response to infection, M1 macrophages, but not MEP macrophages, modulated additional genes known to be associated with susceptibility to Salmonella infection, possibly contributing to the differences in resistance at later time points. Application of the JAK inhibitor Ruxolitinib before infection reduced resistance in M1 macrophages, supporting the importance of early JAK-STAT signalling in M1 resistance to Salmonella.

overall_design: Samples represent monocyte-dervied macrophages which are stimulated with one of IFNy, IL4, or LPS to induce states of polarization, plus an untreated control. Half of the samples then undergo infection from Salmonella enterica serovar Typhimurium strain SL1344, while the other half remain uninfected (untreated). Each combination of Polarization and Treatment has three or four replicates, representing blood drawn from different donors.

first: Katharine

last: Sedivy-Haley

first: Reza

last: Falsafi

first: Amy

last: Lee

first: Robert

last: Hancock


title: Effects of propranolol exposure to Pimephales promelas (fathead minnow) larva across age and duration

city: Cincinnati

first: Gregory

middle: Peter

last: Toth

state: OH

address: 26 W ML King Jr. Dr.

department: CCTE

institute: USEPA/ORD

summary: Given that larval fish stages provide opportunities for development of stressor-selective screening level tests, this work aimed to investigate the optimal age of fathead minnow larva and duration of exposure for the pharmaceutical, propranolol, found in the environment.  Differentially expressed genes were studied as well as gene set enrichment analysis.

overall_design: mRNA reads from fathead minnow (FHM) larvae (4 days; 5 days; 6 days post fertilization) were exposed for 6, 24, and 48 h to two concentrations of propranolol (0.66 and 3.3 mg/l).  RNASeq reads were mapped against 47K known FHM mRNA transcripts

middle: P

first: David

last: Bencic

first: John

last: Martinson

last: Flick

last: Lattier

first: Adam

last: Biales


title: Epigenome wide Association and Stochastic Epigenetic Mutation analysis on 23 twin pairs heterogeneously affected by Congenital Hypothyroidism (CH).

city: Cusano Milanino

first: Luciano

last: Calzari

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

summary: We performed a whole-genome DNA methylation analysis (Infinium HumanMethylation450 BeadChip) on peripheral whole blood of 23 twin pairs (10 monozygotic and 13 dizygotic)  heterogeneously (4 concordant and 19 discordant) affected by Congenital Hypothyroidism (CH) at birth.

overall_design: Genome-wide DNA methylation analysis on peripheral whole blood from 23 twin pairs affected by Congenital Hypothyroidism (CH) using Illumina Human Methylation 450K Beadchip.

first: Luca

last: Persani

first: Davide

last: Gentilini