title: Stress regulates Alzheimer's Disease progression via selective enrichment of CD8+ T cells

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

institute: Tsinghua University

summary: This study investigates stress's impact on Alzheimer's disease (AD) using male APP/PS1 transgenic mice. Negative stressors (chronic social defeat, restraint) and positive hedonia (environmental enrichment, EE) were applied. Stress worsens AD pathology, while EE slows progression. Brain RNA-seq reveals IL-6 and IL-10 as key stress-related AD regulators. Flow cytometry shows CD8+/CD4+ T cell ratio shifts in response to SE and EE. SE increases CD8+/CD4+ ratio, opposite in EE. Depletion and enrichment of CD8+ T cells both accelerate AD, indicating immune intervention's negative impact. Stress management and balanced immunity may aid AD therapy, highlighting novel potential treatment.

overall_design: After behavioral testing and peripheral blood flow cytometry, mice were gas anesthetized with isoflurane. Anesthetized mouse was perfused systemically with 20 mL of ice-cold PBS transapically to ensure high cell viability. The abdominal cavity was opened and the splenectomy was performed for flow cytometry of splenocytes. Then the mouse brain was immediately removed. The posterior half of the left hemisphere was isolated and fixed in ice-cold 4% paraformaldehyde for overnight for immunofluorescence staining. The posterior half of the right hemisphere is used for lysing by RIPA lysate to extract brain proteins. The brain stem and the anterior half of the brain were used to extract RNA for RNA sequencing.

first: Yilin

last: Feng


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [RNA-seq]

status: Public on Dec 15 2023

city: Los Angeles

first: Kathrin

last: Plath

state: CA

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. Dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our results identify XIST as the regulator of X-chromosome dampening, uncover an evolutionarily conserved trans-acting role of XIST/Xist, and reveal a correlation between XIST/Xist dispersal and autosomal targeting.

overall_design: mRNA profiles of female naive hESCs (H9, UCLA1), female naive iPSCs,  female naive hPSCs (HNES3), male naive hPSCs (WIN1 and HNES1), XIST KO in naive hESCs (H9), siSPEN in female naive hESCs (UCLA1), in male naive hPSCs (WIN1), and in XIST KO (H9)

first: Iris

last: Dror

first: Anna

last: Sahakyan

first: Tsotne

last: Chitiashvili


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [RAP-seq_mouse]

summary: X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

overall_design: We examined the genomic localization of the XIST lncRNA using RNA Antisense Purification (RAP) in multiple cells: female mouse D2 and D4 of EpiLCs differentiation and female and male MEFs

first: Shawn

last: Tan


title: Sex-specific epigenetics drive low GPER expression in gastrointestinal smooth muscles in Type 2 diabetic mice

city: Tuskegee

first: Sunila

last: Mahavadi

state: Alabama

address: 1200 W. Montgomery Rd, Carver Research Building, Room #1

department: Biology

institute: Tuskegee University

type: Methylation profiling by high throughput sequencing

summary: Type 2 diabetes mellitus (T2DM) causes gastroparesis, delayed intestinal transit, and constipation, for unknown reasons. Complications are predominant in men and postmenopausal women, suggesting a female hormone-mediated mechanism. Low G-protein coupled estrogen receptor (GPER) expression from epigenetic modifications may explain it. We explored sexually differentiated GPER expression and gastrointestinal symptoms related to GPER alterations in wild-type (WT) and T2DM mice (db/db). GPER mRNA and protein expression, DNA methylation and histone modifications were measured from stomach and colon samples of db/db and WT mice. We found that WT female tissues have the highest GPER mRNA and protein expressions. The expression is lowest in all db/db. The lowest mRNA levels are in the male stomach and female colon. GPER downregulation is associated with promoter hypermethylation and reduced enrichment of H3K4me3 and H3K27ac marks around the GPER promoter. T2DM impairs gut GPER expression, and epigenetic sex-specific mechanisms matter in the downregulation.

overall_design: To investigate the GPER expression in male and female gastric and colonic smooth muscle of wild-type and db/db (type 2 diabetic) mice, we performed DNA-methylation measurement at the GPER promoter region by targeted bisulfite sequencing assay. This was performed in the colonic and gastric tissue of 5 male wild-type, 5 male db/db, 4 female wild-type, and 6 db/db female mice. The DNA methylation data was analyzed by comparative analysis, using ANOVA.

first: Aliyu

last: Muhammad


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [RAP-seq_human]

overall_design: We examined the genomic localization of the XIST lncRNA using RNA Antisense Purification (RAP) in multiple cells: female human naive hESCs (H9, UCLA1, and iPSCs), NHFD (2 replicates), female human primed hESCs (H9 and iPSC), and XIST KO in H9

first: Clara

middle: T

last: Cano


title: Differential effects of PTH (1-34), PTHrP (1-36) and abaloparatide on the murine osteoblast transcriptome

city: New York

first: Nicola

last: Partridge

state: NY

address: 345e 24th Street

department: Department of Molecular Pathobiology

institute: New York University

summary: Teriparatide (PTH(1-34)) and its analogs, PTHrP(1-36) and abaloparatide (ABL) have been used for the treatment of osteoporosis, but their efficacy over long-term use is significantly limited. The 3 peptides exert time- and dose-dependent differential responses in osteoblasts, leading us to hypothesize that they may also differentially modulate the osteoblast transcriptome. We show that treatment of mouse calvarial osteoblasts with 1 nM of the 3 peptides for 4 h results in RNA-Seq data with PTH(1-34) regulating 367 genes, including 194 unique genes; PTHrP(1-36) regulating 117 genes, including 15 unique genes; and ABL regulating 179 genes, including 20 unique genes. There were 83 genes shared among all 3 peptides. Gene ontology analyses showed differences in Wnt signaling, cAMP-mediated signaling, bone mineralization, morphogenesis of a branching structure in biological processes; receptor ligand activity, transcription factor activity, cytokine receptor/binding activity and many other actions in molecular functions. The 3 peptides increased Vdr, Cited1 and Pde10a mRNAs in a pattern similar to Rankl, i.e., PTH(1-34) > ABL > PTHrP(1-36). mRNA abundance of other genes based on gene/pathway analyses, including Wnt4, Wnt7, Wnt11, Sfrp4, Dkk1, Kcnk10, Hdac4, Epha3, Tcf7, Crem, Fzd5, Pp2r2a, and Dvl3 showed that some genes were regulated similarly by all 3 peptides; others were not. Further delineation of which signaling events are attributable to PTH(1-34), PTHrP(1-36) or ABL exclusively and which are shared among all 3 will help improve our understanding of the effects these peptides have on the osteoblast and lead to the refinement of PTH-derived treatments for osteoporosis.

overall_design: Comparative gene expression profiling analysis and GO analyis of PTH (1-34), PTHrP (1-36), and Abaloparatide Effects on Murine Osteoblast Transcriptome with RNA-seq data

first: Michael

middle: J

last: Mosca

first: Zhiming

last: He

first: Florante

middle: R

last: Ricarte

first: Carole

last: Le Henaff

middle: C


title: RNA sequencing of lungs from WT and GSDMD knockout mouse lungs after influenza virus H1N1 strain PR8 infection

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

summary: WT and GSDMD KO mice were infected with 50 TCID50 influenza virus strain PR8.  7 days post infection, RNA was extracted from lung tissue using TRIzol.  RNA library preparation and sequencing was performed by Genewiz.

overall_design: Lung mRNA analysis at 7 days post infection of WT and GSDMD KO mice with influenza virus H1N1 strain PR8.


title: Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences

city: Evanston

first: Heather

last: Pinkett

state: IL

address: 2205 Tech Dr, Cook Hall 4161

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The PDR network is an important regulatory system in yeast involved in the transport of various toxins and drugs out of the cell. The transcription factors Pdr1p and Pdr3p, key regulators of this network, bind to specific sequences called PDREs in the promoter region of PDR genes to control expression. However, the exact mechanism underlying the differences in the regulons of these proteins are not well understood. A combination of genomic occupancy profiling (CUT&RUN) and in vitro binding assays were employed to characterize the differences in sequence specificity between transcription factors. The results indicate that interaction between the transcription factors and PDRE sites is not solely determined by the core sequence, but also influenced by the surrounding regions.

first: Evan

last: Buechel


title: Staphylococcus aureus lipoteichoic acid-stimulated undifferentiated and neutrophil-like differentiated HL-60 cells

city: Kaohsiung

first: Meng-Chi

last: Yen

address: No.100, Shih-Chuan 1st Road

country: Taiwan

institute: Kaohsiung Medical University

summary: HL-60 is a human promyelocytic leukemia cell line and differentiated HL-60 is an alternative to human primary neutrophils. The transcriptomic profile of undifferentiated HL-60 and dimethyl sulfoxide-differentiated HL-60 were determined at 4 and 24 hours after stimulation with high and low concentrations of Staphylococcus aureus lipoteichoic acids.

overall_design: RNA sequencing of whole cell RNA was performed on undifferentiated and differentiated HL-60 that stimulated with Staphylococcus aureus (S. aureus) lipoteichoic acids (LTA). Undifferentiated HL-60 (uHL-60) which was stimulated with 1 μg/ml of S. aureus LTA were collected after 4 and 24 hours. Unstimulated uHL-60 at the same time point were collected and used as control group. There is 1 biological replication in each sample of uHL-60. In addition, differentiated HL-60 (dHL-60) which was stimulated with 1 μg/ml or 10 μg/ml of S. aureus LTA and unstimulated dHL-60 were collected after 4 and 24 hours. Duplicate samples of dHL-60 were collected.

first: I-Jeng

last: Yeh

first: Ya-Ling

last: Hsu

first: Kuan-Ting

last: Liu


title: Serpine1 functions as a non-coding RNA regulating post-transcriptionally epithelial mesenchymal transition [iCLIP]

city: Seville

first: Jose

middle: Antonio

last: Guerrero-Martinez

state: Seville

address: Av. Americo Vespucio, N 24

department: Genome Biology

country: Spain

institute: CABIMER

summary: Serpine1 mRNA is abundantly induced during EMT. Paradoxically, this mRNA is enriched in the RISC complex, blocking its translation and acting as an endogenous RNA competitor for several miRNAs. Cells that overexpress Serpine1 mRNA have a greater capacity for migration, invasiveness, and resistance to anoikis. These cells show an altered proteomic profile, highlighting the increased levels of expression of the splicing factor TRA2b. This splicing factor is posttranscriptionally regulated during EMT by upregulation of Serpine1 mRNA and the resulting sequestration of miR-130b-5p by this mRNA, which contains three binding sites for miR-130b-5p. Through transcriptomic analysis, we confirmed that Serpin 1 mRNA expression modulates the expression of numerous genes, most of which (>60%) are also modulated by TRA2b overexpression.

overall_design: iCLIP, NMuMG mouse glandular epithelial cells treated with TGFb for 4h or 48h, in triplicates.

first: José

middle: A

last: Pintor-Toro

first: Salvador

last: Polo Generelo

first: Belén

last: Torres

last: Guerrero-Martínez

last: Reyes


title: Serpine1 functions as a non-coding RNA regulating post-transcriptionally epithelial mesenchymal transition [RNA-seq]

overall_design: Transcriptome profiles of NMuMG mouse glandular epithelial cells which overexpress mRNA Serpine1 or Tra2b were generated by deep sequencing, in duplicates, using Illumina.


title: Single cell-guided prenatal derivation of primary fetal epithelial organoids from the human amniotic and tracheal fluids

city: London

first: Mattia

middle: Francesco Maria

last: Gerli

address: Rowland hill street

department: Department of Surgical Biotechnology

country: United Kingdom

institute: University College London

summary: Isolation of tissue-specific fetal stem cells and derivation of primary organoids is currently limited to post-termination samples. This hampers the prenatal investigation of fetal development and congenital diseases. Therefore, novel patient-specific in vitro models are needed. To this aim, isolation and expansion of fetal stem cells during pregnancy, without the need for tissue or cellular reprogramming, would be advantageous. The amniotic fluid (AF) is a source of cells originating from multiple developing organs. Using single cell analysis, we characterised the cellular identities present in the human AF. We identified and isolated viable epithelial stem/progenitor cells of fetal gastrointestinal, renal and pulmonary origin. Upon culture, these cells formed clonal epithelial organoids, manifesting small intestine, kidney tubule and lung identity. AF organoids (AFO) exhibit transcriptomic, protein expression and functional features of their tissue of origin. With relevance for prenatal disease modelling, we derived lung organoids from the amniotic and tracheal fluid cells of Congenital Diaphragmatic Hernia (CDH) fetuses. CDH organoids show differences to non-CDH controls recapitulating some features of the disease. AFO are derived in a timeline compatible with prenatal intervention, potentially allowing investigation of therapeutic tools and regenerative medicine strategies personalised to the fetus at clinically relevant developmental stages.

overall_design: scRNAseq of amniotic fluid cells and fetal fluid-derived organoids. Bulk RNAseq of fetal fluid-derived organoids and fetal tissue-derived organoids.

middle: M

first: Giuseppe

last: Calà

first: Max

last: Beesley

first: Beatrice

last: Sina

first: Lucinda

last: Tullie

first: Kylin

middle: Y

last: Sun

first: Francesco

last: Panariello

first: Federica

last: Michielin

first: Joseph

last: Davidson

first: Francesca

last: Russo

first: Brendan

last: Jones

first: Dani

last: Lee

first: Savvas

last: Savvidis

first: Theodoros

last: Xenakis

first: Ian

last: Simcock

first: Anna

last: Straatman-Iwanowska

first: Robert

last: Hirst

middle: L

last: David

first: Christopher

last: O’Callaghan

first: Alessandro

last: Olivo

first: Simon

last: Eaton

first: Stavros

middle: P

last: Loukogeorgakis

first: Davide

last: Cacchiarelli

first: Jan

last: Deprest

first: Vivian

middle: W

last: Li

first: Giovanni

middle: G

last: Giobbe

first: Paolo

last: De Coppi


title: Whole blood transcriptome identifies interferon-regulated genes as key drivers in thrombotic primary antiphospholipid syndrome

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

summary:
Objective: Pathogenesis of antiphospholipid syndrome (APS) isn't fully elucidated. We aimed to identify gene signatures characterizing thrombotic primary APS (thrPAPS) and subgroups at high risk for worse outcomes.
Methods: We performed whole blood next-generation RNA-sequencing in 62 patients with thrPAPS and 29 age-/sex-matched healthy controls (HCs), followed by differential gene expression analysis (DGEA) and enrichment analysis. We trained models on transcriptomics data using machine learning.
Results: DGEA of 12.306 genes revealed 34 deregulated genes in thrPAPS versus HCs; 33 were upregulated by at least 2-fold, and 14/33 were type I and II interferon-regulated genes (IRGs) as determined by interferome database. Machine learning applied to deregulated genes returned 79% accuracy to discriminate thrPAPS from HCs, which increased to 82% when only the most informative IRGs were analyzed. Comparison of thrPAPS subgroups versus HCs showed an increased presence of IRGs among upregulated genes in venous thrombosis (21/23, 91%), triple-antiphospholipid antibody (aPL) positive (30/50, 60%), and recurrent thrombosis (19/42, 45%) subgroups. Enrichment analysis of upregulated genes in triple-aPL positive patients revealed terms related to 'type I interferon signaling pathway' and 'innate immune response'. DGEA among thrPAPS subgroups revealed upregulated genes, including IRGs, in patients with venous versus arterial thrombosis (n = 11, 9 IRGs), triple-aPL versus non-triple aPL (n = 10, 9 IRGs), and recurrent versus non-recurrent thrombosis (n = 10, 3 IRGs).
Conclusion: Upregulated IRGs may better discriminate thrPAPS from HCs than all deregulated genes in peripheral blood. Taken together with DGEA data, IRGs are highly expressed in thrPAPS and high-risk subgroups of triple-aPL and recurrent thrombosis, with potential treatment implications.

overall_design: Whole blood RNA sequencing of human whole blood. 29 Healthy controls and 62 Antiphospholipid Syndrome (APS) samples

first: Petros

last: Sfikakis


title: KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells

status: Public on Dec 14 2023

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

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

overall_design: Refer to individual Series


title: ZFP281 coordinates DNMT3 and TET1 in pluripotent state transitions [MapR (CUT&Run)]

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: The progression and transition between the naïve, formative, and primed pluripotent states are accompanied by a sharp activation of the de novo DNA methyltransferases and the reorganization of transcriptional and epigenetic landscapes. Here we identified Zinc Finger Protein 281 (ZFP281) as an essential factor in the formative-to-primed pluripotent state transition. Using a knockout mouse model and a knockin degron cell system, we revealed that transcription of Dnmt3a/3b depends on the activity of ZFP281 in embryonic stem cells, epiblast-like cells, and epiblast stem cells. Mechanically, chromatin-bound ZFP281 and DNA hydroxylase TET1 are decreased in the formative state but recovered in the primed state to compete with DNMT3A/3B for establishing the DNA methylation and gene expression programs of primed pluripotency. In addition, chromatin occupancy of ZFP281 and TET1 depend on the R-loop structures formed at the ZFP281 target gene promoters devoid of DNA methylation. Our study demonstrates a comprehensive role of ZFP281 in modulating DNA methylation and demethylation for the establishment and maintenance of primed pluripotency.

overall_design: R-loop profiling by MapR in pluripotent stem cells

first: Xin

last: Huang


title: Serpine1 functions as a non-coding RNA regulating post-transcriptionally epithelial mesenchymal transition

first: Jose

last: Guerrero-Martinez


title: Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements, thus representing cornerstones of genomic regulation in eukaryotes. Restrictor, a complex conserved from worms to humans and composed of the RNA-binding protein ZC3H4 and of WDR82, a Pol II-carboxyterminal repeat domain (CTD)-interacting protein, is required to suppress long-range, processive transcription at thousands of extragenic sites, with instead comparatively limited effects on gene transcription. Restrictor contains no RNA cleavage subunit and does not coopt known cleavage complexes, indicating alternative termination mechanisms. Here we show that Restrictor-driven termination involves Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent, phosphatase-dependent termination of non-coding RNAs in yeast. Competition among Restrictor, the cleavage and polyadenylation specificity complex (CPSF) and the histone cleavage complex for a limited pool of Symplekin resulted in mutual regulation, thus revealing unexpected regulatory interactions among multiple transcription termination pathways and a general role of Symplekin in both genic and extragenic cleavage-independent termination pathways.

overall_design: Transcriptome analysis to measure transcription in HCT-116 cell depleted by ZC3H4, SYMPK  and SYMPK + ZC3H4. Genotipe = ZC3H4-mAID:dTAG-SYMPK. 2 Replicates.

first: Marta

last: Russo

first: Danilo

last: Polizzese

first: Elena

last: Prosperini

first: Carolina

last: Borriero

first: Sara

last: Polletti

first: Fabio

last: Bedin

first: Mattia

last: Marenda

last: Michieletto

first: Chiara

last: Soriani

first: Gaurav

last: Mandana

first: Simona

last: Rodighiero

last: Cuomo

first: Gioacchino

last: Natoli


overall_design: Transcriptome analysis to measure transcription in HCT-116 cell depleted by ZC3H4, PNUTS and PNUTS + ZC3H4. Genotype = ZC3H4-mAID:dTAG-PNUTS 2 Replicates.

first: Davide

first: Alessandro


overall_design: Transcriptome analysis to measure transcription in HeLa TREx Flp-In cells, overexpressed by NH2, COOH and ZC3H4 full length


overall_design: Transcriptome analysis to measure transcription in HCT-116 cell depleted by ZC3H4, SYMPK  and SYMPK + ZC3H4. Genotipe = ZC3H4-mAID+ siCTRL or siSYMPK. 3 Replicates.


title: ZFP281 coordinates DNMT3 and TET1 in pluripotent state transitions [STEM-seq]

first: Jianlong

last: Wang

overall_design: STEM-seq of WT, Zfp281+/-, and Zfp281-/- E6.5 embryos


title: Male embryos produced in vitro deviate from their in vivo counterparts in placental gene expression on day 32 of pregnancy

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: This study compared the gene expression of extraembryonic membranes (EEM) from in vitro produced (IVP) and in vivo (AI) derived embryos. Samples of EEM from AI and IVP pregnancies were collected on days 18 and 32. A piece of the conceptus (day 18) or chorioallantois (day 32) were used for DNA and RNA isolation and subsequent determination of the sex by amplification of a Y-linked region of the DNA. The male and female ratios were analyzed by Chi-square of SAS. A subset of three female and three male EEM samples from each group (AI and IVP, days 18 and 32) were used for transcriptome analysis. Differentially expressed genes (DEGs) between groups, sex, and days were determined using edgeR-robust. A false discovery rate (FDR) <0.05 was used for statistical significance, and Toppgene platform was used for biological processes analysis. Sex ratio was similar on day 18 for AI and IVP groups. On day 32, the IVP group had a greater number of females than males (75 vs 25%, P=0.004). On day 18 female embryos, out of 71 DEGs identified, 50 were upregulated in IVP, and 21 in AI. The trophectoderm marker, TKDP2, was upregulated in the AI group, whereas IGF2, which is involved in placenta development, and APOA2, APOB, and APOE, which are important for lipid metabolism, were upregulated in the IVP group. Male embryos on day 18 had 22 DEGs, being 15 upregulated in AI and 7 in IVP. Female embryos on day 32 had 74 DEGs, with 21 upregulated in AI and 53 in IVP embryos. Some of the genes with increased expression in the IVP group were PTGIS, APOB, and APOH, which are related to lipid synthesis and metabolism. Male embryos on day 32 presented 899 DEGs, 564 upregulated in AI and 335 in IVP. Embryos from IVP had increased expression of genes related to embryo development, morphogenesis, neurogenesis, and developmental growth. In addition, male IVP embryos had decreased expression of genes related to lipid and carbohydrate metabolism. Interestingly, PLAC8B, BRB, pregnancy-associated glycoproteins (PAG) 7, 9, 10, and 19, were also downregulated in IVP male EEM. When comparing IVP males and females, there were 6753 DEGs, with 3091 being upregulated in females, and 3662 in male conceptuses on day 18. Some of the genes upregulated in females were related to placental function such as TKDP4, PLAC8A and PAGs 6, 8, 10, 12, 17, 18 and 19. On males, IFNT-related genes were upregulated (IFNT, IFNT2 IFNT3 and IFN-T). On day d32, there were 6772 DEGs, with 3252 genes with increased expression in female, and 3520 in male placentas. Among the genes increased in female placentas are genes involved in placentation: PAGs 17, 19, 9 and PLAC8B. On the other hand, PAG1 was detected as highly expressed in male placentas. In conclusion, IVP-derived male embryos were more susceptible to alterations in gene expression and these effects extend to the peri-implantation period including genes associated with placental development and markers of placental function.

overall_design: Samples of extraembryonic membranes from artificial insemination and in vitro produced pregnancies were collected on days 18 and 32. A piece of the conceptus (day 18) or chorioallantois (day 32) were used.

first: M

middle: S

first: Jessica

middle: N

last: Drum

first: Guilherme

last: Madureira

first: Camila

last: Rosa

first: Marcelo

last: Seneda

first: Milo

last: Wiltbank

first: Roberto

last: Sartori


title: Effect of depletion of ATP3 and ATP22 on gene expression of C. glabrata

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

country: China

institute: Chinese Academy of Sciences

summary: To uncover the underlying mechanism of fluconazole resistance upon genetic depletion of ATP3 and ATP22, we performed transcriptomic analysis by RNA-seq for atp3Δ, atp22Δ, and WT cells during standard log phase growth.

overall_design: We conducted three independent replicates and compared the transcriptomes of atp3Δ and atp22Δ with that of WT cells to profile the differentially expressed genes (DEGs).

first: Eve

last: Chow

first: Jiaxin

last: Gao

first: Yue


title: miRNA expression data from Taenia solium ESP treated human macrophages

city: Kamand

first: Amit

last: Prasad

state: Himachal Pradesh

address: Parashar Road

department: School of Basic Sciences

country: India

institute: Indian Institute of Technology Mandi

summary:
This study aims to investigate the immunemodulatory effects of excretory-secretory products (ESPs) from the parasite Taenia solium on human macrophages to understand immunopathogenesis of neurocysticercosis (NCC). NCC is an infection of the central nervous system caused by the larvae of T. solium and is a major contributor to acquired epilepsy. Although ESPs from parasites are known to possess immune-modulating properties, the specific mechanisms of their action in NCC remains unclear. Therefore, this expression study seeks to shed light on the exact mechanism by which T. solium ESPs exert their immune-suppressive effects on human macrophages. Understanding this mechanism can provide valuable insights into the pathogenesis of NCC and potentially contribute to the development of novel therapeutic strategies for managing the disease.
The study employed miRNA microarray technology to investigate the post-translational effects of excretory-secretory products (ESPs) from Taenia solium on human macrophage function. microRNAs, are small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. The aim of study is to identify specific miRNAs that might be responsible for modulating macrophage function. Altered expression of miRNAs can influence the translation and stability of target mRNA molecules, subsequently affecting the production of proteins and the overall function of macrophages, thus affecting immune homeostasis in infection. Understanding the miRNA-mediated regulatory mechanisms involved in the immune response to T. solium infection can contribute to a better understanding of the pathogenesis of neurocysticercosis and potentially uncover novel therapeutic targets for managing the disease.

overall_design: T.solium ESP was cultured in vitro and human macrophages were treated with ESP. The treated macrophages were processed for RNA extraction and expression study as per the manufacturer's guideline.

first: Naina

last: Arora


title: ZFP281 coordinates DNMT3 and TET1 in pluripotent state transitions


title: ZFP281 coordinates DNMT3 and TET1 in pluripotent state transitions [RNA-seq]

overall_design: RNA-seq of WT and Zfp281degron pluripotent stem cells

first: Xin

last: Huang


title: Defying Gravity: WEEP promotes negative gravitropism in Prunus persica by establishing asymmetric auxin gradients

status: Public on Dec 13 2023

city: East Lansing

first: Courtney

last: Hollender

state: MI

address: 1066 Bogue St

department: Horticulture

institute: Michigan State University

summary: Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The Prunus persica (peach) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Until now, little was known about the function of WEEP protein despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size-exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide new insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.

overall_design: To investigate WEEP function in the development of the gravitropic polar auxin gradient, we compared gene expression in upper and lower tissues of the first two internodes of horizontal lateral shoots from standard and weeping peaches.

first: Andrea

last: Kohler


title: ZFP281 coordinates DNMT3 and TET1 in pluripotent state transitions [ChIP-seq]

first: Jianlong

overall_design: ChIP-seq of ZFP281 and TET1 in pluripotent stem cells


title: The impact of timing and injury mode on induced neurogenesis in the adult mammalian retina

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

institute: University of Washington

summary: Regeneration of neurons has enormous implications for human health and is a topic of interest both from the biological and translational perspective. The retina poses an excellent system to study the potential of replacing neurons following injury and the impact different lesions can have on this process. We have established mouse models where proneural transcription factors are expressed in Müller glia to stimulate neurogenesis, which is analogous to how zebrafish regenerate the retina after injury. Our previous studies have shown that Müller glia overexpressing either Ascl1 or Ascl1-Atoh1 will respond to inner retinal damage, caused by a neurotoxic dose of NMDA, by acquiring a progenitor-like state and giving rise to bipolar cells or retinal ganglion-like cells, respectively. It was not known however whether neurogenesis would still occur if the retina suffered outer retinal injury and if the timing of injury relative to the expression of proneural factors was critical for the process. To address these questions, we explored whether timing or mode of injury affect the induced neurogenesis from MG. We show that reprogramming MG with Ascl1 is not impacted by the mode or timing of injury, since all paradigms resulted in similar ratios of new bipolar neurons. By contrast, MG that express Ascl1-Atoh1 respond to outer retinal damage by producing a new type of retinal ganglion-like cell that is not generated after NMDA injury. Therefore, although the fate of reprogrammed neurons is mostly dictated by the proneural transcription factors, there is a context-dependent effect of the injured retinal microenvironment.

overall_design: The aim of this work was to study the impact of timing and injury mode on induced neurogenesis from Müller glia in the adult mammalian retina. We used transgenic mice in which the reporter GFP and transcription factor Ascl1 or combination of factors Ascl1-Atoh1 are expressed in Müller glia in a Cre-inducible manner. Following different injury modes (light-damage or NMDA injection in the vitreal cavity of the eye) GFP+ cells were harvested from retinas and processed for scRNA-seq  using the Chromium Next GEM Single Cell 3' v3.1 (dual index) protocol.

first: Marina

last: Pavlou

first: Marlene

last: Probst

first: Nicolai

last: Blasdel

first: Aric

last: Prieve


first: Viviana

last: Piccolo


title: Low sucrose availability reduces basal spikelet fertility by inducing abscisic acid and jasmonic acid synthesis in wheat

first: SUN

last: WAN

address: o. 2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

summary: Within a spike of wheat, the central spikelets usually generate three to four fertile florets, while the basal spikelets hardly achieve this. The physiological and transcriptional mechanism behind the difference in fertility between the basal and central spikelets is unclear. This study reports a high temporal-resolution investigation of transcriptomes, number and morphology of floret primordia, and physiological traits. The W6.5–W7.5 stage was regarded as the boundary to distinguish between fertile and abortive floret primordia; those floret primordia reaching the W6.5–W7.5 stage during the differentiation phase (3–9 d after terminal spikelet stage) usually developed into fertile florets in the next, dimorphism phase (12–27 d after terminal spikelet stage), whereas the others aborted. The central spikelets had a greater number of fertile florets than the basal spikelets, which was associated with more floret primordia reaching the W6.5–W7.5 stage. Physiological and transcriptional results demonstrated that the central spikelets had a higher sucrose content and lower abscisic acid (ABA) and jasmonic acid (JA) accumulation than the basal spikelets due to down-regulation of genes involved in ABA and JA synthesis. Collectively, we propose a model in which ABA and JA accumulation is induced under limiting sucrose availability (basal spikelet) through up-regulating genes involved in ABA and JA synthesis; this leads to floret primordia in the basal spikelets being hardly able to reach their fertile potential (W6.5–W7.5 stage) during the differentiation phase and then aborting. This fertility repression module may also regulate spikelet fertility in other cereal crops and potentially provides genetic resources to improve spikelet fertility.

overall_design: To investigate the transcriptional difference between basal and central spikelets, a dynamic transcriptome analysis was conducted at 6, 9, 12, 15, 21, and 27 DAT

first: Wan

last: SUN

first: Chongjing

last: Lu

first: Liangyun

last: Wen

first: Yaqun

last: Liu

first: Xiaohan

last: Zhou

first: Xuechen

last: Xiao

first: Xiaolei

last: Guo

first: Zhimin

last: Wang

first: Zhencai

last: Sun

first: Zhen

last: Zhang

first: Yinghua


title: The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen

city: Detroit

first: Laila

last: Poisson

address: 2799 W Grand Blvd

institute: Henry Ford Health

type: Methylation profiling by genome tiling array

summary: Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histological progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neo-angiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution towards an IDHwt-like phenotype.

overall_design: The GLASS epigenomic cohort consists of 357 DNA methylation samples profiled by either Illumina 450K or EPIC Beadchip methylation arrays. Newly generated DNA methylation data was collected from four different institutions: Henry Ford Hospital (N=103), University of Leeds (UK) (N=8), Chinese University of Hong Kong (N=6), and Luxembourg Institute of Health (N=54) and is available in this series. Previously published data is not included here (they can be accessed at:EGAS00001001255, EGAS00001001854, and EGAS00001001588 .

first: Tathiane

last: Malta

first: Indrani

last: Datta


title: UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors

city: Farmington

first: Duomeng

last: Yang

address: 263 Farmington Avenue

institute: Uconn health

summary: RIG-I like receptors (RLRs) are the major viral RNA sensors essential for the initiation of antiviral immune responses to numerous RNA viruses. RLRs are subjected to stringent transcriptional and posttranslational regulations, of which ubiquitination is one of the most important. However, the role of ubiquitination in RLR transcription is unknown. Here, we generated, screened 375 definite ubiquitin ligase knockout cell lines and identified UBR5 as a positive regulator of RLR transcription. UBR5 deficiency (UBR5-/-) reduced antiviral immune responses to RNA viruses, while increased viral replication in primary cells and mice. Ubr5-/- mice were more susceptible to lethal RNA virus infection than Ubr5+/+ littermates. Mechanistically, UBR5 mediated the Lysine 63-linked ubiquitination of TRIM28, an epigenetic repressor of RLRs. This modification prevented intramolecular SUMOylation of TRIM28, thus disengaged the TRIM28-imposed brake on RLR transcription. In sum, UBR5 enables rapid upregulation of RLR expression to boost antiviral immune responses by ubiquitinating and de-SUMOylating TRIM28.

overall_design:
To identify new E3 ligases critical for RLR signaling by a systemic approach, we performed an unbiased screening of 375 individual ubiquitin E3 ligase knockout cell lines by a CRISPR-Cas9 knockout screening system and identified Ubiquitin Protein Ligase E3 Component N-Recognin 5 (UBR5) as a positive regulator of RLR transcription.
UBR5 regulates RLR transcriptional expression throug posttranslational modification of TRIM28, we then performed ChIP-seq analysis using DNA obtained from TRIM28 IP in WT and UBR5 knockout HEK293T cells with VSV infection.
The ChIP-seq analysis were designed to identify if UBR5 specific control of TRIM28 binding to RLR alleles.


title: UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors (ChIP-Seq)

first: Tingting

last: Geng

first: Andrew

last: Harrison

first: Jason

last: Cahoon

first: Jian

last: Xing

first: Baihai

last: Jiao

first: Mark

first: Chao

last: Cheng

first: Robert

middle: E

last: Hill

first: Huadong

first: Anthony

middle: T

last: Vella

first: Gong

first: Yanlin

first: Penghua


title: Conductive Electrospun Polymer Platforms Improve Stem Cell-Derived Cardiomyocyte Function and Maturation

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

summary: Despite efforts to mature human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) for disease modeling and high throughput screening, cells remain immature and may not reflect adult biology. Recent advancements utilize electro-mechanical and paracrine stimulation to functionally mature cardiomyocytes, but the resulting engineered constructs continue to lack a microenvironment conducive to electrical signal propagation and maturity. Conductive polymers are attractive candidates to facilitate electrical communication between gaps in sparse hPSC-CM clusters or between hPSC-CMs to repair conduction defects. To create a conductive polymer platform for improved electrical signal propagation between hPSC-CMs and achieve electrical maturity, we electrospun poly(3,4-ethylendioxythiophene):polystyrene sulfonate (PEDOT:PSS) blended with 8% (w/v) poly(vinyl alcohol) (PVA). Matrix fiber structure remained stable over 4 weeks in buffer, stiffness remains near cardiac stiffness in vivo, and electrical conductivity scaled with PEDOT:PSS concentration. When fibroblasts were added to fibers, cells had higher initial attachment to PEDOT:PSS compared to PVA-only scaffolds, and after 5 days, over 90% of fibroblasts remained viable on PEDOT:PSS scaffolds compared to PVA-only scaffolds. Electrically excitable hPSC-CMs cultured on conductive substrates exhibited an upregulation of cardiac and muscle-related genes as opposed to non-conductive substrates. These cells further displayed increased desmoplakin (DP) localization on conductive scaffolds, indicating an improvement in the mechanical stability of our hPSC-CMs. Sarcomere organization also scaled with increasing PEDOT:PSS concentration, even in sub-monolayer cell densities, suggesting that improved organization of the contractile machinery in these cells was due to the electrical condition of the matrix. Calcium handling indicated higher calcium flux with a shorter time to peak, further suggesting improved electrical maturity, even when sub-confluent. Taken together, these data suggest that PEDOT:PSS/PVA scaffolds are stable, of a stiffness relevant to cardiomyocytes, and supportive of electrical coupling even in the absence of a monolayer, which may improve cardiac disease modeling and drug development.

overall_design: Day 50 RUES2 hPSC-CMs were cultured on either 8% PVA (non-conductive control) or 9.75% PEDOT:PSS/PVA (conductive) electrospun scaffolds across 3 biological replicates, with 2 technical replicates per sample to compare cardiac gene expression after 3 days of substrate exposure.

first: Gisselle

last: Gonzalez

first: Aileena

last: Nelson

first: Alyssa

middle: R

last: Holman

first: Alexander

middle: J

last: Whitehead

first: Erin

last: LaMontagne

first: Rachel

last: Lian

first: Ritwik

last: Vatsyayan

first: Shadi

last: Dayeh


title: UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors (RNA-Seq)

first: Duomeng

last: Yang

overall_design:
To identify new E3 ligases critical for RLR signaling by a systemic approach, we performed an unbiased screening of 375 individual ubiquitin E3 ligase knockout cell lines by a CRISPR-Cas9 knockout screening system and identified Ubiquitin Protein Ligase E3 Component N-Recognin 5 (UBR5) as a positive regulator of RLR transcription.
We then performed gene expression profiling analysis using data obtained from RNAseq of WT and UBR5 or TRIM28 knockout HEK293T cell lines with/or without poly (I:C) stimulation.
Gene expression analysis busing data from RNAseq of WT and UBR5 or TRIM28 knockout HEK293T cell lines with/or without IFN-β stimulation as control.

first: Tingting

last: Geng

first: Andrew

first: Jason

first: Jian

first: Baihai

first: Mark

last: Wang


title: AP-1 signaling modulates cardiac fibroblast stress responses

summary: This study aimed to evaluate the genomic effects of single nucleotide polymorphisms (SNPs) at the 9p21 locus that are clinically correlated with heart disease. We performed ATAC sequencing on  iPSC-derived cardiac fibroblasts  and found large differences in AP-1 and GATA family motifs between cells containing the SNPs and those lacking them.

overall_design: Three isogenic pairs of iPSCs from two patients were differentiated into cardiac fibroblasts and submitted for ATAC sequencing.

first: James

last: Hocker

first: Bing

last: Ren

first: Hamza

last: Atcha


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells

city: Los Angeles

first: Kathrin

last: Plath

institute: UCLA

summary: X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: NGFR regulates germinal center B-cell activation and negative selection

city: Madrid

first: Alberto

last: Hernández-Barracno

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center

summary: The expression of the Nerve growth factor receptor (NGFR) was described in follicular dendritic cells (FDCs), the major lymphoid stromal cell (LSC) compartment regulating B-cell activation within germinal centers (GCs). However, the role of NGFR in humoral response is not well defined. In this work, we have studied the effect of Ngfr KO in LNs organization and function. Ngfr KO led to spontaneous GC formation and expansion of GC B-cell compartment that were related on Ngfr depletion in non-hematopoietic radioresistant compartment. In agreement, Ngfr KO mice showed alterations in LSC with an increased frequency of FDCs harboring an activated phenotype characterized by the overexpression of CD21/35, MAdCAM-1, and VCAM-1. Moreover, Ngfr KO mice showed GC ectopic location, loss of polarization, impaired high-affinity antibody production, and increased circulating autoantibodies. In addition, Ngfr KO/Bcl2 Tg mice displayed increased levels of autoantibodies, higher incidence of autoimmunity, and decreased overall survival. Our work shows that NGFR maintains GC structure and functionality being involved in the regulation of antibody production and immune tolerance.

overall_design:
To investigate differences in gene expression profiles we isolated FDCs from WT and Ngfr KO popliteal lymph nodes by FACS. Lymph nodes from several animals were pooled for each sample.
Gene expression profiling was performed using 4 WT and 3 Ngfr KO independent samples

last: Hernández-Barranco

last: Benguría

first: Enrique

last: Vazquez

first: Ana

last: Dopazo

first: Héctor

last: Peinado


title: single-nucleus RNA-seq of human SGs

status: Public on Dec 12 2023

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

country: Germany

institute: Technical University of Munich

summary: The sympathetic nervous system (SNS) is pivotal in orchestrating the body's response to stress,maintaininghomeostasis, andfacilitatingadaptive physiological changes. The executing neurons responsible for these responses are localized in ganglia, positioned along the sympathetic chain. Here, we performedsingle-nucleussequencingof human sympathetic ganglia from heart healthy specimens obtained at autopsy. Unbiased clustering and trajectory analyses allowed a comprehensive analysis ofthissequencing data, offering valuable insights intoganglionic physiology includinggene expression patterns,cellular composition, intercellular communication as well as cellstatetransitions anddynamics. Strikingly, identifying previously uncharacterized cell types suggests aremarkablyhigher level of complexity than previously appreciated.Our findings highlightthe dynamic and complex physiology of sympathetic ganglia, shedding light on mechanismsgoverning fundamental physiological processes and the intricate interplay of various cell types coordinating the underlying pathways on the transcriptional level. This dataset enhances our knowledge of the SNS and opens avenues for further investigation into its role in health and disease.

overall_design: Sympathetic ganglia from human specimens were subjected to single-nucleus RNA-seq (10x Genomics).

middle: A

first: Sandro

last: Meunier

first: Stefan

last: Engelhardt


title: Testing SIPA1L2 as a modifier of CMT1A using mouse models

city: Bar Harbor

first: George

middle: C

last: Murray

state: ME

address: 600 Main St.

department: Research

institute: The Jackson Laboratory

summary: Charcot-Marie-Tooth 1A is a demyelinating peripheral neuropathy caused by the duplication of peripheral myelin protein 22 (PMP22), which produces muscle weakness and loss of sensation in the hands and feet.  A recent case-only genome wide association study by the Inherited Neuropathy Consortium identified a strong association between variants in signal induced proliferation associated 1 like 2 (SIPA1L2) and strength of foot dorsiflexion.  To validate SIPA1L2 as a candidate modifier, and to assess its potential as a therapeutic target, we engineered mice with a deletion in SIPA1L2 and crossed them to the C3-PMP22 mouse model of CMT1A.  We performed neuromuscular phenotyping and identified an interaction between Sipa1l2 deletion and muscular endurance decrements assayed by wire-hang duration in C3-PMP22 mice, as well as several interactions in femoral nerve axon morphometrics such as myelin thickness.  Gene expression changes suggested an involvement of Sipa1l2 in cholesterol biosynthesis, which was also implicated in C3-PMP22 mice.  Though several interactions between Sipa1l2 deletion and CMT1A-associated phenotypes were identified, validating a genetic interaction, the overall effect on neuropathy was small.

overall_design: We are primarily investigating the effect of genotype on gene expression in sciatic nerve in contrasts: C3-PMP22 vs WT, Sipa1l2-/- vs WT, and C3-PMP22::Sipa1l2-/- vs WT.

first: Robert

last: Burgess


title: Mesenchymal stem/stromal cells from human pluripotent stem cell-derived brain organoid enhance the ex vivo expansion and maintenance of hematopoietic stem/progenitor cells

city: Chengdu

first: ya

last: zhou

state: Sichuan

address: huacai road No.26, chenghua district

institute: Institute of blood transfusion

summary: We report a novel method for harvesting MSCs from 3D human brain organoids under serum-free culture condition. The stromal cells, derived from both H1-hESCs and human induced pluripotent stem cells (hiPSCs) forebrain organoids, were capable of differentiating into the classical mesenchymal-derived cells (osteoblasts, chondrocytes, and adipocytes). These cells expressed MSC markers, thus named pluripotent stem cell-derived MSCs (pMSCs).To investigate the role of pMSCs, we compared the RNA sequencing of pMSCs ,umbilical cord-MSC,hiPSCs and H1 hESCs.To investigate the function pMSC  in the regulation of umbilical cord blood HSPCs, we compared the RNA sequencing of CD34+ cells after co-culturing with and without pMSC and UC-MSCs,respectively.We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 kinds of different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pMSCs and UC-MSC,CD34+ cells co-cultured with and without MSC.

first: Ya

last: Zhou

first: Feng

last: Ma


title: PBRM-1/PBAF-regulated genes in a multipotent progenitor in C. elegans

city: Richmond

first: Laura

last: Mathies

state: VA

address: 1220 East Broad St.

institute: Virginia Commonwealth University

summary: The Caenorhabditiselegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The two SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates and the other dies by programmed cell death. The PBAF chromatin remodeling complex promotes the multipotent SGP fate. Complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae.

overall_design: Two strains were compared for this study. One strain uses the hnd-1 promoter to drive Cre/lox recombination and GFP nanobody-directed protein degradation in mesodermal tissues; this is pbrm-1(TS-KO). A control strain containing all the selectable markers found in pbrm-1(TS-KO) but lacking the GFP nanobody and Cre expression was used for comparisons, this is prbrm-1(control). L1 larvae were collected from pbrm-1(TS-KO) and pbrm-1(control). Five replicates were performed. Collections were made in parallel, on different days. RNA sequencing was used to identify differentially expressed genes between pbrm-1(TS-KO) and pbrm-1(control).

middle: D


title: Spatial transcriptomics sequencing profiles of human breast tissue

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: 10x Visium spatial transcriptomics expression profiles of breast tissues from BRCA2 mutation carriers and normal patients.

first: Bianca

last: Capaldo

first: Rachel

last: Joyce

first: Gordon

middle: K

last: Smyth

first: Jane

last: Visvader


title: Apically localized PANX1 impacts neuroepithelial expansion in human cerebral organoids

city: St. John's

first: Jessica

middle: L

last: Esseltine

state: NL

address: 300 Prince Philip Drive

department: Division of Biomedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Dysfunctional paracrine signaling through Pannexin 1 (PANX1) channels is linked to several adult neurological pathologies and emerging evidence suggests that PANX1 plays an important role in human brain development. It remains unclear how early PANX1 influences brain development, or how loss of PANX1 alters the developing human brain. Using a cerebral organoid model of early human brain development, we find that PANX1 is expressed at all stages of organoid development from neural induction through to neuroepithelial expansion and maturation. Interestingly, PANX1 cellular distribution and subcellular localization changes dramatically throughout cerebral organoid development. During neural induction, PANX1 becomes concentrated at the apical membrane domain of neural rosettes where it co-localizes with several apical membrane adhesion molecules. During neuroepithelial expansion, PANX1-/- organoids are significantly smaller than control and exhibit significant gene expression changes related to cell adhesion, WNT signaling and non-coding RNAs. As cerebral organoids mature, PANX1 expression is significantly upregulated and is primarily localized to neuronal populations outside of the ventricular-like zones. Ultimately, PANX1 protein can be detected in all layers of a 21-22 post conception week human fetal cerebral cortex. Together, these results show that PANX1 is dynamically expressed by numerous cell types throughout embryonic and early fetal stages of human corticogenesis and loss of PANX1 compromises neuroepithelial expansion due to dysregulation of cell-cell and cell-matrix adhesion, perturbed intracellular signaling, and changes to gene regulation.

overall_design: To investigate the role of PANX1 in neural induction, we established an iPSC in which the PANX1 gene has been knocked out by CRISPR gene editing.

first: Rebecca

last: Noort

first: Thomas

last: Belbin


title: Simvastatin overcomes resistance to tyrosine kinase inhibitors in patient-derived, oncogene-driven lung adenocarcinoma models

city: Sacramento

first: Tianhong

last: Li

address: 2700 Stockton Blvd

institute: UC Davis Health

summary: There is an unmet clinical need to develop novel strategies to overcome resistance to tyrosine kinase inhibitors (TKIs) in patients with oncogene-driven lung adenocarcinoma (LUAD). Statins is a class of drugs that act as competitive inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR). The objective of this study was to determine if simvastatin could overcome TKI resistance using the vivo LUAD models. Mice implanted with patient-derived xenografts (PDXs) from osmertinib-resistant LUAD were treated with simvastatin, either alone or in combination with osmertinib. Tumors were assessed by RNA sequencing. RNA sequencing  identified the proliferation, migration, and invasion-related genes (such as PI3K/Akt/mTOR, YAP/TAZ, focal adhesion, extracellular matrix receptor), proteasome-related genes, and integrin (α3β1, αvβ3) signaling pathways are significantly changed in these PDX tumors treated with simvastatin and the combo therapy.

overall_design: A PDX model was generated from patients with metastatic LUAD harboring oncogenic mutations (EGFR L858) and implanted into the flank of NSG mice at 5-6 weeks of age. Treatment was initiated at week three or when tumors reached an average size of 150-200 mm3. Mice were randomized into control and treatment groups, with 4 mice per group. They received vehicle control, single-agent treatment (osimertinib or simvastatin), or osimertinib and simvastatin combination therapy.  Total RNA was isolated from 10 mg of tumor tissue using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA-sequencing was performed at Novogene Corporation Inc. (https://en.novogene.com), which performed the quality control analysis and constructed the library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). The sequencing was performed on the NovaSeq 6000 system (NovaSeq PE150) at the Novogene UC Davis Sequencing Center. The raw sequencing data were obtained for analysis. Reads were aligned to Human hg38 using Salmon with standard settings

first: Weijie

first: Sixi

last: Wei

first: Qianping

first: Jie

last: Zeng

first: Wenwu

last: Xiao

first: Chihong

first: Ken

last: Yoneda

first: Amir

last: Zeki


title: Chronic endoplasmatic reticulum stress in myotonic dystrophy type 2 promotes autoimmunity via mitochondrial DNA release

city: Dresden

first: Sarah

last: Rösing

address: Fetscherstr. 74

institute: University hospital Carl Gustav Carus, TU Dresden

summary: In this study, next generation sequencing of fibroblasts from healthy controls and patients with myotonic dystrophy type 1 or 2 was performed. The aim is to compare the obtained profiles (RNA-seq) and to find differences between controls and patients or between the two types of the disease. These results may help to further clarify the origin of the autoimmune disease that some patients develop.

overall_design: RNA sequencing of transcripts isolated out of native cell (fibroblast) samples

first: Claudia

last: Günther


title: RNA-sequencing of ERBB3hi and ERBB3lo breast luminal progenitor cells from n=3 premenopausal BRCA2 mutation carriers and n=3 non-carriers [RNASeq_4_ERBB3]

first: Yunshun

summary: RNA-sequencing was performed on patient luminal progenitor breast cell subsets from premenopausal, preneoplastic BRCA2 mutation carriers and non-carriers to interrogate early transcriptional alterations in BRCA2mut/+ cells.

overall_design:
Lin-EPCAM+CD49f+ERBB3hi and Lin-EPCAM+CD49f+ERBB3lo luminal progenitor cells were isolated from n=3 premenopausal BRCA2 mutation carriers and n=3 non-carriers by FACS, then subjected to RNA-sequencing. Fluorescence minus one (FMO) controls were used to determine ERBB3lo versus ERBB3hi cells for each patient.
** Submitter declares that the raw data files are not provided due to privacy concerns about the human samples***

first: Michael

last: Milevskiy

first: Rachel


title: The tRNA methyltransferase dTrmt10A impacts m6A levels and the stress response in the Drosophila brain

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

summary: The tRNA methyltransferase TRMT10A was previously shown modulating the level of N6-methyladenosine (m6A) in polyadenylated RNA (polyA+ RNA). Here, we focus on the function of the Drosophila homolog of human TRMT10A, CG14618/dTrmt10A, and its impact on m6A regulation in the Drosophila brain and acute stress response. Using m6A-IP RNA sequencing from head tissue, we find that altering the levels of dTrmt10A modulates the levels of m6A on polyA+ RNA in the brain. Specifically, dTrmt10A affects m6A levels on transcripts enriched for signaling pathways, with a particular impact on 3' UTR m6A in response to heat shock. Furthermore, our findings indicate that upregulation of dTrmt10A results in a global decrease in m6A levels and decreases resilience to acute heat stress. Collectively, our data affirm the crucial role of m6A in the biological response of the brain to stress, and reveal that dTrmt10A acts as an additional regulator of m6A in the Drosophila brain and stress response.

overall_design: head m6A-IP used to investigate the role of the m6A RNA modification in heat shock stress and dTrmt10A knockdown and upregulation.

first: Nancy

middle: M

last: Bonini


title: LncRNA U90926 is dispensable for the development of obesity-associated phenotypes in vivo

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Obesity is a global health problem, which is characterized by the excessive fat accumulation or adiposity in the body and associated with other chronic metabolic disorders. Excess energy induces adipogenesis and lipid accumulation inside the existing adipocytes during obesity, which involves transcriptional changes and regulation. Recently, long non-coding RNAs (lncRNAs) have been implicated in regulation of adipogenesis and adipose tissue function. Mouse lncRNA U90926 was previously identified as a repressor of in vitro adipogenesis in 3T3-L1 preadipocytes. Based on this, we hypothesized that U90926 may repress weight gain and adiposity in vivo. To test the hypothesis, we leveraged U90926-deficient (U9-KO) mice, which we recently generated, with a generalized high-throughput phenotyping pipeline and focused follow-up phenotyping experiments. Compared with WT, U9-KO mice showed no major differences across a wide range of behavioral, neurological, and other physiological parameters. In mice fed a standard diet, we have found no differences in obesity-related phenotypes such as weight gain, fat mass accumulation, and plasma concentration of glucose, insulin, triglycerides, and free fatty acids in U9-KO mice in comparison with WT. U90926 deficiency did not have a major effect on perigonadal white adipose tissue morphology and gene expression profile. Furthermore, in mice fed a high fat diet, we found increased expression of U90926, yet no effect of U90926 deficiency on weight gain, fat mass, adipogenesis marker expression, and immune cell infiltration into the adipose tissue. Taken together, these data suggest that the lncRNA U90926 lacks an essential role in obesity-related phenotypes as well as adipocyte biology in vivo.

overall_design: We analysed perigonadal white adipose tissue  from U90926 knock-out mice and controls

first: Bristy

last: Sabikunnahar

first: Sydney

last: Caldwell

first: Stella

last: Varnum

first: Tyler

last: Hogan

first: Karolyn

middle: G

last: Lahue

first: Birgit

last: Rathkolb

first: Raffaele

last: Gerlini

first: Nathalia

last: Dragano

first: Antonio

last: Aguilar-Pimentel

first: Martin

last: Irmler

first: Adrián

last: Sanz-Moreno

first: Patricia

last: da Silva-Buttkus

first: Eckhard

last: Wolf

first: Valérie

last: Gailus-Durner

first: Helmut

last: Fuchs

last: Hrabé de Angelis

first: Matthew

last: Poynter

first: Dimitry

last: Krementsov


title: RNA-sequencing of mammary epithelial cell subpopulations from normal premenopausal and postmenopausal breast tissue [RNASeq_2_PrePost]

first: Yunshun

last: Chen

summary: RNA-sequencing was performed on patient mammary epithelial cell subsets from premenopausal and postmenopausal women undergoing breast reduction surgeries to interrogate transcriptional changes in postmenopausal cells.

overall_design:
Lin-EPCAM+CD49F- ML, Lin- EPCAM+CD49F+ LP and Lin-EPCAM-CD49F+ basal cells were isolated from normal premenopausal (n=4 patients) and postmenopausal (n=4 patients) human breast tissue by FACS and subjected to RNA-sequencing. The postmenopausal patients included in the study were not taking hormone-replacement therapies at time of surgery.
** Submitter declares that the raw data files are not provided due to privacy concerns about the human samples***

first: Rachel

last: Joyce

first: Rosa

last: Pascual

first: Gordon

last: Smyth

first: Jane

last: Visvader


title: RNA-sequencing of ERBB3hi and ERBB3lo breast luminal progenitor cells from n=3 premenopausal BRCA2 mutation carriers and n=5 non-carriers [RNASeq_3_ERBB3]

overall_design:
Lin-EPCAM+CD49f+ERBB3hi and/or Lin-EPCAM+CD49f+ERBB3lo luminal progenitor cells were isolated from n=3 premenopausal BRCA2 mutation carriers and n=5 non-carriers by FACS, then subjected to RNA-sequencing. Fluorescence minus one (FMO) controls were used to determine ERBB3lo versus ERBB3hi cells for each patient.
** Submitter declares that the raw data files are not provided due to privacy concerns about the human samples***


title: Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer.

city: Oxford

first: Andrew

last: Blake

state: Oxfordshire, UK

address: Old Road Campus

institute: Department of Oncology

summary:
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC; PDS1 tumours are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis. PDS2 which is regenerative/ANXA1+ stem-rich, with elevated stromal/immune tumour microenvironmental lineages. PDS3 tumours represent a previously overlooked slow-cycling subset of tumours within CMS2, with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are under-represented in pre-clinical models currently and are not identified using existing subtyping classifiers
Mutations: https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_mutations.txt, CNA per gene : https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_cna_gene_subselection_for_paper.txt, CNA segments SPINAL https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws4_spinal_cna.zip, CNA segments FOCUS https://www.s-cort.org/sites/default/files/exports/scort_spinal_focus_paper/ws2.focus_cna.zip

overall_design: 258 Samples analysed, no replicates nor reference samples used


title: The Mediator kinase module regulates transcriptional memory after heat stress by resolving blocked RNA polymerase complexes

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: In nature, plants are often exposed to recurring adverse environmental conditions. Acclimation to high temperature stress entails transcriptional responses that are mediated by heat-shock transcription factors (HSFs), and they are primed to better withstand subsequent stress events. This heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurring HS. However, the mechanisms by which HSFs recruit and enact the transcriptional machinery remain unclear. Here, we identified two subunits of the kinase module of the Mediator transcriptional co-regulator complex, CDK8 and MED12, as regulators of HS memory in Arabidopsis thaliana. Enhanced re-induction of gene expression after recurrent HS and physiological HS memory, as well as H3K4 methylation are compromised in cdk8 and med12 mutants. HSFA2 interacts with CDK8 during and after HS and recruits it to memory gene loci, where CDK8 binds in the promoter but also the gene body, together with core Mediator and RNA polymerase II (Pol II). Our data suggest that CDK8 resolves stalled Pol II complexes or promotes efficient recycling for subsequent cycles of transcription. As HSFA2, CDK8 is largely dispensable for the initial induction of gene expression after HS and thus promotes transcriptional memory independently of HS-dependent primary gene induction. Our findings provide a model for the complex role of the Mediator kinase module during transcriptional memory in multicellular eukaryotes through interaction with transcription factors, chromatin modifications and promotion of Pol II productivity.

overall_design: Gene expression comparison. Wild-type, hsfa2 and cdk8 mutants. Heat stress priming (P), treatment (T), priming and treatment (P+T) and controls. Three biological replicates.

first: Tim

last: Crawford

first: Lara

last: Siebler

first: Aleksandra

last: Sulkowska

first: Bryan

last: Nowack

first: Li

last: Jiang

first: Yufeng

last: Pan

first: Matija

last: Stanic

first: Christian

last: Kappel


title: Comprehensive multi-omics analysis revealed WEE1 as a synergistic lethal target with hyperthermia through CDK super-activation

city: 武汉

first: Hu

last: Xingyuan

state: Hubei

address: 湖北武汉

institute: 同济医院

summary: To explore the translational expression on  mRNA levels after hyperthermia，we exposed OVCAR8 cells to hyperthemia (42℃) for 90 mins.

overall_design: We then performed RNA-seq on OVCAR8 cells with or without hyperthermia stimulation.

first: Sun

last: Chaoyang

first: Yang

last: Xiaohang

last: xingyuan


title: Identification of aberrant luminal progenitors and mTORC1 as a potential chemoprevention target in BRCA2 mutation carriers

first: Yunshun

last: Chen

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

overall_design: Refer to individual Series


title: Spatial transcriptomics analysis of soft tissue sarcomas.

city: Stanford

first: Ajay

last: Subramanian

state: CA

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used spatial transcriptomics to analyze the spatial distribution of malignant, immune, and other stromal cells present within soft tissue sarcomas.

overall_design: Spatial transcriptomics was performed on 4 soft tissue sarcomas.

first: Everett

last: Moding


title: Bulk RNA-sequencing of soft tissue sarcomas from patients undergoing chemotherapy and/or immunotherapy

summary: The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We performed bulk RNA-sequencing of tumors from patients with soft tissue sarcomas undergoing chemotherapy and/or immunotherapy to identify gene expression signatures associated with response to treatment.

overall_design:
Bulk RNA-sequencing was performed on 87 soft tissue sarcoma specimens from 54 patients.
T1 is timepoint 1, and T2 is a later timepoint. An "a" or "b" from the same timepoint represent different regions.


title: i-shaped antibody engineering enables conformational tuning of biotherapeutic receptor agonists

status: Public on Dec 18 2023

city: South San Francisco

first: Daniel

last: Le

address: 1 DNA Way

institute: Genentech

summary: The ability to leverage antibodies to agonize disease relevant biological pathways has the potential to unlock new drug targets for clinical investigation. While antibodies have been successful as antagonists, immune mediators, and targeting agents, they are not readily effective at recapitulating the biological activity of natural ligands. Among the important determinants of antibody agonist activity is the geometry of target receptor engagement. Herein, we describe a novel engineering approach inspired by a naturally occurring Fab-Fab homotypic interaction that constrains IgG in a unique i-shaped conformation. i-shaped antibody (iAb) engineering enables potent intrinsic agonism of five tumor necrosis factor receptor superfamily (TNFRSF) targets. When applied to bispecific antibodies against the heterodimeric IL-2 receptor pair, constrained bispecific IgG formats recapitulate IL-2 agonist activity. Thus, iAb engineering represents a new tool to tune agonist antibody function and this work provides a framework for the development of intrinsic antibody agonists with the potential for generalization across broad receptor classes.

overall_design: We aim to assess the effect of antibody based mimetics of IL2 on gene expression in primary CD8 T cells as compared to recombinant IL2. We have found that constrained antibody formats are capable of inducing signaling and proliferation comparable to IL2 in multiple assays and would like to extend this study to transcriptomic analysis. Each condition was tested in triplicate.

first: Matthew

last: Romei

first: Brandon

last: Leonard

first: Jonathan

last: Sockolosky

first: Greg

last: Lazar


title: RNA-sequencing of epithelial cell subpopulations from human breast tissue [RNASeq_1_BRCA2]

summary: Molecular profiling of mammary epithelial cell subpopulations from premenopausal BRCA2 mutation carriers and premenopausal non-carriers was performed to identify early transcriptional perturbations in preneoplastic BRCA2-mutant breast.

overall_design:
Mammary epithelial cell subpopulations (Lin- EPCAM+CD49f- ML, Lin- EPCAM+CD49f+ LP and Lin-EPCAM-CD49f+ basal cells)  were isolated from preneoplastic breast tissue by FACS and subjected to bulk RNA-sequencing (n=3 premenopausal BRCA2 mutation carriers and n=3 premenopausal non-carriers).
** Submitter declares that the raw data files are not provided due to privacy concerns about the human samples***

first: Rachel

last: Joyce

first: Gordon

last: Smyth

first: Jane

last: Visvader


title: Trps1 predicts poor prognosis in advanced high grade serous ovarian carcinoma

status: Public on Dec 11 2023

city: Fuzhou

first: sun

middle: jian

last: dong

address: 1 North Road, Xuefu

institute: Fujian medical university

summary: TRPS1 is aberrantly expressed in a variety of tumors, including breast, prostate, and gastric cancers, and is strongly associated with tumorigenesis or prognosis. However, the role of TRPS1 in high grade serous ovarian carcinoma (HGSC) is unknown. We investigated the relationship between TRPS1 expression and clinicopathology in HGSC patients. The tumor-related regulatory mechanisms of TRPS1 was explored through in vivo and vitro experiments. The results showed that TRPS1 was highly expressed in HGSC compared to normal tissues. It was also linked to the cell proliferation index Ki67 and poor prognosis. In vivo experiments showed that knockdown of TRPS1 could inhibit tumor growth. In vitro experiments, knockdown of TRPS1 inhibited the proliferation of ovarian cancer cells. TRPS1 exerted its regulatory role as a transcription factor, binding to the PSAT1 promoter and promoting the expression of PSAT1 gene. Meanwhile, PSAT1 was positively correlated with CCND1 expression. These results suggest that TRPS1 affects HGSC proliferation and cell cycle by regulating PSAT1 and thus CCND1 expression.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for TRPS1 in SKOV3 cell lines.

first: Shie

last: Wang

first: Yue

last: Liu

first: Jiandong

last: Sun

first: Xiaojiang


title: Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA-Seq]

city: Guangzhou

first: Gaofei

last: Li

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

summary: Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model, we have identified an eosinophil lineage-specific marker, eslec. Using this marker we have established a Tg(eslec:eGFP) reporter line, which specifically labels zebrafish eosinophil lineage cells from early life through adulthood. Spatial-temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single-cell RNA-Seq of eslec+ cells, tissue-distributed eosinophils were found to have similar differentiation paths but different tissue-specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpβ transcriptional axis that regulated eosinophilopoiesis, in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment, differentiation, and maturation of the eosinophil lineage. In summary, this study characterized eosinophil development in multiple dimensions including spatial-temporal patterns, expression profiles, and genetic regulators. The results provide for a better understanding of eosinophilopoiesis.

overall_design: For the RNA-Seq analysis of eosinophils from different genotypes, eslec:eGFP+ eosinophils were sorted from whole larvae (7 dpf) and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented, adpator tagged, and purified for further sequencing.

first: Yiyue

last: Zhang


title: Bulk RNA Sequencing of sorted LepR+ Sympathetic Associated Perineurial Cells

city: Singapore

first: Jinmiao

last: Chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Adipose tissues (ATs) are innervated by sympathetic nerves, which drive reduction of fat mass via lipolysis and thermogenesis. Here, we report a population of immunomodulatory leptin receptor (LepR)-expressing barrier cells which ensheath sympathetic axon bundles in adipose tissues. These LepR-expressing Sympathetic Perineurial Cells (SPCs) produce IL33, a factor for maintenance and recruitment of regulatory T cell (Treg) and eosinophils in AT. Brown adipose tissues (BAT) of mice lacking IL33 in SPCs (SPCIL33cKO) have fewer Treg and eosinophils, resulting in increased BAT inflammation. These SPCIL33cKO mice are more susceptible to diet-induced obesity, independently of food intake. Furthermore, SPCIL33cKO mice have impaired adaptive thermogenesis, and are unresponsive to leptin-induced rescue of metabolic adaptation. We, therefore, identify LepR-expressing SPCs as a source of IL33 which orchestrate an anti-inflammatory environment in BAT, preserving sympathetic-mediated thermogenesis and body weight homeostasis. LepR+ IL33+SPCs provide a cellular link between leptin and immune regulation of body weight, unifying neuroendocrinology and immunometabolism as previously disconnected fields of obesity research.

overall_design: LepR+ cells from the Superior Cervical Ganglia of LepRCRE::Ai32 mice were sorted and sequenced. 3 biological replicates

first: Bernardo

last: Arús

first: Noelia

last: Martínez-Sánchez

first: Svetoslav

last: Chakarov

first: Florent

last: Ginhoux

first: Ana

last: Domingos


title: Pericytes contribute to pulmonary vascular remodeling via HIF2α signaling [lung]

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Vascular remodeling is the process of structural alteration and cell rearrangement of blood vessels in response to injury and is the cause of many of the world's most afflicted cardiovascular conditions, including pulmonary arterial hypertension(PAH). Many studies have focused on the effects of vascular endothelial cells and smooth muscle cells(SMCs) during vascular remodeling, but pericytes, an indispensable cell population residing largely in capillaries, are ignored in this maladaptive process. Here we report that hypoxia-inducible factor 2α(HIF2α) expression is increased in human PAH patient lung tissues and HIF2α overexpressed pericytes result in greater contractility and an impaired endothelial-pericyte interaction. Using single-cell RNAseq and hypoxia-induced pulmonary hypertension(PH) models, we show HIF2α as a major molecular regulator for pericytes’ transformation into SMC-like cells. HIF2α overexpression in pericyte-selective mice exacerbate PH and right ventricular hypertrophy. Temporal cellular lineage tracing shows that HIF2α overexpressing reporter NG2+ cells (pericyte-selective) relocate from capillaries to arterioles and co-express SMA. This novel insight into the potential role of NG2+ pericytes in pulmonary vascular remodeling via HIF2α signaling suggests a potential drug target for PH.

overall_design: single-cell RNA-seq analysis on mouse lungs after three weeks of hypoxia or without hypoxia

first: Ke

last: Yuan


title: Non-invasive detection of neuroendocrine prostate cancer through targeted cell-free DNA methylation

city: Trento

first: Gian Marco

last: Franceschini

state: Trentino Alto Adige

address: via Sommarive 9, Povo

department: CIBIO

institute: University of Trento

summary: Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive differences in therapy response and outcomes. Histologic transformation to castration-resistant neuroendocrine prostate cancer (CRPC-NE) is associated with distinct epigenetic alterations, including acquired changes in DNA methylation. The current diagnosis of CRPC-NE is challenging and relies on metastatic biopsy. Here, we developed a targeted DNA methylation assay based on the analysis of large tissue datasets to detect CRPC-NE using plasma cell-free DNA (cfDNA) non-invasively. The assay quantifies tumor content and a phenotype evidence score that captures the spectrum of CRPC phenotypes, leveraging a few hundred informative genomic regions to also inform the expression and/or transcriptional state of genes of interest. We qualified the assay in independent clinical cohorts, including 158 plasma samples, achieving a phenotypic evidence score AUC > 0.93 for detecting pathology-confirmed CRPC-NE, and revealing associations between methylation-defined tumor content and clinical outcomes in two prospective phase 2 clinical trials (NCT01799278 and NCT00514540) designed toward aggressive variant CRPC and CRPC-NE, supporting the application of targeted DNA methylation for CRPC-NE detection and patient stratification.

overall_design: To demonstrate the capability of our DNA methylation targeted assay we profiled a large collection of preclinical models, patient derived data and healthy controls. This includes a series of experiments on prostate cancer models, white blood cells, and circulating tumor DNA from patients.

first: Gian

first: Francesca

last: Demichelis

first: Himisha

last: Beltran


title: Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA-Seq]

summary: Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model, we have identified an eosinophil lineage-specific marker, eslec. Using this marker we have established a Tg(eslec:eGFP) reporter line, which specifically labels zebrafish eosinophil lineage cells from early life through adulthood. Spatial-temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single-cell RNA-Seq of eslec+ cells, tissue-distributed eosinophils were found to have similar differentiation paths but different tissue-specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpβ transcriptional axis that regulated eosinophilopoiesis, in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary, this study characterized eosinophil development in multiple dimensions including spatial-temporal patterns, expression profiles, and genetic regulators. The results provide for a better understanding of eosinophilopoiesis.

overall_design: For scRNA-Seq analysis of eosinophils in kidney, eosinophils were sorted from adult Tg(eslec:eGFP) kidneys. For scRNA-Seq analysis of renal cells of different genotypes, kidneys were collected from WT, cebp1-/-, and cebpb-/- individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x 3' scRNA-Seq analysis. The scRNA-Seq data of WT, cebp1-/-, and cebpb-/- KM cells were integrated and analyzed together.

first: Yicong

first: Shuai

last: He

first: Wan

last: Peng


title: Effects of Tibetan tea consumption on white adipose tissue microenvironment and metabolic network in high-fat diet-fed mice

city: Ya'an

first: Songqi

last: Duan

address: No.46, Xinkang Road, Yucheng District

department: College of Food Science

institute: Sichuan Agricultural University

summary: Metabolic disorders, such as obesity and type 2 diabetes, are major public health concerns worldwide. Dietary interventions, such as tea consumption, have been suggested as an effective strategy to prevent and treat metabolic disorders. White adipose tissue, as the main energy storage organ in mammals, plays a critical role in the regulation of whole-body metabolism. Recent studies have shown that the microenvironmental cell composition and metabolic network of white adipose tissue can be modulated by dietary factors, including tea consumption. However, the underlying mechanisms and the effects of tea consumption on white adipose tissue in the context of high-fat diet-induced metabolic disorders are not fully understood. Therefore, this study aimed to investigate the effects of tea consumption on the microenvironmental cell composition and metabolic network of white adipose tissue in high-fat diet-fed mice.

overall_design: In this study, mice were randomly assigned to one of four treatment groups (n=5 per group): chow diet with water, chow diet with Tibetan tea, high-fat diet with water, and high-fat diet with Tibetan tea. The mice were housed under standardized conditions with a 12-hour light/dark cycle and provided ad libitum access to food and water for 10 weeks. Tibetan tea used in this study was prepared as water extract. At the end of the study, mice were euthanized, and white adipose tissue samples were collected for transcriptome sequencing.

first: Ziqi

last: Wang


title: Skin biopsy expression from the faSScinate phase 2 study of tocilizumab in systemic sclerosis

status: Public on Dec 10 2023

first: Jason

middle: Anthony

last: Vander Heiden

department: Biological Research AI Development

summary: Gene expression profiling via microarray was performed for control donors and systemic sclerosis (SSc) patients.

overall_design:
Total RNA was collected from skin biopsies of 20 control donors, 39 placebo patients and 34 tocilizumab treated partients from the Roche faSScinate phase 2 study of tocilizumab in systemic sclerosis (SSc).

**RAW data not provided**

first: Thierry

last: Sornasse


title: Neoadjuvant CD40 agonism remodels the tumor immune microenvironment in locally advanced esophageal/gastroesophageal junction cancer [CITE-seq]

city: San Francisco

first: Bridget

middle: P

last: Keenan

address: 505 PARNASSUS AVE, ROOM 1296

department: Medicine

institute: University of California San Francisco

summary: Sotigalimab (sotiga) is an agonistic anti-CD40 monoclonal antibody that can modulate anti-tumor immune responses. In a clinical trial of sotiga combined with neoadjuvant chemoradiation (CRT) in locally advanced esophageal/gastroesophageal junction cancer, treatment induced pathologic complete responses in 38% of patients. Using high-dimensional single cell techniques, we found that sotiga dramatically re-modeled both peripheral immune responses and the tumor microenvironment (TME), increasing components of antigen processing and presentation and altering metabolic pathways in myeloid cells. Concomitant with myeloid cell alterations, sotiga primed new T cell clonotypes, increased T cells with enhanced cytotoxic activity, and decreased the frequency of Tregs in the TME. Clinical responses were associated with both baseline and treatment-induced T cell states. These findings indicate that sotiga induces antigen presentation leading to enhanced T cell activation and clinical response, and that the immune composition of the TME at baseline is important in conferring sensitivity to this treatment approach.

overall_design: Blood samples were obtained from patients pre- and on-treatment as part of a phase II clinical trial clinical trial (NCT03165994). Treatment regimen was carboplatin (AUC 2)/paclitaxel (50 mg/m2) weekly for 5 weeks and concurrent radiation 5040 cGy in 28 fractions, and up to 4 doses of sotigalimab 0.3mg/kg IV between weeks 1-10, followed by Ivor-Lewis esophagectomy. Blood samples were collected from patients at baseline, at 2 weeks following the initial dose of sotigalimab, at weeks 8-11 following chemoradiation (approximately corresponding with the surgical resection), and at 2-6 months following surgery (long term follow up).

first: Maira

last: Soto

first: Erin

last: Filbert

first: Hai

last: Yang

first: Stephanie

last: Starzinski

first: Alec

first: Marissa

last: Gin

first: Brandon

first: Phi

last: Le

first: Tony

last: Li

last: Bol

first: Alexander

last: Cheung

first: Li

last: Zhang

first: Frank

last: Hsu

first: Andrew

last: Ko

first: Lawrence

last: Fong


title: Nuclear export of circular RNA

status: Public on Dec 09 2023

city: Adelaide

first: John

last: Toubia

address: Frome Rd

institute: Centre for Cancer Biology

summary: Circular RNAs (circRNAs), which can function as regulators of gene expression, are formed by back-splicing of precursor mRNAs in the nucleus. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here, we uncover a pathway specific for nuclear export of circular RNA. This pathway requires Ran-GTP, Exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter, CRM1, selectively increases nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Analysis of nuclear circRNA binding proteins reveals that interaction of IGF2BP1 with circRNA is enhanced by Ran-GTP, whereas its interaction with linear RNA is inhibited by Ran-GTP. Depletion or knockout of Exportin-2 specifically inhibits nuclear export of circRNA, while formation of an Exportin-2 circRNA export complex requires Ran-GTP and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Exportin-2 to export circRNAs in a mechanism analogous to protein export, rather than mRNA export.

overall_design: The study is composed of 14 individually matched nuclear and cytoplasmic fractionated RNA samples, 28 samples in total. Of these, 12 samples were treated with either siRNA negative controls or IGF2BP1 siRNA to produce 3 matched replicate samples for each fraction and treatment. Likewise, the remaining 16 samples were treated with either siRNA negative controls or XPO2 siRNA to produce 4 matched replicate samples for each fraction and treatment

last: Bert

first: Gregory

last: Goodall

first: Vihandha

middle: O

last: Wickramasinghe


title: Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish [ChIP-seq]

first: Gaofei

overall_design: For the ChIP-Seq analysis of Cebp1 or Cebpβ binding regions, Tg(hsp70:cebp1-eGFP) or Tg(hsp70:cebpb-eGFP) larvae were heatshocked for the overexpression of Cebp1-eGFP or Cebpβ-eGFP. Then, the binding regions were enriched by ChIP with the anti-GFP antibody.

first: Yiyue


title: ZFP36L1 is suppressed in ASCL1-positive lung adenocarcinoma and represses tumorigenic function

city: Bunkyo-ku

first: Takayoshi

last: Enokido

state: Tokyo

address: 7-3-1 Hongo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

summary:
To investigate the function of ZFP36L1 in ASCL1-positive lung adenocarcinoma, we established VMRC-LCD cell line in which the target gene has been overexpressed by plasmid vector.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VMRC-LCD cell and its OE derivatives (OE_ZFP36L1).

first: Naoya

last: Miyashita

first: Akira

last: Saito