title: RNA-seq of AFP-positive and negative liver tissues in LiKM mice

city: Suita

first: Yuki

last: Makino

state: Osaka

address: 2-2, Yamadaoka

institute: Osaka University Graduate School of Medicine

summary: RNA-seq of AFP-positive and negative liver tissues in LiKM (KrasG12D mutation and Mdm2 loss in the liver) mice. This study was aimed to clarify gene expression profile of AFP-positive cells in LiKM mice to clarify their characteristics.

overall_design: Total RNA was collected from AFP-positive and negative liver tissues of LiKM mice at 4 months of age.

first: Kazuhiro

last: Murai

first: Hayato

last: Hikita

first: Tetsuo

last: Takehara


title: Oxidative stress-mediated alterations of the microRNA expression profile in porcine granulosa cells using RNA-Seq technique

status: Public on Aug 24 2022

city: Zhengzhou

first: Jiaqing

last: Zhang

address: No. 116 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

country: China

institute: Henan Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the effects of oxidative stress induced by hydrogen peroxide(H2O2) on miRNA expression in porcine granulosa cells,we examined the impact of H2O2-mediated oxidative stress in procine GC through miRNA-Seq. We identified 33 (19 upregulated, 14downregulated) and 22 (14 upregulated, 8 downregulated miRNAs) differentially expressed miRNAs (DEmiRNAs) at 300μM and 100μM H2O2, respectively, compared with the control group.

overall_design: miRNA profiles of control and H2O2 treatment groups (100 and 300μM) were generated by deep sequencing using Illumina HiSeqTM 2500

first: Jia-Qing

first: Bao-Song

last: Xing


title: RNA-seq of non-tumorous liver tissues in LiK and LiKM mice after normal diet or ACR diet

country: Japan

type: Expression profiling by high throughput sequencing

summary: KrasG12D mutation and Mdm2 loss in the liver (LiKM) accelerated liver carcinogenesis in mice, compared with LiK (KrasG12D mutation in the liver) mice.  Acyclic retinoid (ACR) diet suppressed tumor development in LiKM mice. The goal of RNA-seq of non-tumorous liver tissues is to identifiy the effect of ACR diet on the transcriptomic profile of the liver and clarify the mechamism of ACR-mediated tumor suppression in LiKM mice.

overall_design: LiK and LiKM mice were fed a normal diet or a diet containing 0.06% ACR from 5 weeks of age until sacrifice at 4 months of age. Non-tumorous liver tissues were obtained at the time of sacrifice.


title: single cell-RNA sequencing for Immune cells from mouse brain post high-salt diet

city: Daejeon

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: To identify the effect of high-salt diet on immune cells of brain tissues, we isolated immune cells of brain from mice fed with control diet or high-salt diet.

overall_design: Examination of transcriptional changes on brain immune cells post high-salt diet

first: Chae

middle: W

first: Heung

middle: K

last: Lee


title: Analyses of prometastasic gene profile and immune infiltration in K7M2 osteosarcoma mouse model after treatment with SFV vectors expressing galectin-3 inhibitor.

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

summary: RNA profiling of orthotopic K7M2 osteosarcoma mouse model treated with SFV-Gal3-N-C12, SFV-Luc or PBS (mock group). To better understand the mechanism underlying the therapeutic effect of SFV-Gal3-N-C12 we analyzed, in primary tumors of treated mices, the changes in expression of osteosarcoma-specific prometastasic genes as well as immunomodulatory molecules genes, and differences in immune cell infiltration.

overall_design: Comparison of the RNA pofiling in K7M2 osteosarcoma mouse model treated with SFV-Gal3-N-C12 (n = 4), SFV-Luc (n = 3) or PBS (n = 5). Seven days after orthotopic K7M2 cell implantation (0D),  we treated mice by intratumorally injection with SFV-Gal3-N-C12, SFV-Luc or PBS (mock group). Then, the expression of osteosarcoma-specific prometastasic gene set, expression of immunomodulatory molecules genes and tumor immune infiltrate was analyzed by RNA-seq (14 days posttreatment).

middle: M

last: Alonso

first: Guillermo

last: Herrador Cañete


title: Extracellular Vesicles Derived from Wharton’s Jelly Mesenchymal Stem Cells Inhibit the Tumor Environment via the miR-125b/HIF-1a Signaling Pathway

city: Tsukuba

first: Yun Hsuan

last: Chang

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

summary:
Purpose: small RNAseq analyses were conducted to identify the key miRNAs which involves in the regulation of tumor development in the Wharton's Jelly Mesehchymal Stem Cell-derived EV (WJ-EV) treated breast cancer cell (BCC)
Methods: MDAMB231, a triple negative breast cancer cell line, were treated with WJ-EV at 0 and 24 hours, then the cell samples were harvested at 48 hours. The cells were cultured under a hypoxic condition (1%O2).
Results: 1169 miRNAs were identified in original BCC and WJ-EV treated BCC (pBCC), respectively.

overall_design: miRNA profiles of BCC and pBCC

first: Yun

middle: H

first: Nhat

last: Ngo

first: Cat

last: Vuong

first: Toshiharu

last: Yamashita

first: Xiucai

last: Ye

first: Yasunori

last: Futamura

first: Mana

last: Obata-Yasuoka

first: Hiromi

last: Hamada

first: Motoo

last: Osaka

first: Yuji

last: Hiramatsu

first: Masafumi

last: Muratani

first: Tetsuya

last: Sakurai

first: Osamu

last: Ohneda


title: Single-cell RNA sequencing of small intestine neurons in Hirschsprung disease mice

city: Boston

first: Allan

last: Goldstein

state: MA

address: 185 Cambridge St

department: Pediatric Surgery

country: USA

institute: Massachusetts General Hospital

summary: This study was undertaken to identify gene expression changes in enteric neurons of Hirschsprung disease mice. Methods: We performed single-cell RNA sequencing of enteric nervous system cells isolated from the small intestine of Ednrb-knockout mice at age P14. Results: Through comparisons with published datasets of WT small intestine enteric neurons, we identify a missing neuronal population in the ganglionated small intestine of Hirschsprung disease mice. Conclusion: Single-cell RNA sequencing permits identification of cellular perturbations in Hirschsprung disease models.

overall_design: Use of 10X Genomics technology to analyze single-cell transcriptomics myenteric plexus neurons in an Ednrb-knockout model of Hirschsprung disease.


title: CRELD2 is a novel modulator of calcium mobilisation and calcineurin-NFAT signalling during osteoclast differentiation

city: Newcastle-Upon-Tyne

first: Ella

middle: Patricia

last: Dennis

address: Inst. of Genetic Medicine, Int’l Centre for Life, Central Parkway

country: United Kingdom

institute: Newcastle University

summary: Cysteine rich with epidermal growth factor (EGF)-like domains 2 (CRELD2) is an endoplasmic reticulum (ER) resident chaperone protein with calcium binding properties. CRELD2 is an ER-stress regulated gene that has been implicated in the pathogenesis of skeletal dysplasias and has been shown to play an important role in the differentiation of chondrocytes and osteoblasts. Despite CRELD2 having an established role in skeletal development and bone formation, its role in osteoclasts is currently unknown. Here we show for the first time that CRELD2 plays a novel role in trafficking transforming growth factor beta 1 (TGF-β1), which is linked to an upregulation in the expression of Nfat2, the master regulator of osteoclast differentiation in early osteoclastogenesis. Despite this finding, we show that CRELD2 is dispensable for osteoclastogenesis. Indeed, the overexpression of Creld2 impaired osteoclast differentiation due to a reduction in the activity of the calcium-dependent phosphatase calcineurin. This in turn led to a subsequent block in the dephosphorylation of nuclear factor of activated T cells 1 (NFATc1) dephosphorylation preventing its nuclear localisation and activation as a pro-osteoclastogenic transcription factor. Our exciting results show that the overexpression of Creld2 in osteoclasts impaired calcium mobilisation which is essential for activating calcineurin and promoting osteoclastogenesis. Therefore, our data proposes a novel inhibitory role for this calcium-binding ER-resident chaperone in modulating calcium flux during osteoclast differentiation which has important implications in our understanding of bone remodelling and the pathogenesis of skeletal diseases.

overall_design: RNA was extracted from CONTROL and CRELD2 overexpressing RAW264.7 osteoclasts 48 hours after RANKL stimulation using Promega ReliaPrep Cell Miniprep System following the manufacturer’s protocol, and was sequenced using an Illumina NextSeq 500.

first: Adam

last: Duxfield

first: Jennifer

last: Munkley

first: Michael

middle: D

last: Briggs

middle: P


title: Whole transcriptome analysis of HK1EBV exosome-treated fibroblasts.

city: Taoyuan

first: Po-Ju

middle: Gordon

last: Lee

address: No. 300, Zhongda Rd, Zhongli District

department: Biomedical Sciences and Engineering

country: Taiwan

institute: National Central University

summary: We aimed to investigate whether EBV exosomes will affect gene expression in primary fibroblasts. By obtaining normalized read counts of genes generated from RNA-sequencing, we compared the transcriptomic alterations between fibroblasts treated with HK1EBV exosomes and untreated fibroblasts.

overall_design: mRNA profiles of untreated fibroblasts and HK1EBV exosome-treated fibroblasts

first: Shu-Chen

last: Liu

first: Tzu-Tung


title: RNA-seq of liver tissues in LiK and LiKM mice

first: Yuki

last: Makino

summary: LiKM (KrasG12D mutation and Mdm2 loss in the liver) accelerated liver carcinogenesis in mice compared with LiK (KrasG12D mutation in the liver) mice. This study was aimed to clarify mRNA expression pforile to elucidate the mechanism of accelerated liver carcinogenesis in LiKM mice.

overall_design: Total RNA was collected from the liver of LiK and LiKM mice at 6 weeks of age.


title: RNA-Seq of KRAS-regulated genes in a KPAR1.3-G12C murine cell line and lung tumours

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

institute: The Francis Crick Institute

summary: KPAR1.3-G12C murine lung cancer cell line, and derived lung tumours, were treated with a KRASG12C inhibitor for different time points

overall_design: RNA-Seq of KRASG12C-inhibited cells and tumours

last: Arcas

middle: L

last: Sopena

first: Julian

last: Downward


title: Mettl14-driven senescence-associated secretory phenotype (SASP) facilitates somatic reprogramming

city: 上海

first: xiang

middle: chen

last: xi

address: siping road 1239

institute: tongji university

summary: The METTL3-METTL14 complex, as the "writer" of N6-methyladenosine (m6A), plays an important role in many biological processes. Previous studies have shown that overexpression of Mettl3 can increase the level of m6A and promotes somatic cell reprogramming. Here, we demonstrate that Mettl14, another component of the methyltransferase (MTase) complex, can significantly enhance the generation of induced pluripotent stem cells (iPSCs) in m6A independent manner. Cooperating with Oct4, Sox2, Klf4 and c-Myc (OSKM), Mettl14 transiently increased the senescence-associated secretory phenotype (SASP) gene expression in the non-reprogramming cells at the late reprogramming stage. The conditional medium in reprogramming intermediates overexpressing Mettl4 or its mutant could enhanced the reprogramming, so do IL-6, a component of SASP. Corespondingly, blocking of SASP using senolytic agent or NF-κB inhibitor impairs the effect of Mettl14 on reprogramming. . Our work highlights the m6A independent function of Mettl14 and provides new insight into the interplay between senescence and reprogramming in vitro.

overall_design: The reprogrammable MEFs derived from the transgenic mice carrying the tetO-OSKM transgene and Oct4-GFP/Rosa26-M2rtTA were used in the experiments. The reprogrammable MEFs that were not induced with doxycycline were designated as “MEF” . The reprogrammable cells with or without Obox1’s overexpression were induced with doxycycline (1ug/ml) for 3 days. The cells were harvested and performed RNA sequencing (RNA-seq) .

first: ChenXiang

last: Xi

first: Li

last: Wu

first: XiaoCui

last: Xu


title: Telomere shortening is associated with over-expression of subtelomeric genesin thyroid tumors.

city: Madrid

first: CRISTINA

last: Montero-Conde

address: C/Melchor Fdez Almagro, 3

institute: CNIO

summary: To determine whether telomere shortening in thyroid tumors delineates gene expression of subtelomeric regions, we performed RNA sequencing in a set of tumors (n = 15) and compare gene expression profiles of subtelomeric and non-subtelomeric genes between short telomere tumors and normal telomere tumors. We defined as subtelomeric genes, those located within the 5 megabase windows (Mb) adjacent to the telomeres.

overall_design: Fifteen thyroid tumors comprising 10 tumors with short telomere telomeres and 5 tumors with telomere length within the range of normal thyroid tissues were included in the study. Telomere length was measured by Q-FISH.

first: Ángel

last: Martínez-Montes

first: Rafael

last: Torres-Perez

first: Cristina

first: Mercedes

last: Robledo


title: Downstream targeted genes of Satb2 regulate synaptic formation and axonogenesis in developing cerebral cortex

city: Shanghai

first: Yaqiong

last: Wang

address: 399 Wanyuan Rd

institute: Children's hospital of Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RB1 loss triggers dependence on ESRRG in retinoblastoma

city: Miami

first: Matthew

last: Field

state: FL

address: 900 NW 17th St

institute: University of Miami

summary: Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 16 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify novel Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death which is exacerbated in hypoxia. These findings reveal a novel dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.

overall_design: RNA-Sequencing of primary retinoblastoma tumors, RNA-Sequencing of low-passaged primary cultured retinoblastoma cell lines with and without knockdown of ESRRG, ChIP-Sequencing of low-passaged retinoblastoma cell lines with pulldown of ESRRG

middle: G

first: J

last: Harbour


city: Worcester

first: Mariya

last: Ivshina

address: 373 Plantation st

institute: Umass Medical School

summary: RNA seq of microglia from CPEB1-deficient and LPS-treated mice establish that RNA levels, splicing, and 3' poly(A) site selection are under complex regulation that mediate inflammation and phagaocytosis.

overall_design: RNA-seq from triplicate biologic samples of total microglia from WT and CPEB1 KO mice, some of which were injected with LPS for 24 hours prior to harvesting cells.

first: Maria

first: Joel

last: Richter


title: Next Generation Sequencing Facilitates Quantitative Analysis of control, TNFα and TNFα+JNK I treated GSCs Transcriptomes

city: Tianjin

first: xudong

address: Qixiangtai Road

institute: Tianjin medical university

summary: Among 830 TNFα-induced genes (at least 1.5 folds of upregulation in TNFα-treated TPC2-4 cells compared with control), the expression of 268 genes is significantly suppressed by JNKi treatment (TPC2-4 TNFα+JNKi/TPC2-4 TNFα, JNKi: JNK-IN-8, a kinase inhibitor specific for JNK (c-Jun N-terminal kinase) that inhibited phosphorylation of c-JUN)

overall_design: The mRNA profiles of TPC2-4 con, TPC2-4 TNFα, TPC2-4 TNFα+JNKi

first: Xudong

first: Xuejiao

last: Lv


title: ATAC-seq comparatively analyse chromatin accessibility varition of control, TNFα and TNFα+JNK I treated GSCs

summary: Among 3,673 TNFα-induced gain of accessibility (at least 2 folds of upregulation in TNFα-treated TPC2-4 cells compared with control), and most of the gained peaks were significantly suppressed by JNKi treatment (TPC2-4 TNFα+JNKi/TPC2-4 TNFα, JNKi: JNK-IN-8, a kinase inhibitor specific for JNK (c-Jun N-terminal kinase) that inhibited phosphorylation of c-JUN)

overall_design: Examination  chromatin accessibility varition of TPC2-4 con, TPC2-4 TNFα, TPC2-4 TNFα+JNKi


title: PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas

first: Kirsi

middle: J.

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Oligodendrogliomas are typically associated with the most favorable prognosis among diffuse gliomas. However, many of the tumors progress, eventually leading to patient death. To characterize the changes associated with oligodendroglioma recurrence and progression, we analyzed two recurrent oligodendroglioma tumors upon diagnosis and after tumor relapse based on whole-genome and RNA sequencing. Relapsed tumors were diagnosed as glioblastomas with an oligodendroglioma component before the World Health Organization classification update in 2016. Both patients died within 12 months after relapse. One patient carried an inactivating POLE mutation leading to a clearly hypermutated progressed tumor. Strikingly, both relapsed tumors carried focal chromosomal rearrangements in PTPRD and CNTNAP2 genes with associated decreased gene expression. TP53 mutation was also detected in both patients after tumor relapse. In The Cancer Genome Atlas (TCGA) diffuse glioma cohort, PTPRD expression decreased by tumor grade in all diffuse glioma subtypes, while CNTNAP2 expression was associated with diffuse glioma subtypes and with tumor grade in oligodendrogliomas and IDH wild-type astrocytomas. Low expression of the genes was associated with poor overall survival. Our analysis provides information about aggressive oligodendrogliomas with worse prognosis and suggests that PTPRD and CNTNAP2 expression could represent an informative marker for their stratification.

overall_design:
Examination of two oligodendroglioma patient cases with gene expression from primary and relapsed tumors.
Raw data not provided due to patient privacy concerns.

middle: J

last: Granberg

first: Serafina

last: Jaatinen

first: Aliisa

last: Tiihonen

first: Matti

last: Annala

first: Elisa

last: Vuorinen

first: Anni

last: Kivinen

first: Minna

last: Rauhala

first: Kendra

last: Maass

first: Kristian

last: Pajtler

first: Olli

last: Yli-Harja

first: Pauli

last: Helén

first: Joonas

last: Haapasalo

first: Hannu

first: Wei

last: Zhang

last: Nykter


title: Spatial transcriptomics of the ageing ovary

city: Lone Tree

first: Mary

middle: E

last: Haywood

state: CO

address: 10290 RidgeGate Circle

institute: CCRM

summary: Ageing is a physiological process that manifests through progressive molecular, cellular, and systemic changes. Female reproductive potential gradually declines with age as oocyte quality and quantity decline. The purpose of this study was to better understand the spatiotemporal dynamics of the ovary.

overall_design: The Visium Spatial Gene Expression technology from 10x Genomics was used to evaluate expression in ovary sections from young (3-4 months) and aged (15-16 months) mice. RNA was captured and sequenced from 4 capture areas, each containing 2 ovary sections (one young, one aged) for a total of 4 young and 4 aged samples.

first: Jennifer

last: Russ

first: Sydney

middle: C

last: Lane

first: William

middle: B

last: Schoolcraft

first: Mandy

last: Katz-Jaffe


title: STAT1 and Head and Neck Cancer

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

summary: This study examines the role of host STAT1 expression during oral carcinogenesis using an orthotopic model of metastatis oral cancer.

overall_design: LY2 oral cancer cell lines were injected into the oral cavity of WT or Stat1 deficient BALB/C mice. Tumors were subjected to bulk RNA sequencing


title: SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days [RNA-seq]

city: Yokohama

first: David

middle: Seth

last: Favero

state: International

address: 1-7-22 Suehirocho, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that SOB3 inhibits hypocotyl growth in SD, similar to its effects in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-Seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes affected by SOB3 were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data indicate that SOB3 mostly binds to similar genes throughout the day. Collectively, these data indicate that SOB3 affects gene expression in a time point-specific manner irrespective of changes in binding throughout SD.

overall_design: Identification of AHL regulated genes at different time points in Arabidopsis seedlings grown in short days

first: D

middle: S

first: C

middle: N

last: Jacques

first: K

last: Sugimoto

first: M

last: Neff


title: SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days [ChIP-seq]

overall_design: Genome-wide identification of SOB3 binding sites at different time points in Arabidopsis seedlings grown in short days

middle: M


title: Macrophages trigger injury-induced hepatocyte reprogramming via IL-6/gp130/STAT3 axis [RNA-Seq]

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: The liver is a pivotal organ possessing remarkable regenerative capacity. By employing murine liver injury models and lineage tracing strategy, recent studies have demonstrated that differentiated hepatocytes undergo reprogramming to SOX9+HNF4α+ liver progenitor-like cells (LPLCs), and serve as a totally new cell source for mammalian liver regeneration. However, it is largely unknown how hepatocyte reprogramming is regulated. In this study, we focus on analyzing the microenvironment cues in triggering hepatocyte reprogramming in liver injuries. By performing single-cell RNA sequencing (scRNA-seq) of hepatocyte reprogramming in liver injury, we find immune response is significantly activated. Notably, by lineage depletion, macrophages, especially kupffer cells, but not T cells, B cells, natural killer cells or neutrophils, are found essential for hepatocyte reprogramming and liver regeneration. IL-6, derived specifically from activated kupffer cells, triggers hepatocyte reprogramming via gp130/STAT3 signaling. Furthermore, STAT3 triggers gene expression by binding to Arid1a-dependent pre-opened regeneration-responsive enhancers (RREs) of reprogramming genes. Collectively, this study provides key insights into kupffer cells/IL-6/STAT3-mediated hepatocyte reprogramming and liver regeneration, which may serve as the base for new therapeutic strategies in facilitating endogenous repair mechanisms.

overall_design: Liver immune cell RNA profiling in DDC injury; Hepatocyte mRNA profiles of IL-6 treatment, DDC injury and STAT3Δhep mice.

first: Lu

last: Li

first: Lei

last: Cui

first: Ping

last: Lin


title: Cell-type specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

type: Methylation profiling by high throughput sequencing

summary: We report the application of an affinity purification approach (INTACT) to isolate tagged nuclei for GABAergic (GABA), Glutamatergic (Glu), and Purkinje neurons in mice. We performed whole-genome bisulfite sequencing (WGBS) to explore the cell type-specific DNA methylation signatures for the three neuronal types, together with matched transcriptomics. We found a substantial number of differentially methylated regions (DMRs) between cell types, characterized cell-type specific DMRs, and estimated the effects of DNA methylation on gene expression. Finally, we revealed that DNA methylation altered in a cell-type specific manner in a mouse model of Rett syndrome, a neurodevelopmental disorder caused by Mecp2 loss of function. The presented data emphasize the important role of DNA methylation-mediated epigenetic regulation in neuronal diversity and disease.

overall_design:
WGBS and RNA-Seq for mouse GABAergic, Glutamatergic and Purkinje neurons, as well as for GABAergic and Glutamatergic neurons with Mecp2 KO.
Only male mice were included in this project. For the nuclei isolated from one mouse, half of them were used for DNA extraction, and another half were used for RNA-Seq extraction. Therefore, each sample has DNA and matched RNA for WGBS and RNA-Seq, respectively.

first: Peng


title: LINE-1 antisense oligonucleotide ameliorate HGPA and WRN aging phenotype.

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

institute: Sequientia Biotech

summary: Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. In higher eukaryotes, constitutive  heterochromatin is mostly segregated at the nuclear periphery, where the interaction with the nuclear lamina makes the genome more resistant to transcription. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here we show that LINE-1 (L1) RNA accumulation is an early event in both typical and atypical progeroid syndromes. L1 RNA negatively regulates Suv39H1 enzymatic activity, resulting in heterochromatin loss and onset of senescent phenotypes. Depletion of L1 RNA in cells from different progeroid syndrome patients using specific antisense oligonucleotides (ASO) restores the levels of heterochromatin epigenetic marks, preserves DNA methylation and counteracts the expression of senescence-associated genes. Moreover, systemic delivery of ASO rescues the histophysiology of all tissues and increases the lifespan of Hutchinson-Gilford Progeria Syndrome (HGPS) mouse model. Furthermore, the transcriptional profiling following L1 RNA depletion shows that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response and DNA damage were downregulated. Our results show a key role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.

overall_design: all treatments have been performed in biological triplicates

first: Francesco

last: Della Valle

first: Pradeep

last: Reddy

first: Valerio

last: Orlando

first: Juan

last: Izpisua Belmonte


title: Gene Expression Dynamics in Late Embryonic and Early Postnatal Mouse Ovaries

city: Providence

first: Kathryn

last: Grive

state: RI

address: 200 Chestnut Street, Kilguss Research Institute, Rm 108, Grive Lab

department: OB-GYN

institute: Women & Infants Hospital of RI

summary: This analysis represents one of the first unbiased sampling of germ cells in the developing murine ovary over time, at high-resolution, single-cell depth, revealing novel genetic regulatory signatures of murine female germ cells and somatic cells over time.

overall_design: Single-cell suspensions of mammalian ovaries ranging from E18.5 to PND5 were created, processed for 10x Genomics and sequencing on an Illumina NextSeq.

last: Woodman

last: Ozcan

last: Gura


title: Macrophages trigger injury-induced hepatocyte reprogramming via IL-6/gp130/STAT3 axis [ChIP-Seq]

overall_design: Hepatocytes were perfused and isolated from normal diet feeding and DDC diet feeding Sox9-CreERT2; Rosa-LSL-tdTomato  (LPLC tracing tools) mice livers, analysis of genomic occupancy of H3K27ac in hepatocytes by ChIP-seq. Hepatoblasts were FACS from E12.5 fetal liver via DLK1 expression and were analyzed in genomic occupancy of H3K27ac. For high-quality pSTAT3 ChIP-seq, hepatocyte were perfused and isolated from normal diet liver with HTVi of IL6 plasmids (5ug/mL) for 3 days.


title: Control, TNFα and TNFα+JNK I treated GSCs

first: xudong

last: Wu


title: Global tibialis anterior skeletal muscle transcript data from male Carm1 skm-/- (HSAcre Tg/0 x Floxed Carm1) and Carm1 skm+/+ mice (HSAcre 0/0 x Floxed Carm1) on a chow diet.

city: Ottawa

first: Goutham

last: Vasam

state: ON

address: 451 Smyth Rd

department: Faculty of Health Sciences

country: Canada

institute: University of Ottawa

summary:
Transcript data from tibialis anterior muscle from male muscle-specific Coactivator-Associated Arginine Methyltransferase 1 (Carm1 ) knockout mice (Carm1 skm-/- ) and wild-type mice (Carm1 skm+/+) generated by using the Cre-loxP system (on a C57BL6J/129 background) with HSA-Cre mice (from Jackson laboratories).
We used RNA-Seq to detail the effects of muscle-specific loss of Carm1  on the global program of gene expression in tibialis anterior muscle.

overall_design: Chow diet fed 12-weeks-old male mice were etuhanized using cervical dislocation, then tibialis anterior skeletal muscles were snap-frozen in liquid nitrogen for RNA extraction. Samples included 4 animals for each geneotype which were prepared  for RNA-Seq.

first: Tiffany

last: vanLieshout

first: Derek

middle: W

last: Stouth

first: Nicolas

last: Hartel

first: Sean

middle: Y

last: Ng

first: Erink

middle: K

last: Webb

first: Irena

middle: A

last: Rebalka

first: Nicholas

last: Graham

first: Keir

last: Menzies

first: Thomas

last: Hawke

first: Vladimir

last: Ljubicic


title: SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days

first: David

last: Favero


title: Gut-derived short-chain fatty acids modulate skin barrier integrity by promoting keratinocyte metabolism and differentiation

city: Clayton

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: Barrier integrity is central to the maintenance of a healthy immunological homeostasis. Impaired skin barrier function is linked with enhanced allergen sensitization and the development of diseases such as atopic dermatitis (AD), which can precede the development of other allergic diseases such as food allergies and asthma.  Epidemiological evidence indicates that children suffering from allergies have lower levels of dietary fibre-derived short-chain fatty acids (SCFA). Using an experimental model of AD, we report that a fermentable fibre-rich diet alleviates AD severity and systemic allergen sensitization. The gut-skin axis underpins this phenomenon through SCFA, which strengthen skin barrier integrity by altering mitochondrial metabolism of epidermal keratinocytes. SCFA promote keratinocyte differentiation and the production of key structural lipids, resulting in enhanced barrier function. Our results demonstrate that dietary fibre and SCFA mitigate AD by improving barrier integrity, ultimately limiting early systemic allergen sensitization and development of disease.

overall_design: 16 Samples, 4 groups in duplicate

first: Aurélien

last: Trompette

first: Nick

first: Benjamin

last: Marsland


title: The establishment of human low-grade glioma xenografts requires CD4 T cell-mediated suppression of astrocyte Cxcl10 production

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: One of the major barriers to identifying improved treatments for pediatric low-grade brain tumors (gliomas) is the inability to reproducibly generate reliable human xenografts. This limitation reflects the dependency of these tumors on trophic support from non-neoplastic cells in the tumor microenvironment. In an effort to surmount this barrier, we leveraged human induced pluripotent stem cell (hiPSC) engineering to generate low-grade glioma (LGG)-like lesions in immune-compromised mice, representing the two most common pediatric LGG (pilocytic astrocytoma) molecular alterations. This platform also enabled the identification of the likely cells of origin for these tumors. In addition, we discovered a CD4+ T cell-astrocyte immune circuit in which CXCL10 was both necessary and sufficient for human hiPSC-LGG formation, enabling the successful growth of patient-derived pediatric LGGs in vivo. Taken together, these avatars establish experimental platforms to elucidate pediatric LGG pathogenesis, cellular origins, and signaling pathway dependencies relevant to future precision medicine strategies.

overall_design: Examination of different transcript expression in WT or Rag1-/- mouse brainstem cells

first: Corina

last: Anastasaki

first: Jit

last: Chatterjee

first: Amanda

last: De Andrade Costa

first: Suzanne

last: Schaeffer

first: Olivia

last: Cobb

first: Xia

last: Ge

first: Fausto

last: Rodriguez

first: Joel

middle: R

last: Garbow

middle: H


title: Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

city: Athens

first: Robert

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here, we report that a monocot plant, Spirodela polyrhiza, has lost CG gene body methylation, genome-wide CHH methylation, and the presence or expression of several genes in the highly conserved RNA-directed DNA methylation (RdDM) pathway. It has also lost the CHH methyltransferase CHROMOMETHYLASE 2. Consequently, the transcriptome is depleted of 24-nucleotide, heterochromatic, small interfering RNAs that act as guides for the deposition of 5mC to RdDM-targeted loci in all other currently sampled angiosperm genomes. Although the genome displays low levels of genome-wide 5mC primarily at LTR retrotransposons, CG maintenance methylation is still functional. In contrast, CHG methylation is weakly maintained even though H3K9me2 is present at loci dispersed throughout the euchromatin and highly enriched at regions likely demarcating pericentromeric regions. Collectively, these results illustrate that S. polyrhiza is maintaining CG and CHG methylation mostly at repeats. S. polyrhiza reproduces rapidly through clonal propagation in aquatic environments, which we hypothesize may enable low levels of maintenance methylation to persist in large populations.

overall_design: We generated MethylC-seq and small RNA-seq for two lines of S. polyrhiza, Sp7498 and Sp9509. Additionally, we generated H3K9me2 ChIP-seq and input gDNA as a control for line 9509.

first: Adam

last: Bewick

first: Alex

last: Harkess

first: Zefu

last: Lu

first: Blake

last: Meyers

first: R


title: Differential gene expression in SMC Ctrl vs TAZ4SA

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

summary: Poor prognosis of small cell lung cancer (SCLC) is mainly attributed to its highly metastatic capability. Here we identify the SMC and Non-SMC from Rb1L/L/Trp53 L/L mouse model through FACS with NE and mensenchymal markers. In order to identify functions of these two subpopulations during SCLC malignant progression, we compared their metastatic capability by allograft experiment. In addition, we find that the SMC is progressively transited from the Non-SCLC during mouse SCLC malignant progression. Further investigation reveals that genetic disruption of the SWI/SNF chromatin-remodeling complex, in RP model abrogates SMC phenotype maintenance and SCLC metastasis. In search of important downstream regulators, we find that TAZ, the core transcription cofactor of the Hippo pathway, is epigenetically silenced by SWI/SNF complex during this process. Collectively, our data link phenotypic transition to cancer metastasis and identify TAZ as a critical molecular switch that controls SCLC plasticity.

overall_design: SMC were derived from Rb1L/L, Trp53L/L mouse model through FACS. SMC was infected with the Ctrl or TAZ4SA (activated muation) virus. RNA-seq was performed to compare the gene expression profile between SMC with or without TAZ4SA overexpression.  Three replicates for each sample were included.

first: Yujuan

last: Jin

first: Hongbin

last: Ji


title: Differential gene expression in paired SMC vs. Non-SMC

overall_design: Paired SMC and Non-SMC were derived from Rb1L/L, Trp53L/L mouse model through FACS. RNA-seq was performed to compare the gene expression profile between paired SMC and Non-SMC. Two paired SMC and Non-SMC were used for the RNA-seq. Three replicates for each sample were included.


title: RNA-Seq of KRAS-regulated genes in a murine cell line and lung tumours

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

institute: The Francis Crick Institute

summary: A murine lung cancer cell line, and derived lung tumours, were treated with a KRASG12C inhibitor for different time points

overall_design: RNA-Seq of KRASG12C-inhibited cells and tumours

first: Molina

last: Miriam

first: Llorian

first: Downward

last: Julian


title: ATAC-seq in paired SMC vs. Non-SMC

overall_design: Paired SMC and Non-SMC were derived from Rb1L/L, Trp53L/L mouse model through FACS. ATAC-seq was performed to compare the chromatin remodeling between paired SMC and Non-SMC.


title: Genetic background and diet induce hepatic gene expression of different regulatory pathways associated with obesity in the Collaborative Cross

city: Davis

first: Brian

last: Bennett

state: CA

address: 430 West Health Sciences Drive

institute: USDA ARS-WHNRC

summary: In this study, we used 123 Collaborative Cross female mice fed either a high protein (HP) or high fat high sucrose (HS) diet to perform differential gene expression and analyses in the liver. We also determined the correlation of liver gene expression levels with phenotypic data of adiposity and obesity-related traits.

overall_design: Female mice from 22 CC strains were obtained from University of North Carolina’s CC Mouse Core at 6-9 weeks of age. Mice were then acclimated for 2 weeks on a synthetic diet, housed 3 mice per cage. Then, mice were put on experimental diets, randomized into different cages by experimental diet, and housed 3-5 mice per cage.  Mice were challenged on their respective diets for 8 full weeks and sacrificed the following week after a 4-hour fast and anesthetization to obtain liver samples for microarray analysis. Microarray data were available for 127 samples.

first: Phoebe

last: Yam


title: RNA-Seq of KRAS-regulated genes

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The Hippo kinase MST1 negatively regulates the differentiation of follicular helper T cells

status: Public on Aug 23 2022

city: Beijing

first: Lin

last: Dong

address: No. 19, Xinjiekouwai Street, Haidian District

institute: Beijing Normal University

summary: In order to explore the regulatory mechanism of MST1 kinase on Tfh differentiation and function, we sorted Tfh cells in the spleen of WT and Mst1 KO mice 8 days after intraperitoneal sensitization, and extracted total RNA from the collected cells as samples for sequencing analysis.

overall_design: RNA-sequencing samples were derived from sorted Tfh cells from mouse spleen  after intraperitoneal OVA sensitization of WT and Mst1 KO mice

first: Yejin

last: Cao

first: Hui

last: Yang

first: Yueru

last: Hou

first: Ying

last: He

first: Yufei

last: Wang

first: Qiuli

first: Yujing

last: Bi

first: Guangwei

last: Liu


title: Rab11FIP1-Deficient Mice Develop Spontaneous Inflammation and Show Increased Susceptibility to Colon Damage

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

summary: We hypothesized that deficiency of Rab11-FIP1 would affect mucosal integrity in the intestine and generated global Rab11FIP1 knockout (KO) mice. Transcription signatures indicated that Rab11FIP1 deletion downregulated genes that mediate stress tolerance response, while genes mediating the response to infection were significantly upregulated, consistent with the inflammatory responses in the steady state. These findings suggest that Rab11FIP1 is important for cytoprotection mechanisms and for the maintenance of colonic mucosal integrity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated colonic epithelial cells was compared between proximal and distal colons from Rab11FIP1KO, Rab11FIP2KO, and BL6J wild type mice.

first: James

last: Goldenring


title: LPS-induced IFN networks predict severe viral Lower Respiratory tract Infections in infancy

city: Perth

last: Read

state: WA

address: 15 Hospital Ave.

institute: Telethon Kids Institute

summary: Severe LRIs are a major cause of infant/child hospitalization and a risk factors for asthma pathogenisis. Innate immune interactions with microbial pathogens, esp. in early life,  underpin risk. We aimed to characterize cord blood mononuclear cell (CBMC) responses to activation of micriobial recognition receptors (TLRs 3, 4, & 7) and identify response pattern variations associated withsLRI susceptibility in infancy.

overall_design: 308 samples in total. Human cord blood mononuclear cells (CBMC) were available from 50 individuals, 27 of these subjects had matched PBMCs collected at 5 years. Samples were block randomized and cultured in the presence of each of three innate immune stimuli (LPS, Imiquimod, & Poly(I:C)), alongside an untreated control.

middle: F

first: Anthony

last: Bosco


title: Single‑cell analysis of peripheral CD8+ T cell responses in patients receiving checkpoint blockade immunotherapy for cancer

city: St. Louis

first: Michelle

last: Brennan

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

summary: Checkpoint blockade immunotherapy has become a first-line treatment option for cancer patients, with success in increasingly diverse cancer types. Still, many patients do not experience durable responses and the reasons for clinical success versus failure remain largely undefined. Investigation of immune responses within the tumor microenvironment can be highly informative but access to tumor tissue is not always available, highlighting the need to identify biomarkers in the blood that correlate with clinical success. Here, we used single-cell RNA sequencing coupled with T cell receptor sequencing to define CD8+ T cell responses in peripheral blood of two patients with melanoma before and after immunotherapy with either anti-PD-1 (nivolumab) alone or the combination of anti-PD-1 and CTLA-4 (ipilimumab). Both treatment regimens increased transcripts associated with cytolytic effector function and decreased transcripts associated with naive T cells. These responses were further evaluated at the protein level and extended to a total of 53 patients with various cancer types. Unexpectedly, the induction of CD8+ T cell responses associated with cytolytic function was variable and did not predict therapeutic success in this larger patient cohort. Rather, a decrease in the frequency of T cells with a naive-like phenotype was consistently observed after immunotherapy and correlated with prolonged patient survival. In contrast, a more detailed clonotypic analysis of emerging and expanding CD8+ T cells in the blood revealed that a majority of individual T cell clones responding to immunotherapy acquired a transcriptional profile consistent with cytolytic effector function. These results suggest that responses to checkpoint blockade immunotherapy are evident and traceable in patients’ blood, with outcomes predicted by the simultaneous loss of naive-like CD8+ T cells and the expansion of mostly rare and diverse cytotoxic CD8+ T cell clones.

overall_design: T Cells were isolated from human PBMCs, purified by FACS based on CD8+ and CD4+ staining and processed for single cell RNAseq using the 10X Genomics platform.

first: Niloufar

last: Khojandi

first: Ryan

last: Teague


title: Generation of TCR-negative CD8αβ+ CAR T cells from T cell-derived induced pluripotent stem cells

city: New York

first: Sjoukje

middle: van der

last: Stegen

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary:
The production of autologous T cells expressing a chimaeric antigen receptor (CAR) is time-consuming, costly and occasionally unsuccessful. T cell-derived induced pluripotent stem cells are a promising source for the generation of ‘off-the-shelf’ CAR T cells, but their in vitro differentiation often yields T cells with suboptimal features. Here we show that premature expression of the T cell receptor (TCR) or a constitutively expressed CAR promote the acquisition of an innate phenotype, which can be averted by disabling the TCR and relying on the CAR to drive T cell differentiation. Delaying CAR expression and calibrating its signalling strength enabled the generation of human CD8αβ+ TCR– CAR+ T cells that perform overall similarly to peripheral blood CD8αβ+ CAR+ T cells in achieving effective tumour control upon systemic administration in a mouse model of leukaemia, without causing graft-versus-host disease. Driving T cell maturation in the absence of a TCR by taking advantage of a CAR may facilitate the large-scale development of potent allogeneic CD8αβ+ T cells for a broad range of immunotherapies.
TRAC-1XX-iT cell generation: TiPS were differentiated to the DP T cell stage, and matured to CD8ab SP cells on 3T3-CD19-41BBL. CD8ab SP cells were purified by flow cytometry.
Peripheral Blood Mononuclear cells were purified from healthy donor whole blood. CD4 and CD8 T cells were targeted with CD19-28z-1XX CAR into the TRAC locus, NK and gdT cells were retrovirally transduced to express the CD19-28z-1XX CAR. Cells were purified for CAR expression by flow cytometry.

overall_design: mRNA profiles of PBMC-derived ab-TCR CD8ab T cells, gd-TCR T cells, CD8ab TRAC-1XX-iT cells.

last: van der Stegen

first: Michel

last: Sadelain


title: Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia

first: Sean

middle: Akira

last: Montgomery

address: C/ del Dr. Aiguader 88

institute: Centre for Genomic Regulation


title: Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia [CUT&RUN]

summary: Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

overall_design: Histone modifications of Marchantia embryos


title: Conditioned medium of PC-3 prostate cancer influences mRNA profiles in mechanically strained osteoblasts

city: Guilin City

first: Cao

last: Zhen

address: 1 Zhiyuan Road, Lingui, Guilin, Guangxi 541004, P.R. China

institute: Guilin medical university

summary: Bone is the main site of metastasis from prostate cancer, it is important to investigated miRNAs and mRNAs of bone metastases from prostate cancer. Considering that bone is in an appropriate mechanical environment in physiological state, in this study, the miRNA, mRNA, lncRNA profiles of mechanically strained osteoblasts treated with conditioned medium of PC-3 prostate cancer cells were studied. MC3T3-E1 osteoblastic cells were treated with conditioned medium of PC-3 prostate cancer cells, at the same time stimulated with mechanical tensile strain of 2,500 microstrain (με) at 0.5 Hz, the osteoblastic differentiation of the MC3T3-E1 cells were assayed

overall_design: In this study, MC3T3-E1 osteoblastic cells were treated with conditioned medium of PC-3 prostate cancer cells, at the same time stimulated with mechanical tensile strain of 2,500 microstrain (με) at 0.5 Hz, the osteoblastic differentiation of the MC3T3-E1 cells were assayed. Then the differential expressions of mRNAs, lncRNA in MC3T3-E1 cells treated with the conditioned medium of PC-3 cells were screened, and some of the mRNAs were verified by RT-qPCR

first: Zhen

last: Cao

first: Zhixiong

last: Yan

first: Biao

last: Han

first: Yong

last: Guo


title: Distinct global chromatin landscape for Peml-1 CD8+ T cells

city: Houston

first: Xin

last: Li

state: Texas

address: 6670 Bertner ave

institute: Houston methodist hospital

summary: To investigate the distinct global chromatin landscape in CD8+ T cells, we established global chromatin accessibility of CD8+ T cells using ATAC-seq.

overall_design: Comparative gene expression profiling analysis of ATAC-seq data for cd8+ T cells.

last: Lu

first: Gang

last: Xue


title: Gene expression profile at single cell level of total tumor-infiltrating CD8+ T cells

summary: Goblet cells are considered as a homogeneous population in total tumor-infiltrating CD8+ T cells. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of total tumor-infiltrating CD8+ T cells.

overall_design: Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~5000 individual cells per sample.


title: ATAC-Seq Peml-1 CD8+ T cells; scRNA-Seq total tumor-infiltrating CD8+ T cells


title: Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Acipenser ruthenus]

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Acipenser ruthenus. The occurrence of transcript asymmetry in A. ruthenus has been described at a global level only in matured eggs. However not much is known about the asymmetry during oogenesis. In this study we assessed the temporal establishment of the transcript localization at a global level for A. ruthenus. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed an early, predefined and also late pathways for both the vegetally and animally localized transcripts. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.

overall_design: Oocytes from Acipenser ruthenus females were extracted to create two groups: small oocytes (n = 5; size 1320-1500 µm); and big (n = 5, size 1920-2100 µm). Samples were oriented along their animal-vegetal axis and cryosectioned to produce 5 main sections (A (extreme animal) – E (extreme vegetal)). Each section was sequenced and the abundance of the transcript across the section and stages analyzed.

first: Pavel

last: Abaffy

first: Viktoriia

last: Iegorova

first: Ravindra

last: Naraine


title: Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Xenopus laevis]

summary: In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Xenopus laevis. The occurrence of transcript asymmetry in X. laevis has been described at a global level only in matured eggs, while the establishment of the asymmetry during oogenesis has been described only for a few transcripts. In this model it was discerned that there exist three pathways (early, intermediate, late) for the establishment of the vegetal gradient, while for the animal gradient not much is known for its production. In this study we assessed the temporal establishment of the transcript localization at a global level for Xenopus laevis. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed the previously described early, intermediate (predefined) and also late pathways but found more member transcripts within these groups. We also described, perhaps for the first time, an early, intermediate (predefined) and late pathway for the animal genes as well. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.

overall_design: Oocytes from Xenopus laevis females were extracted to create four groups: very small oocytes (n = 3; stage III, size 560-580µm); small oocytes (n = 5; stage IV, size 720-810µm); medium (n =2; stage V, size 1050µm); and big (n = 2; stage VI, size 1140-1200µm). Samples were oriented along their animal-vegetal axis and cryosectioned to produce 5 main sections (A (extreme animal) – E (extreme vegetal)). Each section was sequenced and the abundance of the transcript across the section and stages analyzed.


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes [Hi-C]

city: Dallas

first: Hongtao

last: Yu

address: 6001 Forest Park Rd

institute: University of Texas Southwestern Medical Center

summary: Cohesin folds chromosomes via DNA loop extrusion. Cohesin-mediated chromosome loops regulate transcription by shaping long-range enhancer-promoter interactions, among other mechanisms. Mutations of cohesin subunits and regulators cause human developmental diseases termed cohesinopathy. Vertebrate cohesin consists of SMC1, SMC3, RAD21, and either STAG1 or STAG2. To probe the physiological functions of cohesin, we created conditional knockout (cKO) mice with Stag2 deleted in the nervous system. Stag2 cKO mice exhibit growth retardation, neurological defects, and premature death, in part due to insufficient myelination of nerve fibers. Stag2 cKO oligodendrocytes exhibit delayed maturation and downregulation of myelinationrelated genes. Stag2 loss reduces promoter-anchored loops at downregulated genes in oligodendrocytes. Thus, STAG2-cohesin generates promoter-anchored loops at myelinationpromoting genes to facilitate their transcription. Our study implicates defective myelination as a contributing factor to cohesinopathy and establishes oligodendrocytes as a relevant cell type to explore the mechanisms by which cohesin regulates transcription.

overall_design: Hi-C was performed on duplicates of isolated primary oligodendrocytes from Stag2f/y and Stag2f/y; Cre mice

first: Ningyan

last: Cheng

first: Mohammed

last: Kanchwala

first: Bret

last: Evers

first: Chao

last: Xing


title: Optimal human intestinal organoid model reveals interleukin-22-induced Paneth cell differentiation

city: Utrecht

first: Jeff

last: DeMartino

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Here, we developed an optimal system for culturing human small intestinal organoids (hSIOs) that recapitulate the structural and functional complexity of the intestinal crypt in vitro, including mature Paneth cells. With this model, we found that IL-22 is required for the differentiation of human Paneth cells. Rather than STAT3, the PI3K-mTORC1 axis, downstream of IL-22, mediates Paneth cell differentiation programs. CD-associated variants of the IL-22 receptor (IL10RB) were introduced in our system, resulting in the abolishment of Paneth cells in hSIOs. Moreover, our data demonstrated that long-term IL-22 exposure inhibited the growth of hSIOs, challenging the current perception of IL-22 in promoting intestinal regeneration, but rather in reducing cell viability. As a proof-of-principle, our study demonstrates that this optimal culture system for hSIOs has great potential for modelling human intestinal physiology and pathophysiology.

overall_design: Single-cell RNA-sequencing of human small intestinal organoids cultured in growth medium with or without the addition of IL22

first: Gui-Wei

last: He

first: Lin

last: Lin

first: Eduard

last: Bodewes

first: Thanasis

last: Margaritis

first: Frank

last: Holstege

first: Hans

last: Clevers


title: EZH1 repression promotes generation of mature iPSC-derived CAR T cells with enhanced antitumor activity

city: Boston

first: Mohamad Ali

last: Najia

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Human induced pluripotent stem cells (iPSCs) provide a potentially unlimited resource for cell therapies, but the derivation of functionally mature cell types remains challenging. The histone methyltransferase EZH1 is a negative regulator of lymphoid potential during embryonic hematopoietic development. Here we demonstrate that EZH1 repression facilitates in vitro differentiation and developmental maturation of T cells from iPSCs. Using a stroma-free T cell differentiation system and EZH1 knockdown-mediated epigenetic reprogramming, we generated iPSC-derived T cells, termed EZ-T cells, that display a highly diverse T-cell receptor (TCR) repertoire and mature molecular signatures similar to those of TCRαβ T cells from peripheral blood. Upon activation, EZ-T cells give rise to both effector and memory T cell subsets. When transduced with anti-CD19 chimeric antigen receptors (CARs), EZ-T cells exhibit enhanced anti-tumor activities in vitro and in xenograft models relative to T cells derived by previously established protocols. Epigenetic remodeling via EZH1 repression allows efficient production of developmentally mature T cells from iPSCs for applications in adoptive T cell therapy.

overall_design: EZH1 repression

first: Mohamad


title: Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia [RNA-seq]

city: Barcelona

first: Sean

last: Montgomery


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes


title: Smooth muscle cell-specific Klf4 deletion in Marfan syndrome aortic root aneurysm

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

summary: Aortic smooth muscle cell (SMC) phenotype modulation is a central feature of cell-mediated pathology in Marfan syndrome aortic aneurysm and Klf4 is proposed to contribute to this process. We generated mice with smooth muscle cell-specific Klf4 deletion using an Myh11-creERT2 transgene, induced deletion at 8 weeks and performed single cell RNA sequencing at 24 weeks on whole aortic root tissues.

overall_design: Three experimental groups (Littermate Control, Fbn1-C1041G/+ Marfan syndrome (MFS), and MFS with induced Klf4 deletion) are included. Within each strain, with separate single cell RNA libraries are incuded for lineage-traced SMC populations and non-SMC subsets based on fluorescent sorting.

middle: J

first: Michael

middle: P

last: Fischbein


title: Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis

first: Radek

last: Sindelka

sample_organism:
Acipenser ruthenus
Xenopus laevis

platform_organism:
Acipenser ruthenus
Xenopus laevis


title: RNA-Seq of KRAS-regulated genes in human cell lines

first: Miriam

last: Molina-Arcas

summary: Human cell lines were treated with a KRASG12C inhibitor or tamoxifen to activate KRAS for different time points. Then RNA was extracted for gene expression analysis to assess the role of KRAS signalling on immune-related genes.

overall_design: RNA-Seq of two KRASG12C-mutant lung cancer cell lines and one normal lung cell line

first: Mugarza

last: Edurne

first: Llorian

last: Miriam

first: Downward

last: Julian


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes [ChIP-seq]

first: Hongtao

last: Yu

overall_design: ChIP-Seq was performed on primary oligodendrocytes for the following experiments: one replicate with anti-STAG2 antibody of Stag2f/y cells and one replicate with anti-H3K27ac antibody of Stag2f/y and Stag2f/y; Cre cells

first: Ningyan

last: Cheng

first: Mohammed

last: Kanchwala

first: Bret

last: Evers

first: Chao

last: Xing


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes [scRNA-seq]

overall_design: Single-cell RNA-Seq was performed on duplicates of forebrains from Stag2f/y and Stag2f/y; Cre mice


title: A missense mutation in COP1 SUPPRESSOR 5 causes reversed action in mediating photomorphogenic development

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at the site of 409 in COP1 SUPPRESSOR 5 (CSU5, also called WRKY32) largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. CSU5P409L promotes the hypocotyl growth and inhibits the opening of cotyledons in plants. Loss of CSU5 function mutant seedlings display elongated hypocotyls, whereas overexpression of CSU5 leads to shortened hypocotyls. CSU5 directly associates with the promoter regions of HY5 to activate its transcription. Although COP1 interacts with both CSU5 and CSU5P409L, it negatively controls the stability of CSU5, but not CSU5P409L. CSU5P409L exhibits enhanced DNA binding ability and affects the expression of more genes compared with CSU5. Our results not only reveal the molecular role for CSU5 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.

overall_design: Total RNA was extracted from the 5-d-old Col, csu5-1 and csu5-3 seedlings grown in constant W (14.59 μmol·m-2·s-1) light conditions. Quality control of DNase I treated mRNA was performed with an Agilent 2100 Bioanalyzer. cDNA libraries were generated, and sequencing was performed using the Illumina HiSeq 2500 platform according to the manufacturer's instruction (HiSequation 2500 user guide) by Novogene. Sequenced reads were preprocessed using Trimmomatic to remove reads in low quality and adaptor contamination (Bolger et al., 2014). The high-quality reads were aligned to Arabidopsis genome (TAIR 10) using Hisat2 (version 2.05; Kim et al., 2015) software using default parameters. Then, raw reads for each gene were calculated by HTseq (Anders et al., 2015) before calculating differential gene expression. Genes with a fold change >1.5 (FDR < 0.01) were defined as differentially expressed genes.

first: Dongqing

last: Xu


title: Modulation of multiple gene clusters expression by a single PAS-LuxR transcriptional regulator

city: Toulouse

first: Cláudia

last: Vicente

address: 135 avenue de Rangueil

country: France

institute: Toulouse Biotechnology Institute

summary: PAS-LuxR transcriptional regulators are highly conserved enzymes governing polyene macrolide antifungal biosynthesis. One of such regulators PteF, is located in the polyene macrolide filipin gene cluster from Streptomyces avermitilis and its mutation leads to a drastic decrease in filipin production as well as a severe loss of oligomycin production, an ATP-synthase inhibitor of macrolide structure, and a delay in sporulation. This transcriptomic study aims to understand the regulatory role of PteF and unveil the reach of PAS-LuxR transcriptional regulators in the global metabolism of Streptomyces.

overall_design: Two-colour microarray with common reference. The transcriptomes of S. avermitilis NRRL 8165 (WT) and S. avermitilis MUF (DpteF) were compared. Two time points were included: exponential (t1) and stationary (t2) phase. Biological triplicates were performed for each strain/time point. Genomic DNA of S. avermitilis NRRL 8165 was used as common reference.

first: C

first: F

last: Santos-Beneit

first: A

last: Rodríguez-García

first: J

last: Aparicio


title: Transcriptional behavior of regulatory T cells predicts IBD patient responses to vedolizumab therapy

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

institute: University of Miami

summary: Vedolizumab (VDZ) is used to treat patients with IBD but the exact way it works is not known. We studied the immune system in the blood and intestine of patients treated with VDZ and found immune characteristics that correlated with response.

overall_design:
Mucosal biopsies from UC and CD were digested for single cells and FAC sorted for Treg and Tmem subset  sorted from PBMCs and biopsies
Total RNA sequencing of 940 samples

first: Julie

last: Davies

last: Quintero

first: Amber

last: Delmas

first: Sophia

last: Diaz

first: Catherine

middle: D

last: Martinez

first: Thomas

last: Venables

first: Adrian

last: Reich

first: Gogce

last: Crynen

first: Amar

last: Deshpande

first: David

last: Kerman

first: Oriana

last: Damas

first: Irina

last: Fernandez

first: Ana

last: Santander

first: Judith

last: Pignac-Kobinger

first: Juan

last: Burgueno

first: Mark

last: Sundrud


title: scRNA-seq of triple knockout SCLC mouse models for subtyping

status: Public on Aug 22 2022

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

summary: Small cell lung cancer (SCLC) tumors comprise heterogeneous mixtures of cell states, categorized into neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. NE to non-NE state transitions, fueled by plasticity, likely underlie adaptability to treatment and dismal survival rates. Here, we apply an archetypal analysis to model plasticity by recasting SCLC phenotypic heterogeneity through multi-task evolutionary theory. Cell line and tumor transcriptomics data fit well in a five-dimensional convex polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterparts. These tasks, supported by knowledge and experimental data, include proliferation, slithering, metabolism, secretion, and injury repair, reflecting cancer hallmarks. SCLC subtypes, either at the population or single-cell level, can be positioned in archetypal space by bulk or single-cell transcriptomics, respectively, and characterized as task specialists or multi-task generalists by the distance from archetype vertex signatures. In the archetype space, modeling single-cell plasticity as a Markovian process along an underlying state manifold indicates that task trade-offs, in response to microenvironmental perturbations or treatment, may drive cell plasticity. Stifling phenotypic transitions and plasticity may provide new targets for much-needed translational advances in SCLC.

overall_design: Sample analyzed from a triple knockout mouse model

first: Vito

last: Quaranta

first: Julien

last: Sage

first: Sarah

last: Groves


title: Systems approach for identification of the Escherichia coli K-12 LysR-type transcriptional regulators function.

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: It is now possible to discover the physiological function of LysR-family transcription factors (LLTF) in E. coli using ChIP-Exo (in vivo DNA-binding), growth phenotype, conserved gene clustering, and transcriptional analysis (RNA-seq deletion mutants). The LysR-family regulator phenotype microarray has been detected for YbdO, YbeF, YcaN, YiaU, and YgfI deletion mutants and for the isogenic E. coli BW25113 strain in minimal medium at carbon/nitrogen starvation or L-threonine supplement conditions. The LLTF YbdO and YgfI regulation is important for bacterial growth adaptation to low pH with citrate supplementation or glycerol as the carbon source, respectively. A systems analysis approach allows for the identification of the YneJ (putrescine utilization), YgfI, and YbdO transcription factor regulated genes in Escherichia coli. YgfI regulates DhaKLM, the phosphotransferase system involved in glycerol and dihydroxyacetone utilization. YbdO is a repressor for ybdMN and is  likely involved in citrate lyase regulation. YneJ, re-named PtrR, directly controls the expression of the succinate-semialdehyde dehydrogenase Sad (YneI) and is important for bacterial growth in the presence of L-glutamate as a nitrogen source. The sad promoter is repressed by PtrR. PtrR is also a repressor of the fnrS gene, encoding a small regulatory RNA involved in the regulation of the sodB gene, as shown by RNA-seq data. A 15-bp palindromic PtrR-binding site was identified in the upstream regions of the sad / ptrR and fnrS genes and confirmed by ChIP-Exo and fluorescent polarization assays. The PtrR-dependent regulation of fnrS likely leads to a regulatory cascade induced by this small RNA.

overall_design: Ribosomal RNA removed RNA prepared from cell cultures of Escherichia coli at the exponential phase

last: Rodionova

first: Ye

last: Gao

first: Hyun

middle: G

last: Lim

middle: O


title: Transcription profiling of PfSPZ Vaccine trial subjects (US, malaria naïve) receiving a 3-dose or 5-dose regimen

city: Bethesda

first: Robert

last: Morrison

state: MD

address: 29 Lincoln Drive

department: NIAID

institute: NIH

summary: The Sanaria® PfSPZ Vaccine can confer sterilizing protection against liver stage infection by Plasmodium falciparum (Pf) in malaria naïve individuals. The vaccine consists of aseptically purified irradiated Pf sporozoites. Vaccinees received either 3 doses of 1.8M irradiated sporozoites or 5 doses of 270K. Efficacy was measured by challenged by controlled human malaria infections (CHMI) at 3 weeks and 24 weeks after the last vaccine dose

overall_design: 30 samples from 2 time points, pre-vaccination (Day -7) and post-vaccination (Day 116(3-dose vaccinees) or day 143 (5-dose vaccinees)), for 15 US adult participants who received the PfSPZ vaccine. All 15 participants remained uninfected after the first CHMI, while only 7 participants remained uninfected after both CHMI

first: Patrick

middle: E

last: Duffy

first: Irfan

last: Zaidi


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes [RNA-seq]

first: Hongtao

last: Yu

overall_design: The submission contains two RNA-Seq experiments from brain hemispheres or isolated primary oligodendrocytes of Stag2f/y and Stag2f/y; Cre mice: quadruplicates for brain hemispheres and duplicates for primary oligodendrocytes of each genotype

first: Ningyan

last: Cheng

first: Mohammed

last: Kanchwala

first: Bret

middle: M

last: Evers

first: Chao

last: Xing


title: C28 induced autophagy and the underlying mechanism of female germline stem cells in vitro

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use RNA-seq and ChIP-seq to explore the underlying mechanism of 028-induced autophagy in female germline stem cells in vitro

overall_design: C28-treated and control FGSCs mRNA profiles of 3h were generated by deep sequencing, in triplicate,and C28-treated and control FGSCs H3K27ac profiles of 3h were generated by deep sequencing.

first: Ping

last: Chen

first: Xinyan

last: zhao

first: Geng

last: Tian


title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia [RNA-seq]

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

institute: CRCM

summary: Resistance to treatment is due to the heterogeneity of the tumor which contains a subset of cancer cells that escape treatment and are responsible for the relapse. We took advantage of the PLZF/RARA retinoic acid (RA) resistant acute promyelocytic leukemia (APL) model to catch relapse-initiating cell features and their vulnerabilities. By developing an integrative single-cell multi-omics analysis (scRNA-seq and scATAC-seq), we uncovered transcriptional and chromatin heterogeneity of the PLZF/RARA APL blasts. We highlighted a subset of cells insensitive to RA-induced differentiation with a strong DNA repair signature ("Rep" cluster) and exhibiting a fine tuned transcriptional network targeting the histone methyltransferase Ezh2. Combining epigenomic profiling with mouse-derived models for Ezh2 catalytic inhibition or total KO, we revealed an independent methyltransferase Ezh2 activity linked to RA resistance. These findings demonstrate the power of single-cell multi-omics integration to highlight paths to sensitize therapy-resistant leukemia cells

overall_design: RNAseq was performed on murine PLZF/RARA transformed progenitors treated with GSK126 (inhibitor of Ezh2 catalytic activity) or MS1943 (EZH2 degrader).

first: Mathilde

last: Poplineau

first: Mazuel

last: Adrien


title: Characterization of m6A modifications in the contemporary Zika virus genome and host cellular transcripts

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

summary:
Purpose and Methods: To profile m6A modifications on both the viral genome RNA and cellular transcripts, we used Methylated RNA immunoprecipitation sequencing (MeRIP-seq) on ZIKV SZ1901-infected human hepatocarcinoma cell line Huh7.
Results and conclusions: Using MeRIP-seq, we identified a unique m6A map in the genome of ZIKV strain SZ1901 that is different from all previous isolates. Our study describes unique viral and host m6A profiles in contemporary ZIKV-infected Huh7 cells, highlighting the complexity and importance of m6A modification during viral infection.

overall_design: Using a contemporary Asian ZIKV strain isolated in 2019 (SZ1901) as a model, we profiled m6A modifications (MeRIP-seq) on both the viral genome RNA and cellular transcripts from the ZIKV-infected human hepatocarcinoma cell line Huh7.

first: Yanpeng

last: Xu


title: Investigating tumor radiation response heterogeneity using single-cell sequencing

city: Beijing

first: Xiaofei

last: Zheng

state: Beijing

address: No.27, Taiping Road

institute: Beijing Institute of Radiation Medicine

summary: Tumor cell radioresistance is a major challenge in radiotherapy. By contrast, radiation response heterogeneity of tumor cells is poorly understood. Here, we performed scRNA-seq and scATAC-seq of 6 Gy γ-ray treated human lung adenocarcinoma cells to dissect cellular radiation response heterogeneity from perspective of transcriptional and regulatory cell states. Notably, we observed heterogeneous radioresponsiveness in purified lung adenocarcinoma cells by qualified cellular radiation response based on transcriptional landscape. There was DNA repair and apoptosis related transcriptional cell state appeared post-irradiation. We identified gene markers in this radiation-associated cell state and screened promising targets for LUAD radiosensitization based on 107 transcriptomic data of radiotherapy treated LUAD patients from TCGA database. Besides, transcriptional cell states transition was obvious accompanied with radiation-induced cell cycle arrest in which cell-cell communication was a potential regulatory mechanism. Finally, we identified radiation-associated regulatory cell state and analyzed the regulatory network of key transcriptional factors in cellular radiation response.

overall_design: scRNA-seq of unpurified and purified A549 cells; scRNA-seq of purified A549 cells (control) and 6 Gy γ-ray treated purified A549 cells at 2 h (IR_2h) and 6 h (IR_6h) post-irradiation, scATAC-seq of purified A549 cells (control) and 6 Gy γ-ray treated purified A549 cells at immediate (IR_immediate) and 2 h (IR_2h) post-irradiation.

first: Huan

last: Tao

first: Yaru

first: Hebing


title: USP22 controls type III interferon signaling and SARS-CoV-2 infection through activation of STING

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary:
Within the context of the DUB module in the SAGA complex, USP22 is involved in transcriptional elongation through the regulation of H2AK119ub1 and H2BK120ub1. However, up till now, the spectrum of USP22-regulated target genes largely remains unclear, partially due to organism-, cell- and context-dependent redundancy in alternative DUBs that might compensate for loss of USP22.
To understand which genes are regulated by USP22, we profiled USP22-dependent changes in gene expression in the human intestinal epithelial cell (hIEC) line HT-29.

overall_design: The human intestinal epithelial cell line HT-29 was subjected to CRISPR/Cas9 mediated knockout of USP22 and control (non-human target: nht), followed by single clone selection and confirmation of the knockout using Western blot. Single clones X16 and X62 were cultivated in defined settings to ensure equal conditions.

first: Rebekka

last: Karlowitz

first: Megan

last: Stanifer

first: Jens

last: Rödig

first: Denisa

last: Bojkova

first: Marco

last: Bechtel

first: Sonja

last: Smith

first: Lisa

last: Kowald

first: Ralf

last: Schubert

first: Melanie

last: Boerries

first: Jindrich Jr.

last: Cinatl

first: Steeve

last: Boulant

first: J

middle: L

last: van Wijk


title: Flag-Esrrg Overexpression in SH-SY5Ys [H202SC21091592]

city: Birmingham

first: Rita

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

summary: SH-SY5Y cells were transfected with either 0.5 ul GFP control or Flag-ERRg expressing adenoviruses and isolated with Trizol after 24 hours to compare gene expression and find potential ERRg targets specific to neuron-like cells.

overall_design: Examination of gene expression resulting from flag-ERRg expression in SH-SY5Y cells.

first: Kathlene

last: Joyce

first: David

last: Crossman


title: Mapping MYC binding sites in ONS76 medulloblastoma cells

city: Nashville

first: Jing

last: Wang

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: In this experiment, we identify MYC binding sites in the medulloblastoma cell line ONS76. The purpose of this experiment was to identify genes bound by MYC and compare MYC bound genes to genes differentially expressed when SOX2 or omomyc were elevated in ONS76 cells.

overall_design: The medulloblastoma cell line ONS76 was used for ChIP-seq of MYC.

first: William

last: Tansey

first: Angie

last: Rizzino

first: Tessa

last: Popay

first: Qi

last: Liu


title: The sex difference under non-stressed and chronic-stressed conditions in C57BL/6 mice

city: Taoyuan

first: ChiHui

last: Tsao

address: No. 259, Wenhua 1st Rd., Guishan Dist.

institute: Chang Gung University

summary: Animal models are important tools in scientific research, whereas the animals used are usually single-sex instead of mixed-sex in the experimental design. To better understand the effect of sex difference, we compared several phenotypes between male and female C57BL/6 mice, including behavioral tests, plasma corticosterone levels, adult neurogenesis, and RNA-seq. The experiments were performed under non-stressed and chronic-stressed conditions, respectively. Overall, our results showed several differences between male and female mice in sensorimotor performance while little difference was found in anxiety, depression, learning, and memory. We did not observe a significant difference in adult neurogenesis. There was a sex difference in plasma corticosterone levels under chronic stress conditions, either in 30 min after the restraint stress or after 60min of the recovery. Yet, the corticosterone levels were equivalent between the sexes under non-stressed conditions at any time point. Furthermore, the results of RNA-seq identified the differential expression genes between male and female mice under non-stressed or chronic-stressed conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the hippocampus from C57BL/6 mice under non-stressed and chronic-stressed conditions.

first: Guo-Jen

last: Huang

first: Chi-Hui

first: Nicole

middle: C

last: Su


title: Bioorthogonal Chemical Epigenetic Modifiers Enable Dose-dependent CRISPR Targeted Gene Activation

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

summary: CRISPR-Cas9 systems have been developed to regulate gene expression by using either fusions to epigenetic regulators or, more recently, through the use of chemically mediated strategies. These approaches have armed researchers with new tools to examine the function of proteins by intricately controlling expression levels of specific genes. Here, we present a CRISPR based chemical approach that uses a new Chemical Epigenetic Modifier (CEM) to hone to a gene targeted with a catalytically inactive Cas9 (dCas9) bridged to an FK506-binding protein (FKBP). One arm of the bifunctional CEM recruits BRD4 to the target site and the other arm is composed of a bumped ligand that binds to a mutant FKBP with a compensatory hole at F36V. This bump-and-hole strategy allows for activation of target genes in a dose dependent and reversible fashion with increased specificity and high efficacy.

overall_design: ChIP-seq for BRD4 in conditions sgNT, sgCXCR4, 25nM CEM207, and sgCXCR4+25nM CEM207 to analyze the specificity of BRD4 binding in each.

first: Dongbo

last: Lu

first: Caroline

middle: A

last: Foley

first: Shama

middle: V

last: Birla

first: Jeremy

last: Simon

first: Lindsey

middle: I

last: James

first: Nathaniel

last: Hathaway


title: Sex differences in FGF21-induced changes in hepatic metabolism

city: Davis

first: Karen

middle: K

last: Ryan

address: 1 Shields Ave

department: Neurobiology, Physiology and Behavior

institute: University of California Davis

summary: To investigate sex-dependent changes in hepatic metabolism in response to fibroblast growth factor-21 (FGF21), we administered FGF21 or vehicle to mice on a high-fat diet then performed gene expression profiling analysis using data obtained from RNA-seq from livers of male and female mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from male and female livers in response to FGF21 or saline vehicle (n = 9-11 mice/ group).

first: Aki

last: Chaffin

first: Karlton

middle: R

last: Larson

first: Kuei-Pin

first: Chih-Ting

last: Wu

first: Nadejda

last: Godoroja

first: Yanbin

last: Fang

first: Devi

last: Jayakrishnan

first: Karla

last: Soto Sauza

first: Landon

last: Sims

first: Niloufar

last: Mohajerani

first: Michael

last: Goodson


title: ARID1A-deficient Bladder Cancer is Dependent on PI3K Signaling, and can be Targeted via EZH2 and/or PI3K Pharmacologic Inhibition: Therapeutic Implications

first: Ryan

last: Miller

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

summary: ARID1A-mutant bladder cancer is dependent on PI3K signaling and is sensitive to EZH2 and/or PI3K inhibition. Clinical trials in molecularly selected patients should be considered.

overall_design: Cleavage Under Targets & Release Using Nuclease of RT112 cells in triplicate for ARID1A and H3K4me3

first: Hasibur

last: Rehman

first: Darshan

middle: S

last: Chandrashekar

first: Chakravarthi

last: Balabhadrapatruni

first: Saroj

last: Nepal

first: Sai

middle: H

last: Balasubramanya

first: Abigail

last: Shelton

first: Kasey

last: Skinner

first: Ai-Hong

last: Ma

first: Ting

last: Rao

first: Marie-Lisa

last: Eich

first: Alyncia

last: Robinson

first: Gurudatta

last: Naik

first: Upender

last: Manne

first: George

last: Netto

first: C

first: Chong-xian

last: Pan

first: Guru

last: Sonpavde

first: Sooryanarayana

last: Varambally

first: James

last: Ferguson


title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia [scRNA-seq]

first: Estelle

last: Duprez

overall_design: Single-cell RNA-seq performed on murine purified promyelocytes expressing the PLZF/RARA  oncogenic fusion

first: Mathilde

last: Poplineau

first: Mazuel

last: Adrien


title: Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [ChIP-seq]

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

summary: Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulate only a small subset of genes. Further, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes.

overall_design: Standard ChIP-seq approach including crosslinking, chromatin extraction, DNA fragmentation and immunoprecipitation. All experiments were done in two biological replicates (A and B). Samples were treated with either DMSO or 3-indolacetic acid (IAA), which was used to induce degradation of target proteins.

first: Linda

last: Warfield

first: Lakshmi

last: Mahendrawada

first: Steven

last: Hahn


title: Azithromycin promotes relapse by disrupting immune and metabolic networks after allogeneic stem cell transplantation

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

institute: Assistance Publique des Hôpitaux de Paris

summary: The aim of this experiment was to identify gene expression changes in patients's PBMC from ALLOZITHRO's study cohorte. Following cell clustering according to their phenotype, gene expression was compared between azithromycin treated PBMC's patients  and non-treated PBMC. We identified a downregulation in several pathways such as mTOR, JAK-STAT, NF𝑘B, mitochondrial functions and inflammatory response.

overall_design: 31 Patients's samples (17 treated wit azithromycine and 14 treated with placebo) were thawed before performing CITEseq.

first: Sophie

last: Le Grand

first: Nicolas

last: Vallet

first: Delphine

last: Bouteiller


title: Gene changes associated with deletion of Esrrg in Dopaminergic neurons in mice [H202SC21050050]

first: Rita

last: Cowell

summary:
Purpose: The goal of this study is to understand what gene changes are associated with removal of Esrrg in dopaminerigc neurons from the mouse midbrain using BAC-TRAP and an AAV for Thcre
Methods: Midbrain from mice expressing the L10a transgene used for BAC-TRAP method of RNA isolation both with and without deletion of Esrrg using AAV:THCre were aged 1 month post-injection and midbrains were then extracted and flash frozen on dry ice. RNA was isolated using the BAC-TRAP method and samples were sent for sequencing.

overall_design: Midbrain mRNA profiles of mice 1 month post deletion of Esrrg in the midbrain compared to mice with no Esrrg deletion. All mice were expressing the L10a transgene to allow for BAC-TRAP method of RNA-isolation.

last: Crossman

first: Stephanie

last: Fox


title: Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [ChEC-seq]

overall_design: ChEC-seq method was used to map genome-wide binding of selected subunits of coactivator complexes. Where indicated, samples were treated with either DMSO or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Experiments were done in two, three or four (A,B,C,D) biological replicates.


title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia.

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

overall_design: Refer to individual Series


city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

institute: CSIC-UMH

summary: Axon pathfinding is a key step during the formation of neural circuits but however the transcriptional mechanisms regulating its progression remain poorly understood. The binary decision of crossing or avoiding the midline that neurons make during developmente midline that mammalian retinal ganglion cell (RGC) axons take at the optic chiasm has classically represented a robust model to search for novel mechanisms controlling the selection of axonal trajectories. Here, in order to identify new axon pathfinding regulators, we compared the transcriptome and chromatin accessibility profiles of mammalian retinal ganglion cells RGCs projecting ipsilateral (iRGCs) or contralaterally (cRGCs). Overall, our analyses retrieved dozens of new molecules potentially involved in axon pathfinding and uncovered the regulatory logic behind axon trajectories selection.

overall_design:
Study of 2 different cell types  in Mouse Retina,  with biologic replicates, generated by RNA-seq and ATAC-seq technologies.

Fernández-Nogales M, López-Cascales MT, Murcia-Belmonte V, Escalante A, Fernández-Albert J, Muñoz-Viana R, Barco A, Herrera E. Multiomic Analysis of Neurons with Divergent Projection Patterns Identifies Novel Regulators of Axon Pathfinding. Adv Sci (Weinh). 2022

first: Marta

last: Fernández-Nogales

first: Maria

last: López-Cascales

first: Verónica

last: Belmonte

first: Augusto

last: Rodríguez

first: Ángel

last: Guerrero

first: Eloisa

last: de Molina


summary: The aim of this experiment was to identify gene expression changes in sorted T cells from healthy donors two days after CD3/CD28 activation in the presence of azithromycin or a control. Following cell clustering according to their phenotype, gene expression was compared between azithromycin treated and non-treated activated T cells. We identified a downregulation in mitochondrial genes expression and pro-inflammatory genes and upregulation of anti-inflammatory genes such as SOCS1.

overall_design: Sorted T cells from human healthy donors, untreated and unactivated, activated with azithromycin, activated and untreated mRNA profiles after two days of CD3/CD28 activation


title: Transcriptomic profiling for differential gene expression in ARID1A-wt and ARID1A-deficient bladder cancer cells with and without GSK126 (an EZH2 inhibitor) treatment

first: Ryan

last: Miller

summary: Metastatic urothelial carcinoma of the bladder is generally incurable with current systemic therapies. Chromatin modifiers are frequently mutated in bladder cancer, with ARID1A inactivating mutations present in 20% of tumors. EZH2 is a histone methyltransferase that acts as an oncogene that functionally opposes ARID1A. In addition, PI3K signaling is activated in over 20% of bladder cancers. Here we show that ARID1A-mutant tumors are more sensitive to EZH2 inhibition than ARID1A-wild-type tumors. Mechanistic studies reveal that: 1) ARID1A deficiency results in a dependency on PI3K/AKT/mTOR signaling via upregulation of a non-canonical PI3K regulatory subunit PIK3R3, and: 2) EZH2 inhibitor sensitivity is due to upregulation of PIK3IP1, an inhibitor protein of PI3K signaling. Thus, our studies suggest that a subset of bladder cancers with ARID1A mutations can be treated with inhibitors of EZH2 and/or PI3K, and reveal novel mechanistic insights into the role of non-canonical PI3K constituents in bladder cancer biology.

overall_design: mRNA sequencing of ARID1A-wt and ARID1A-deficient bladder cancer cells (RT112) treated with either DMSO control or GSK126

first: James

last: Ferguson

first: Abigail

last: Shelton

first: Hasibur

last: Rehman


title: Transcriptome response of mouse mammary gland from age 12 to 30 months of age in Esr1 and CYP19A1 genetically engineered mouse models of breast cancer risk in the presence and absence of transgene induction

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Breast cancer is an age-related cancer in women with two peaks, one at 50 and one at 70 years of age. Here we used two conditional genetically engineered mouse models of breast cancer risk to study mammary gland transcriptional changes that occur as female mice age from 12 to 30 months of age, paralleling aging from 58 to 85 years of age in women. The two models express either mammary epithelial cell-targeted Estrogen Receptor (ER) alpha (Esr1) or Aromatase (CYP19A1A) over-expression beginning at age 12 or 18 months of age. Both of these risk factors increase estrogen pathway signaling, either directly though the receptor or by increasing local estrogen production. The goals of the study are to determine how quickly significant transcriptional changes occur in the mammary gland following transgene induction, to determine how the transcriptome becomes modified as the mice age past reproductive senescence through old and very old life stages, and to identify similarities and differences in the transcriptomes between the two risk conditions at different ages and conditions. The first specific objective of this transcriptome-based study is to identify significantly differentially expressed genes within each model between different ages and times of transgene induction. This includes transcriptional changes induced by 1 week, 6, 12 and 18 months of transgene expression with transgene expression initiated at age 12 months as well as transcriptional changes induced by 1 week and 6 months of transgene expression initiated at age 18 months. The second specific objective is to compare the two models at different ages (12, 18, 24 and 30 months of age) and different transgene induction times (6, 12 and 18 months) to identify differentially expressed genes between the models. Comparative control mice from each model include age 18- and 24-month-old mice without transgene induction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mouse mammary gland tissue from 12, 18, 24 and 30 month old Esr1 and CYP19A1 mice with and without transgene induction. Twenty-four month old mice were studied in the absence of transgene induction and in the presence of 12- and 6-month transgene induction. Twelve and 18 month-old-mice were studied in the absence and presence of 1-week transgene induction.

first: Furth

last: Priscilla A.

first: Kang

last: Keunsoo