title: Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region

city: Warsaw

first: Karim

last: Abu Nahia

address: Księcia Trojdena 4

country: Poland

institute: IIMCB Warsaw

summary: The atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks of mammalian AV node, including the expression of genes implicated in its development and those encoding connexins forming low conductance gap junctions. Transcriptome analysis uncovered protein-coding and noncoding transcripts enriched in AVC, which have not been previously associated with this structure, as well as dynamic expression of epithelial-to-mesenchymal transition markers and components of TGF-β, Notch, and Wnt signaling pathways likely reflecting ongoing AVC and valve development. Using transgenic line Tg(myl7:mermaid) encoding voltage-sensitive fluorescent protein, we show that abolishing the pacemaker-containing sinoatrial ring (SAR) through Isl1 loss of function resulted in spontaneous activation in the AVC region, suggesting that it possesses inherent automaticity although insufficient to replace the SAR. The SAR and AVC transcriptomes express partially overlapping species of ion channels and gap junction proteins, reflecting their distinct roles. Besides identifying conserved aspects between zebrafish and mammalian conduction systems, our results established molecular hallmarks of the developing AVC which underlies its role in structural and electrophysiological separation between heart chambers. This data constitutes a valuable resource for studying AVC development and function, and identification of novel candidate genes implicated in these processes.

overall_design: Transcriptome profiling of zebrafish atrioventricular canal at 48 and 72 hours post-fertilization.Intact hearts from transgenic line sqet31Et embryos were chemically dissociated into a single-cell suspension for FACS. Cells were sorted into GFP positive (GFP+) cells within the atrioventricular canal and GFP negative (GFP-) fraction representing rest of heart, three biological replicates each. To identify genes enriched GFP+ cells, differential expression analysis were performed using the GFP- sample as background.

first: Cecilia

middle: L

last: Winata


title: Gene expression profiling of isogenic malignant melanoma A375-BRAFV600E/NRASQ61 and A375-BRAFV600E/NRASQ61K cell lines

status: Public on Sep 23 2021

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

country: USA

institute: University of Arizona

summary: BRAF-inhibitor (BRAFi)-resistance compromises long term survivorship of malignant melanoma patients, and mutant NRAS is a major mediator of BRAFi-resistance. We have employed NanoString nCounterTM transcriptomic analysis of isogenic human malignant melanoma cells that differ only by NRAS mutational status (BRAFi-sensitive A375-BRAFV600E/NRASQ61 versus BRAFi-resistant A375-BRAFV600E/NRASQ61K), identifying modulation of specific gene expression networks as a function of NRASQ61K-status.

overall_design: Differential expression between isogenic human malignant melanoma A375-BRAFV600E/NRASQ61 (n=3) and A375-BRAFV600E/NRASQ61K (n=3) cell lines was assessed using nCounter PanCancer Panel code set.

first: Jana

last: Jandova

middle: T


title: Vacuolar protein sorting 33B deficiency effect on conventional dendritic cell type 1 subpopulation

city: Dongguan

first: Gonghua

last: Huang

address: 1 Xincheng Avenue

country: China

institute: Guangdong Medical University

type: Expression profiling by high throughput sequencing

summary: Analysis of FACS-sorted conventional dendritic cell type 1 (cDC1) subpopulation in mediastinal lymph nodes (mLNs) from mice with vacuolar protein sorting 33B (Vps33B) specific deletion in DCs in response to house dust mite (HDM). Our results provide insight into the role of Vps33B in regulating the function of cDC1s upon HDM stimulation.

overall_design: examination of 3 sets of cDC1s from WT and Vps33B conditional knock-out mice

first: Di

last: Yang

first: Youqiong

last: Ye

first: Jingyu

last: Ma


title: N6-methyladenosine RNA methylome analyses in cyclophosphamide-treated neonatal rat cardiac myocytes.

city: Beijing

first: Min

last: Zhu

state: China

address: 49 North Garden Rd.,Haidian District

institute: Peking University Third Hospital

summary: To identify N6-methyladenosine RNA methylome in cyclophosphamide-treated neonatal rat cardiac myocytes (NRCMs), MeRIP-seq of NRCMs treated with cyclophosphamide (CYP) or solvent control (DMSO) were performed.

overall_design: N6-methyladenosine RNA methylome profiling by high throughput sequencing (MeRIP-seq)

first: Ming

last: Xu


title: Transcriptome (RNA-seq) of HepG2 cells non-infected (NI) or infected (Inf.) with the pathogen Listeria monocytogenes (strain EGD-e)

status: Public on Sep 25 2021

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: Comparisons of gene expression profiles of human hepatocytes (HepG2) infected or not by the bacterium Listeria monocytogenes (strain EGD-e) for 72 hours and analysed by RNA-seq

overall_design: We used  RNA-seq to identify the repertoire of genes differentially expressed after 3 days of infection of HepG2 cells with Listeria monocytogenes EGDe strain.

first: Natalie

last: DESCOEUDRES

first: Luc

last: JOUNEAU

first: Kevin

last: GORRICHON

first: Hélène

last: BIERNE


title: RNA-seq Analysis of Wild-Type and G898D UPC2A Transcriptomes [G898D UPC2A transcriptome]

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

summary:
Purpose: Determine the number of genes that respond to the presence of a gain-of-function mutant form of the UPC2A transcription factor in Candida glabrata.
Methods: Prepare total RNA from wild-type and gain-of-function G898D UPC2A cells.  Use standard RNA-seq to evaluate and compare the transcriptomic changes caused by this allele of UPC2A.
Results: Although a clear increase was seen in fluconazole resistance conferred by the G898D UPC2A allele, elevated transcription was only observed for 11 genes with 9 of these involved in ergosterol biosynthesis.
Conclusions: The presence of the G898D UPC2A allele led to elevated constitutive transcription for genes involved in ergosterol biosynthesis.

overall_design: Candida glabrata mRNA profiles of wild-type (WT) and G898D UPC2A  strains grown to mid-log phase.

first: Yu

last: Li

first: Mark

last: Stamnes

first: W

middle: S

first: P

middle: D

last: Rogers


title: Mesenchymal cell type-specific roles of KLF4 in lung fibrosis [bulk RNA-seq]

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

summary:
Purpose: The goal of this study is to investigate mesenchymal cell-type specific role of KLF4 in the context of lung fibrosis.
Methods:  Adult Pdgfrb-CreERT2, ROSA26R(Zs/+) mice were induced with tamoxifen (1mg/day for 5 days), rested for 5 days. The lungs were harvested and prepared to obtain single cell suspension. Live Zs+ cells were isolated by FACS, cultured, and subjected to Klf4 siRNA or Scr RNA treatment. Total RNA was purified after 72 hrs. and  subjected to bulk RNA-seq. using Illumina HiSeq 2000. Similarly, wild type mice airway smooth muscle cells (cell biologics) were treated  with Klf4 siRNA or Scr RNA. Total RNA was purified after 72 hrs. and  subjected to bulk RNA-seq.
Results: Expression profile of the transcriptome are compared between cell-types; PDGFR-β+ cells and airway smooth muscle cells.
Conclusions: Significant difference in the expression of genes involved in pathogenesis of fibrosis was observed

overall_design: Scr RNA or siKlf4 treated tracheal SMCs and Lung PDGFR-β+ cells

first: Rachana

middle: R

last: Chandran

first: Daniel

last: Greif


title: RNA-sequencing analysis of fluconazole-treated wild-type and upc2A null cells [Fluconazole]

summary:
Purpose: Compare the fluconazole-induced transcriptome of isogenic wild-type and upc2A null cells.
Methods: Prepare total RNA from wild-type and upc2A null cells grown under unstressed conditions or challenged with 50 microgram/ml fluconazole for 6 hours.  Use standard RNA-seq to evaluate and compare the transcriptomic changes caused by fluconazole in the presence or absence of UPC2A.
Results: These data established that over 100 genes were induced by fluconazole in a UPC2A-dependent manner.  However, most fluconazole-induced genes (>500) did not require the presence of UPC2A.  Fluconazole-induced genes included the expected genes involved in ergosterol biosynthesis but also large number of plasma membrane-localized transporters.
Conclusions: These data suggest that Upc2A provided transcriptional co-regulation between membrane transporters and the lipid environment in which these proteins function.  A significant portion of the fluconazole-induced transcriptome does not require the presence of Upc2A, suggesting the presence of other transcriptional circuits responsive to this pharmacologic block of ergosterol biosynthesis.

overall_design: Candida glabrata mRNA profiles of wild-type (WT) and upc2A null strains grown +/- fluconazole treatment.


title: Genomic level analysis of Upc2A-regulated transcription in Candida glabrata

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Nakaseomyces glabratus
Nakaseomyces glabratus CBS 138

overall_design: Refer to individual Series


title: Regulation and role of glycophagy in skeletal muscle energy metabolism

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

summary: We report that short-term knockdown of the enzyme alpha-acid glucosidase in mouse C2C12 myotubes modifies genes involved in PPAR and PI3K-AKT signaling.

overall_design: C2C12 myoblasts were transfected with shscrambled or shGAA lentivirus, puromycin selected, and then differentiated into myotubes which were then harvested for RNA sequencing.

first: Timothy

last: Heden

middle: G


title: ChIP-seq analysis of  transcription factor Upc2A binding across the Candida glabrata genome [Upc2A ChIP-seq]

summary: To determine the genomic binding sites for the Candida glabrata transcription factor Upc2A, we utilized three different strains.  One was the wild-type KKY2001 which contains a wild-type copy of UPC2A but lacks any HA tag.  The other two are both derived from KKY2001 but contain a 3X HA tag immediately after the start codon of UPC2A.  These strains are BVGC82 and BVGC84, respectively.  Both contain a single copy of a loxP element located 252 bp downstream from the UPC2A stop codon.  BVGC82 contains a wild-type copy of the UPC2A gene while BVGC84 contains a mutant form of UPC2A (G898D) that confers elevated resistance to fluconazole.  ChIP was performed with anti-HA antibodies in all cases.  Strains containing the wild-type UPC2A gene (no HA tag) are referred to as C1 and C2.  Strains containing the 3X HA epitope tag at the N-terminus of the wild-type UPC2A gene are referred to as wt1 and wt2.  These same strains challenged with fluconazole prior to ChIP are referred to as wtf1 and wtf2.  The strain containing the G898D UPC2A allele are referred to as M1 and M2 (no fluconazole challenge) and MF1 and MF2 (with fluconazole challenge.

overall_design: ChIP-seq using anti-HA antibody against strains expressing HA-tagged Upc2A as a wild-type protein or a gain-of-function form (G899D Upc2A).  Prior to chromatin preparation and shearing, parallel cultures were either left untreated or challenged with 20 microgram/ml of fluconazole for two hours at 30 degrees C.

first: Bao

last: Vu


title: Regulation of 5-hydroxymethylcytosine by TET2 contributes to Squamous Cell Carcinoma tumorigenesis

city: Boston

first: Matthew

last: Ramsey

state: MA

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a key regulatory event controlling a variety of physiological processes and can have dramatic effects on gene transcription. Methylated Cytosine (5mC) can be oxidized by the TET family of enzymes to 5-hydroxymethylcytosine (5-hmC), a key intermediate in the de-methylation cycle, and 5-hmC levels are reduced in malignancies such as AML and melanoma.  We constructed a tissue microarray of human cutaneous Squamous Cell Carcinoma (SCC) tumors and found a global reduction in 5-hmC levels compared to adjacent skin.  Using a murine K14-CreER system, we have found that loss of Tet2 promotes carcinogen-induced SCC, and cooperates with loss of Tp53 in to drive spontaneous SCC tumors in epithelial tissues.  Loss of Tet2 in the normal epidermis leads to site-specific changes in 5-hmC levels, with many genes showing both increased and decreased levels of 5-hmC.  Importantly, many of these changes were in genes regulating keratinocyte differentiation and self-renewal, consistent with reported roles for Tet enzymes in controlling lineage commitment in hematopoietic stem cells and ES cells.  These results establish a functional role for Tet2 in the regulation of 5-hmC in the epidermis and demonstrate that Tet2 is a bone fide tumor suppressor in SCC.

overall_design: We used ba barcoded hydroxymethylated DNA immunoprecipitation (hMeDIP) method coupled with deep sequencing (hMeDIP-seq) for quantitative comparison of 5-hmC tag density at specific genomic loci in the epidermis of wild-type mice compared to mice which had epidermal specific deletion of Tet2 (K14-CreER Tet2Flox). We performed RNA-seq on the epidermis of K14-CreER Tet2L/L mice treated with vehicle (n=3) or tamoxifen (n=3).

first: Christine

last: Lian


title: Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression [RNA-Seq]

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: A remarkably high frequency of pediatric gliomas and bone tumors harbor monoallelic, missense mutations in genes encoding histone variant H3.3 at Glycine 34. We find that G34 mutations distinctly impede H3K36 methylation by SETD2. Consequently, the reduction of H3K36 methylation leads to high levels of PRC2-mediated H3K27me3 on G34 mutant nucleosomes. We find that H3.3G34W expression in murine mesenchymal stem cells (mMSCs) promotes aberrant gain of H3K27me2/3 and loss of H3K27ac at active enhancers containing SETD2. mMSCs expressing H3.3G34W display a unique transcriptional program that is dependent on PRC2 activity *in cis* and exhibit enhanced tumor development *in vivo*. Altogether, we demonstrate that H3.3G34 oncohistones selectively promote PRC2 activity by interfering with SETD2-mediated H3K36 methylation. We propose that PRC2-mediated silencing of enhancers involved in cell differentiation represents a potential mechanism that drives these malignancies.

overall_design:
To understand the transcriptional profile changes mediated by H3.3 G34 mutations in mouse mesenchymal stem cells
Expression of various histone transgenes in C3H10T1/2 cells, followed by mRNA-Seq

first: Siddhant

middle: U

last: Jain


title: RNA-seq profiles of germinal center B cells from spleens of wild-type and Il21r-deficient mice after immunization with NP-KLH

status: Public on Sep 22 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Humoral immune responses require germinal centres (GC) for antibody affinity maturation. Within GC, B-cell proliferation and mutation are segregated from affinity-based positive selection in the dark zone (DZ) and light zone (LZ) substructures, respectively. While IL21 is known to be important in affinity maturation and GC maintenance, here we show it is required for both establishing normal zone representation and preventing the accumulation of cells in G1 cell cycle stage in the GC LZ.

overall_design: Wildtype and IL21 receptor deficient (Il21r-/-) mice were immunized with NP-KLH in alum. Germinal center B cells were extracted from spleens 7 days, 10 days and 14 days after immunization. RNA was extracted and profiled using RNA-seq. An Illumina HiSeq 2000 was used to generate 100bp single-end sequence reads. Each sample was generated from an independent mouse.

first: Connie

last: Li-Wai-Suen

first: David

middle: M

last: Tarlinton

first: Dimitra

last: Zotos


title: Targeting DNMTs to overcome enzalutamide resistance in prostate cancer

city: Lexington

first: Xiaoqi

last: Liu

address: 760 press Ave

department: Toxicology & Cancer Biology

institute: University of Kentucky

summary: Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is a FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment. After a short positive response period to enzalutamide, tumors will develop drug resistance. In this study, we uncovered that DNA methylation was deregulated in enzalutamide-resistant cells. DNMT activity and DNMT3B expression were upregulated in resistant cell lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role of p53 and pRB in this process. The overexpression of DNMT3B3, a DNMT3B variant, promoted an enzalutamide-resistant phenotype in C4-2B cell lines. Inhibition of DNA methylation and DNMT3B knockdown induced a re-sensitization to enzalutamide. Decitabine treatment in enzalutamide-resistant cells induced a decrease of the expression of AR-V7 and changes of genes for apoptosis, DNA repair and mRNA splicing. Combination treatment of Decitabine and enzalutamide induced a decrease of tumor weight, Ki-67 and AR-V7 expression and an increase of cleaved-caspase3 levels in 22Rv1 xenografts. The collective results suggest that DNA methylation pathway is deregulated after enzalutamide resistance onset and that targeting DNA methyltransferases restores the sensitivity to enzalutamide in prostate cancer cells.

overall_design: To study the impact of DNMT3B in enzalutamide resistance, we designed an RNA sequencing experiment depicted in Figure 6A. In this experiment, we compared enzalutamide-sensitive cell lines, LNCaP and C4-2B to the enzalutamide-resistant cell lines, C4-2B-MDVR as comparison 1 (C1) and comparison 2 (C2),  respectively. Then we compared untreated C4-2B-MDVR cells to C4-2B-MDVR cells treated with decitabine or decitabine plus enzalutamide as comparison 3 (C3) and comparison 4 (C4), respectively. In these comparisons, we explored the changes of genes expression upon different treatments. This approach allowed us to identify high interest genes and pathways involved in responses to treatments. The expression of these highly interest genes were explored in C3 and C4 to identify any reversal in gene expression compared to C1 and C2. These analyses allowed us to identify a subset of genes that changed in resistantC4-2B-MDVR compared to sensitive cell lines after decitabine treatment.

first: Elia

last: Farah

first: Zhuangzhuang

last: Zhang

first: Sagar

last: Utturkar


title: A single-cell atlas of chromatin accessibility in the human genome

city: San Diego

first: Bing

last: Ren

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

summary: Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of gene regulatory elements in diverse cell types and tissues in the human body, we applied single-cell chromatin accessibility assays to 30 adult human tissue types from multiple donors. We integrated these datasets with single-cell chromatin accessibility data from 15 fetal tissue types to reveal the status of open chromatin for approximately 1.2 million candidate cis-regulatory elements (cCREs) in 222 distinct cell types comprised of >1.3 million nuclei. We used these chromatin accessibility maps to delineate cell type-specificity of fetal and adult human cCREs and to systematically interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues, life stages, and organ systems.

overall_design: Applying single cell chromatin accessibility assays to diverse human tissue types from four donors.

first: Kai

first: James

last: Hocker

first: Michael

last: Miller

first: Xiaomeng

last: Hou

first: Olivier

middle: B

last: Poirion

first: Allen

last: Wang

first: Sebastian

last: Preissl


title: Reciprocal YAP1 loss and INSM1 expression in neuroendocrine prostate cancer

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Neuroendocrine prostate cancer (NEPC) is a rare but aggressive histologic variant of prostate cancer that responds poorly to androgen deprivation therapy. Hybrid NEPC-adenocarcinoma (AdCa) tumors are common, often eluding accurate pathologic diagnosis and requiring ancillary markers for classification. We recently performed an outlier-based meta-analysis across a number of independent gene expression microarray datasets to identify novel markers that differentiate NEPC from AdCa, including up-regulation of Insulinoma-associated protein 1 (INSM1) and loss of Yes-associated protein 1 (YAP1). Here, using diverse cancer gene expression datasets, we show that Hippo pathway-related genes, including YAP1, are among the top down-regulated gene sets with expression of the neuroendocrine transcription factors, including INSM1. In prostate cancer cell lines, transgenic mouse models and human prostate tumor cohorts, we confirm that YAP1 RNA and YAP1 protein expression are silenced in NEPC and demonstrate that the inverse correlation of INSM1 and YAP1 expression helps to distinguish AdCa from NEPC.  Mechanistically, we find that YAP1 loss in NEPC may help to maintain INSM1 expression in prostate cancer cell lines and we further demonstrate that YAP1 silencing likely occurs epigenetically, via CpG hypermethylation near its transcriptional start site. Taken together, these data nominate two additional markers to distinguish NEPC from AdCa and add to data from other tumor types suggesting that Hippo signaling is tightly reciprocally regulated with neuroendocrine transcription factor expression.

overall_design: Next generation sequencing of human prostate tumor cell lines with YAP1 knowckdown or overexpression using Novaseq polyA library prep and Illumina sequencing.

first: Kaushal

last: Asrani

first: Alba

middle: F

last: Torres

first: Juhyung

last: Woo

first: Thiago

last: Vidotto

first: Harrison

last: Tsai

first: Jun

last: Luo

first: Eva

last: Corey

first: Brian

last: Hanratty

first: Srinivasan

last: Yegnasubramanian

first: Angelo

last: De Marzo

first: Peter

last: Nelson

middle: C

last: Haffner

first: Tamara

last: Lotan


title: Epigenetic Interaction between UTX and DNMT1 in brown adipocytes

status: Public on Sep 24 2021

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University


title: RNA sequencing of JCPyV infection in primary human astrocytes

city: Orono

first: Melissa

last: Maginnis

state: Maine

address: 5735 Hitchner Hall Room 320

department: Department of Molecular and Biomedical Sciences

institute: University of Maine

summary: Research in JCPyV infection of primary astrocytes is limited. However, viral infection in a transformed glial cell line (SVGAs), mostly composed of astrocytes, is well studied. RNA sequencing was performed at 24 hours post infection (hpi), 48 hpi, and 96 hpi. Timepoints established to be important in both cell types in the JCPyV infectious cycle.

overall_design: Comparitive analysis using RNA sequencing of JCPyV infection during varying timepoints of infection in primary astrocytes versus a transformed glial cell line, mostly composed of astrocytes

first: Michael

middle: P

last: Wilczek

first: Benjamin

last: King


title: Dynamic changes in tRNA modifications and abundance during T-cell activation

status: Public on Oct 13 2021

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

type: Non-coding RNA profiling by high throughput sequencing


title: RNA-seq analysis of FTO depletion effect on gene expression during the type I IFN response

city: DURHAM

first: Stacy

last: Horner

state: NC

address: 213 Research Drive CARL 0049

department: Molecular Genetics & Microbiology

institute: Duke University

summary: FTO is an m6A and m6Am demethylase protein that regulates many biological processes through modulation of RNA biology. The goal of this experiment was to determine the role of FTO in regulation of gene expressoin during the type I interferon response. We found that FTO suppresses the expression of a subset of interferon-stimulated genes at the mRNA level. In follow-up experiment, we determined that FTO regulates the transcription of these ISGs through suppression of activation of the transcription factor STAT3.

overall_design: Huh7 cells were seeded in 10-cm plates and treated with siRNAs (non-targeting control; CTRL or FTO) for 36 hours, followed by IFN-b treatment at 50 units/mL or mock treatment for 8 hours. RNA was extracted and RNA-seq was performed. 3 biological replicates were performed for each condition.

middle: J

last: McFadden

first: Matthew

last: Sacco

first: Nandan

last: Gokhale

first: Kristen

middle: A

last: Murphy

first: Kim

middle: Y

last: Somfleth


title: A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis


title: Transcriptome-wide profiling of thyroid hormone and adrenergic interactions in the mouse heart

city: San Jose

first: Alexander

last: Payumo

address: One Washington Square

department: Biological Sciences

institute: San Jose State University

summary: During the first weeks after birth, cardiomyocytes within the mouse heart progressively exit the cell cycle, binucleate, and lose regenerative capacity. We have determined that combined pharmacological inhibition of thyroid hormone and adrenergic signaling during postnatal development robustly enhances cardiomyocyte proliferation, retention of diploid cardiomyocytes, and functional cardiac regeneration at postnatal day 14. In this study, we perform transcriptome-wide analyses to understand the genetic pathways regulated by thyroid hormone, alpha-adreneric, and beta-adrenergic signaling - individually and in combination -  that promote cardiomyocyte cell-cycle arrest and loss of cardiac regenerative potential.

overall_design: Thyroid hormone was inhibited by treating pregnant female mice with chow containing propylthiouracil (thyroid hormone inhibitor; 0.15% in iodine deficient diet) starting at E13.5 and then maintained thereafter. Newborn pups were injected subcutaneously with phenoxybenzamine (alpha-adrenergic inhibitor; 10 ug/g/day) and/or propranolol (beta-adrenergic inhibitor; 20 ug/g/day) daily from P1 to P14. Using these drug administration protocols, thyroid hormone, alpha-adreneric receptor, and beta-adrenergic receptor signaling were inhibited individually or in combination and hearts were harvested at P14. Heart tissues were harvested at P14 from three animals treated with each experimental condition, total RNA was extracted, and RNA-seq was performed to identify differentially expressed genes.

first: Guo

middle: N

last: Huang


title: A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation [ATAC-Seq]

summary: Human genetics have defined a new autism-associated syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes autism, ADHD, intellectual disability, obesity, and brain anomalies is unknown. Here, we develop a mouse model of this syndrome. Physically, Myt1l haploinsufficiency causes obesity, white-matter thinning, and microcephaly in the mice, mimicking clinical phenotypes. Studies during brain development reveal disrupted gene expression, mediated in part by loss of Myt1l gene target activation, and highlight precocious neuronal differentiation as the mechanism for microcephaly. In contrast, adult studies reveal that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. This results in behavioral features including hyperactivity, hypotonia, and social alterations, with more severe phenotypes in males. Overall, these studies provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.

overall_design: Utilizing MYT1L KO mouse line, we performed ATAC-seq and RNA-seq on developing mouse brain (E14.5 cortex) and adult prefrontal cortex to undertsand chromatin structure changes and transcriptom alternation upon MYT1L loss.

first: Jiayang

last: Chen


title: Mobility of condensin DC is key to its function in repressing transcription [ChIP-seq]

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

institute: NYU

summary: Analyze condensin binding by fluorescence recovery after photobleaching (FRAP) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) in ATP hydrolysis mutant and in mutants that affect the level of histone H4K20 methylation and H4K16ac enrichment and depletion on the X chromosome. We have also performed Hi-C analysis to test how 3D DNA interactions mediated by condensin DC change in the catalytic and null mutant of dpy-21, a H4K20me2 demethylase that increase H4K20me1 on the X.

overall_design: Population ChIP-seq profiles of mixed embryo worms harboring rex site insertions and a dCas9-SunTag block strain

first: Laura

last: Breimann

first: Ana

last: Morao

first: David

middle: S

last: Jimenez

first: Nina

last: Maryn

first: Krishna

last: Bikkasani

last: Carrozza

first: Sarah

middle: E

last: Albritton

first: Maxwell

last: Kramer

first: Lena

last: Street

first: Kustrim

last: Cerimi

first: Vic-Fabienne

last: Schumann

first: Ella

last: Bahry

first: Stephan

last: Preibisch

first: Andrew

last: Woehler

first: Sevinc

last: Ercan


title: Mobility of condensin DC is key to its function in repressing transcription [RNA-seq II]

overall_design: Population mRNA profiles of mixed embryos with genotypes: WT, hsp::dpy-27::gfp or hsp::dpy-27[EQ-TR]::gfp.

first: Jimenez

last: David

first: Michael


title: Impaired attenuation of pluripotency enhancers at the onset of neural crest formation in ARID1B haploinsufficient Coffin-Siris patients

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: De-novo ARID1B haploinsufficient mutations cause many developmental disorders characterized by neurological and craniofacial phenotypes, including Coffin-Siris Syndrome.  ARID1B and its paralog ARID1A encode for mutually exclusive subunits of the BAF chromatin remodeler, yet their role in cell-fate determination is poorly understood.   We discovered a novel neural crest configuration of the BAF complex (ARID1B-BAF), which includes ARID1B, SMARCA4, and eight additional subunits. The ARID1B-BAF regulates lineage commitment upon differentiation cues through attenuation of pluripotency enhancers of the SOX2 network.  Consistently, the ARID1B-BAF interacts with SALL4, which is known to have repressing abilities during lineage commitment.  In iPSCs, pluripotency enhancers are maintained in active state by cooperation between the pioneer activity of SOX2 and the ARID1A-containing BAF.  At the onset of differentiation, ARID1B-BAF replaces ARID1A-BAF at these enhancers, eliciting chromatin repression and coordinating the exit from pluripotency. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout CNCC differentiation.  This correlates with aberrant SOX2 binding at the pluripotency enhancers, and failure to reposition SOX2 at the developmental enhancers. SOX2 dysregulation promotes upregulation of the NANOG regulatory network, impairing CNCC differentiation.  Intriguingly, the patient with the most extreme molecular phenotype is also affected by a more severe version of the syndrome.  These findings have significant biomedical implications, since they suggest a direct connection between ARID1B mutations and developmental disorders.

overall_design: Using patient-derived iPSCs to study ARID1B's function in craniofacial development

first: Luca

last: Pagliaroli

first: Patrizia

last: Porazzi

first: Alyxandra

middle: T

last: Curtis

first: Chiara

last: Scopa

first: Harold

last: Mikkers

first: Christian

last: Freund

first: Lucia

last: Daxinger

first: Sandra

last: Deilard

last: Welsh

first: Bruno

last: Calabretta

first: Elizabeth

last: Kropf

first: Connor

last: Ott

first: Samantha

last: Brugmann

first: Gijs

last: Santen


title: GATM-Mediated Creatine Biosynthesis Enables Maintenance of FLT3-ITD-Mutant Acute Myeloid Leukemia

city: Gainesville

first: Petr

last: Starostik

state: Florida

institute: University of Florida

summary: RNA-seq was used to demonstrate the differential expression genes in MOLM14 and MV4-11 cells after FLT3 inhibition.

overall_design: Transcriptional signature of FLT3-ITD dysregulation

first: Yuan

last: Zhang


title: Understanding COVID-19 in children and adults

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary:
Purpose: This study aims to characterize the early innate and adaptive responses induced by SARS-CoV-2 infection in children and adults over time up to 8 weeks post symptoms onset (POS). We report the gene signature of COVID-19 over the course of the disease in both age groups. The kinetic of infection was divided in 5-time intervals according to the calculated days POS: interval 1 (0-5), interval 2 (6-14), interval 3 (15-22), interval 4 (23-35), and interval 5 (36-81).
Methods: RNA extraction was performed automatically via the PAXgene Blood miRNA Kit and the QIAcube instrument (Qiagen) following the manufacturer’s protocol. RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively. The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq 4000 sequencer for a minimum of 30 million single-end 100 reads per sample.
Main results: (I) we observed an antiviral-IFN-signature and innate-cell-activation within the first 5 days post symptoms onset (POS), while genes associated with CD4 T-cell responses, plasma cells and immunoglobulin were upregulated in both age groups during the first two weeks POS, indicative of SARS-CoV-2-specific adaptive immune responses; (II) in adults, genes associated with IFN antiviral responses and activated dendritic cells were maintained during the second week of disease, and subsided only after 14 days. By contrast, those transcriptome changes subsided already after 5 days in children.

overall_design: Transcriptomic analysis of whole blood from SARS-COV-2 infected participants and their SARS-CoV-2 negative household contacts.

first: Maria

last: Vono

last: Lemeille

first: Arnaud

last: Didierlaurent

first: Claire

last: Siegrist


title: A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation [RNA-Seq]

first: Joseph

last: Dougherty


title: Mobility of condensin DC is key to its function in repressing transcription [Hi-C]

first: Jun

last: Kim

summary: analyze condensin binding by fluorescence recovery after photobleaching (FRAP) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) in ATP hydrolysis mutant and in mutants that affect the level of histone H4K20 methylation and H4K16ac enrichment and depletion on the X chromosome. We have also performed Hi-C analysis to test how 3D DNA interactions mediated by condensin DC change in the catalytic and null mutant of dpy-21, a H4K20me2 demethylase that increase H4K20me1 on the X.

overall_design: Population Hi-C contact matrices of mixed embryo dpy-21 and jmjC mutant

first: Laura

last: Breimann

first: Ana

last: Morao

first: David

last: Jimenez

first: Nina

last: Maryn

first: Krishna

last: Bikkasani

first: Michael

last: Carrozza

first: Sarah

last: Albritton

first: Maxwell

last: Kramer

first: Lena

last: Street

first: Kustrim

last: Cerimi

first: Vic-Fabienne

last: Schumann

first: Ella

last: Bahry

first: Stephan

last: Preibisch

first: Andrew

last: Woehler

first: Sevinc

last: Ercan


title: Mobility of condensin DC is key to its function in repressing transcription

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

overall_design: Refer to individual Series


title: Intrapleural nano-immunotherapy promotes innate and adaptive immune responses to enhance anti-PD-L1 therapy for malignant pleural effusion

status: Public on Sep 21 2021

city: Winston Salem

first: Dawen

last: Zhao

address: Medical Center Blvd

department: Biomedical Engineering

institute: Wake Forest School of Medicine

summary: Malignant pleural effusion (MPE) is indicative of terminal malignancy with uniformly fatal prognosis. Often, two distinct compartments of tumor microenvironment, the effusion and disseminated pleural tumors, co-exist in the pleural cavity, presenting a major challenge for therapeutic interventions and drug delivery. Clinical evidence suggests that MPE comprises abundant tumor associated myeloid cells with the tumor-promoting phenotype, impairing antitumor immunity. Here, we developed liposomal cyclic dinucleotide (LNP-CDN) for targeted activation of STING signaling in macrophages and dendritic cells and showed that, upon intrapleural administration, they induce drastic changes in the transcriptional landscape in MPE, mitigating the immune cold MPE in both the effusion and pleural tumors. Moreover, combination immunotherapy with blockade of PD-L1 potently reduced MPE volume and inhibited tumor growth not only in pleural cavity but also in lung parenchyma, conferring significantly prolonged survival of MPE-bearing mice. Furthermore, the LNP-CDN-induced immunological effects were also observed with clinical MPE samples, suggesting the potential of intrapleural LNP-CDN for clinical MPE immunotherapy.

overall_design: The LLC MPE mice (n = 3/treatment) were treated with intrapleural PBS, LNP-CDN (1 µg), anti-PD-L1 Ab (10F.9G2; 30 µg; BioXCell) or LNP-CDN plus anti-PD-L1 Ab. 48 h later, pleural fluid cells were collected and pooled from n = 3 MPE mice under each treatment. Biological replicates were then processed at the single-cell suspension stage with an equivalent number of cells from each replicate. Four thousand cells from each of the mixed samples for each condition were loaded onto the 10x Genomics Chromium System. Library preparation was performed using 10x Genomics Chromium Single cell 3' reagent kit V3 according to the manufacturer’s instructions by Cancer Genomics Shared Resource (CGSR) of the Wake Forest Baptist Comprehensive Cancer Center and passed quality control. Libraries were sequenced using a NovaSeq 6000 (one library per lane) at the CGSR.

first: Yang

last: Liu

first: Lulu

last: Wang

first: Qianqian

last: Song

first: Muhammad

last: Ali

first: William

last: Crowe

first: Gregory

middle: L

last: Kucera

last: Hawkins

first: Shay

last: Soker

first: Karl

last: Thomas

first: Lance

middle: D

last: Miller

first: Yong

last: Lu

first: Christina

middle: R

last: Bellinger

first: Wei

last: Zhang

first: Amyn

last: Habib

first: W

last: Petty


title: NSD2 amplifies oncogenic transcriptional output to promote lung adenocarcinoma pathogenesis [RNA-seq]

city: Irvine

first: Yumei

last: Li

state: CA

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

summary: RNA-seq of kras and kras;NSD2 driven tumor biopsies and RNA-seq and Cut-and-run of kras;NSD2 derived cells suggests NSD2 amplifies Ras-output at chromatin and separately activates oncogenic-promoting gene expression programs.

overall_design: RNA-seq was performed using tumor biopsies from kras and kras;NSD2 mice and compared to wild type lungs. In a separate study, RNA-seq and cut and run was performed in cell lines derived from the tumor biopsies of kras;NSD2 mice (KN cells±sgNSD2).

first: Deepanwita

last: Sengupta

first: Liyong

last: Zeng

first: Simone

last: Hausmann

first: Debopam

last: Ghosh

first: Gang

last: Yuan

first: Thuyen

last: Nguyen

first: Marcello

last: Caporicci

first: Xiaojie

last: Yang

first: Garry

last: Coles

first: Vladlena

last: Kharchenko

first: Iwona

last: Czaban

first: Dulat

last: Azhibek

first: Wolfgang

last: Fischle

first: Mariusz

last: Jaremko

first: Ignacio

middle: I

last: Wistuba

first: Julien

last: Sage

first: Åukasz

first: Pawel

last: Mazur

first: Or

last: Gozani


title: NSD2 amplifies oncogenic transcriptional output to promote lung adenocarcinoma pathogenesis [CUT&RUN]

first: Yumei

last: Li

first: Deepanwita

last: Sengupta

first: Liyong

last: Zeng

first: Simone

first: Wei

middle: K


title: Role of HNRNPL in human epidermal stem and progenitor cells

first: George

last: Sen

address: 9500 Gilman Drive

institute: UCSD

summary: HNRNPL plays a critical role in regulating epidermal stem and progenitor cell function through regulating integrin gene expression at transcriptional level.

overall_design: HNRNPL ChIP-Seq and RNA-Seq

first: Jingting


title: G-protein-coupled receptor P2Y10 facilitates chemokine-induced CD4 T cell migration through an autocrine feedback loop involving ATP and lysophosphatidylserine

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: G-Protein-coupled receptors (GPCRs), especially chemokine receptors, play a central role in the regulation of T cell migration. Various GPCRs are upregulated in activated CD4 T cells, among them P2Y10, a putative lysophospholipid receptor that is officially still considered an orphan GPCR. P2Y10-deficient CD4 T cells showed normal activation, differentiation, and proliferation, but reduced chemokine-induced migration and polarization. Chemokine-induced activation of RhoA, a central regulator of polarization and migration, was reduced in the absence of P2Y10, and this was due to loss of an autocrine feedback loop involving chemokine-triggered release of lysophosphatidylserine and adenosine triphosphate and consecutive P2Y10-dependent RhoA activation. In line with impaired chemokine-induced T cell migration, we found that mice with CD4 T cell-specific P2Y10 deficiency showed reduced T cell infiltration into the spinal cord in experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis

overall_design: samples from 3 control mice and 3 CD4 T cell-specific P2Y10-deficient mice

first: Nina

last: Wettschureck

first: Malarvizhi

last: Gurusamy


first: Dawen

last: Zhao

overall_design: The LLC MPE mice (n=3/group) were randomly grouped and treated on day 11 as follows: (i) PBS, (ii) LNP-CDN (intrapleural injection of 1 ug LNP-CDN), (iii) anti-PD-L1 Abs (intrapleural injection of 10F.9G2), (iv), (v) LNP-CDN +PD-L1 Abs. Cells from pleural fluid and pleural tumors of individual mice were gathered and total RNA was isolated by TRIzol Reagent for library preparation and further sequencing.

first: Yang

last: Liu

first: Lulu

last: Wang

first: Qianqian

last: Song

first: Muhammad

last: Ali

first: William

last: Crowe

first: Gregory

last: Kucera

last: Hawkins

first: Shay

last: Soker

first: Karl

middle: W

last: Thomas

first: Lance

last: Miller

first: Yong

last: Lu

first: Christina

last: Bellinger

last: Zhang

first: Amyn

last: Habib

first: W

last: Petty


title: DNA methylation maintains integrity of higher order genome architecture (Nanopore)

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research

type: Genome variation profiling by high throughput sequencing

summary: DNA replication timing and 3D chromatin organisation are associated with epigenomic changes across large domains during human differentiation and cancer progression. However, it is unclear if epigenome changes, in particular cancer-associated DNA hypomethylation, is a consequence or cause of changes observed in higher order genome architecture. Here, we compare replication timing profiles and three dimensional (3D) genome organisation, using Hi-C and single cell Repli-Seq in the DNMT1 and DNMT3B DNA methyltransferases double knockout hypomethylated DKO1 colorectal cancer cell line and its parental HCT116 cell line. We find that the hypomethylated cells show a profound loss of replication timing precision, gain of single cell replication timing heterogeneity and loss of chromatin conformation integrity. Discrete regions, that undergo a large change in replication timing in the hypomethylated cells, are associated with a loss of allelic replication timing and shrinking of late replicating Partially Methylated Domain (PMD) boundaries. In contrast, conservation of replication timing after DNA methylation depletion at PMDs is associated with the formation of new H3K9me3/H3K4me3 bivalent domains which may serve to prevent ectopic transcription and maintain cell viability. Together our results show that a loss of global methylation, a common hallmark of cancer, directly impacts on the precision of replication timing and contribute to deregulation of the 3D chromatin architecture.

overall_design: Repli-Seq, single cell Repli-Seq, Hi-C, WGBS and Nanopore sequencing was conducted in HCT116 human colorectal cancer cell line and the same cell line with knockout of DNMT1 and DNMT3B (DKO1) (Rhee et al. 2002).

first: Susan

last: Clark


title: DNA methylation maintains integrity of higher order genome architecture (RNA-Seq)


title: NSD2 amplifies oncogenic transcriptional output to promote lung adenocarcinoma pathogenesis

first: Yumei

last: Li


title: DNA methylation maintains integrity of higher order genome architecture (WGBS)


title: DNA methylation maintains integrity of higher order genome architecture


title: DNA methylation maintains integrity of higher order genome architecture (single cell Repli-Seq)


title: DNA methylation maintains integrity of higher order genome architecture (Repli-Seq)


title: DNA methylation maintains integrity of higher order genome architecture (Hi-C)


title: Characterization of duck peripheral blood cells at single-cell resolution

city: Xi'an

first: Hai

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: We performed scRNA-seq for duck peripheral white blood cells.

overall_design: Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks were subjected to scRNA-seq using the 10 × Chromium platform and transcriptional profile of subgroups of duck PWBCs separated according to their physical properties were also generated. The peripheral blood cells pretreated with erythrocyte lysis buffer were firstly separated by density gradient centrifugation using a duck lymphocyte isolation kit (Tianjin Haoyang Biological Technology, Tianjin, China). The cells in pallet were washed with 1640 culture medium and named as “high-density cells”(HDC) . The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs. The cells that tightly adhered to the coverslips situated in the culture dishes within one hour of seeding were named “adherent PBMCs” (ADP). The suspended cells were then transferred into new dishes and cultured for another 24 hours. Then the remaining suspended cells were collected and named as “suspended PBMCs” (SPP).

first: Shengwang

last: Liu


title: Mobility of condensin DC is key to its function in repressing transcription [RNA-seq I]

first: Jun

last: Kim

overall_design: Population mRNA profiles of mixed embryo and larval sir2.1 mutant worms

first: Laura

last: Breimann

first: Ana

last: Morao

first: David

last: Jimenez

first: Nina

last: Maryn

first: Krishna

last: Bikkasani

first: Michael

last: Carrozza

first: Sarah

last: Albritton

first: Maxwell

last: Kramer

first: Lena

last: Street

first: Kustrim

last: Cerimi

first: Vic-Fabienne

last: Schumann

first: Ella

last: Bahry

first: Stephan

last: Preibisch

first: Andrew

last: Woehler

first: Sevinc

last: Ercan


title: SARS-CoV-2 infection and replication in human  gastric organoids

status: Public on Sep 20 2021

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: COVID-19 typically manifests as a respiratory illness but several clinical reports described gastrointestinal (GI) symptoms. This is particularly true in children, whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. These observations raise the question of whether the virus can replicate within the stomach. Here we show the novel derivation of gastric organoids from fetal, pediatric and adult biopsies and prove their value as in vitro models for SARS-CoV-2 infection. To facilitate infection, we induced a reversed polarity in our organoids (RP-GOs). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, while the viral replication is significantly lower in organoids of fetal and adult origin. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we show how the virus can efficiently infect gastric epithelium, suggesting that the stomach might have an active role in fecal-oral SARS-CoV-2 transmission.

overall_design: Transcriptomic analysis of organoids derived from fetal, pediatric and adult gastric samples infected by SARS-CoV-2 virus at MOI 1, and paired negative controls.

first: Giovanni

middle: G

last: Giobbe

first: Francesco

last: Bonfante

first: Elisa

last: Zambaiti

first: Onelia

last: Gagliano

first: Brendan

last: Jones

first: Camilla

last: Luni

first: Cecilia

last: Laterza

first: Silvia

last: Perin

first: Georg

last: Busslinger

first: Hannah

last: Stuart

first: Matteo

last: Pagliari

first: Alessio

last: Bortolami

first: Eva

last: Mazzetto

first: Anna

last: Manfredi

first: Chiara

last: Colantuono

first: Alessandro

last: Pellegata

first: Vivian

last: Li

first: Simon

last: Eaton

first: Nikhil

last: Thapar

first: Davide

last: Cacchiarelli

first: Hans

last: Clevers

first: Nicola

last: Elvassore

first: Paolo

last: De Coppi


title: Potent androgen receptor inhibition unleashes oncogenic action of the KLF5 stem cell transcription factor in castration-resistant prostate cancer [ChIP-seq]

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

summary: Advanced prostate cancer (PC) can be treated with endocrine therapies that inhibit transcriptional activity of the androgen receptor (AR). However, PC will ultimately evolve under the selection pressure of these therapies and progress to a lethal phenotype termed castration-resistant PC (CRPC). Recent studies suggest that de-differentiation away from an AR-driven luminal cell identity may be a key, early step. However, early therapy-induced mechanisms of prostate cancer cell de-differentiation are poorly understood. Here we show that the stem cell transcription factor Kruppel-like factor 5 (KLF5) is transcriptionally repressed by AR, and de-repressed by enzalutamide. KLF5 expression is high in a subset of CRPC tissues, but low in primary adenocarcinoma. KLF5 functioned as oncogene in CPRC cells, promoting cellular migration, anchorage-independent growth, expression of basal cell markers, and transcriptional signatures of CRPC lineage plasticity, but had modest effects on cell proliferation. Chromatin immuno-precipitation (ChIP)-sequencing, RNA-sequencing, and co-immunoprecipitation experiments established a physical interaction between KLF5 and AR, and integrative analysis revealed that KLF5 and AR drive opposing transcriptional programs. We identified ERBB2 as a point of transcriptional convergence that was activated by KLF5 and repressed by AR. Accordingly, KLF5 expression levels in CRPC tissues correlated with predicted sensitivity to the dual EGFR inhibitor lapatanib, and the ERBB2-specific inhibitor mubritinib blocked KLF5-driven cell migration. Collectively, these findings implicate KLF5 as an AR-suppressed oncogene that drives early steps in CRPC de-differentiation and disease progression.

overall_design: KLF5 ChIP-seq in R1-AD1 prostate cancer cells cultured in medium supplemented with 10% charcoal-stripped serum (CSS) and stimulated 4h with 1 nM DHT (or 0.1% ethanol as vehicle control) as well as KLF5 ChIP-seq in AR gene-engineered R1-D567 prostate cancer cells cultured in medium supplemented with 10% CSS.

first: Meixia

last: Che

first: Sarah

last: Munro


title: Transcriptomic profiling of bone marrow stromal cell subsets during chronic viral infection with LCMV

city: Zurich

first: Cesar

last: Nombela-Arrieta

address: Häldeliweg, 4

department: Medical Oncology and Hematology

institute: University of Zurich

summary: RNA sequencing of two stromal cell subsets of the bone marrow, namely CXCL12-abundant reticular cells (CARc) and sinusoidal endothelial cells (SECs) isolated from untreated mice (day 0) and mice infected with Lymphocytic Choriomeningitis Virus cl-13, 56 days after infection (day 56)

overall_design: RNA-sequencing of two FACS-sorted mouse bone marrow stromal cells based on phenotypic marker expression from uninfected control (day 0) and LCMV-cl13 infected mice (56 day post infection-day 56). Cell subsets were sorted according to previously defined phenotypic signatres. CARc; CD45-Ter119-Cd31-CD140b+Sca-1- .  SECs; CD45-Ter119-CD31+Sca-1+CD105hi

first: César

first: Stephan

last: isringhausen

first: Patrick

last: Helbling


title: Potent androgen receptor inhibition unleashes oncogenic action of the KLF5 stem cell transcription factor in castration-resistant prostate cancer [RNA-seq]

overall_design: RNA-seq analysis of the prostate cancer cell line R1-AD1 infected with lentivirus encoding control shRNA (shCon) or two independent shRNAs targeting KLF5 (shKLF5), cultured in medium supplemented with 10% charcoal-stripped serum (CSS) and stimulated 24h with 1 nM DHT or 0.1% (v/v) ethanol as vehicle control. RNA-seq analysis was also performed with AR gene-engineered R1-D567 prostate cancer cells infected with lentivirus encoding shCon or shKLF5, cultured in medium supplemented with 10% CSS.


title: Potent androgen receptor inhibition unleashes oncogenic action of the KLF5 stem cell transcription factor in castration-resistant prostate cancer


title: Polymorphic endogenous retroviral element gives rise to differential epigenomic states and gene expression between distinct genetic backgrounds

city: HONG KONG

first: Danny

last: Leung

state: HONG KONG

address: Clear Water Bay

institute: HONG KONG UNIV OF SCIENCE & TECHNOLOGY

summary: Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset is capable of influencing the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Here, utilizing wildtype murine embryonic stem cells (mESCs) derived from distinct genetic backgrounds, we discovered a polymorphic MMERGLN element capable of regulating H3K27ac enrichment, transcription and higher-order chromatin structure of neighboring loci. We demonstrated that this polymorphic element enhanced the neighboring Klhdc4 gene’s expression in cis, which in turn altered activity of downstream stress response genes. The results suggest that the polymorphic ERV-derived cis-regulatory element contribute to strain-specific phenotypes from particular stimuli. Moreover, we identified thousands of potential polymorphic ERVs in mESCs from both strains and illustrated their potential to regulate nearby histone modifications and transcription. Overall, our findings show the mechanism of how polymorphic ERVs can shape the epigenome and transcriptional networks that give rise to phenotypic divergence between individuals.

overall_design: ChIP-seq, WGS, Tri-4C and RNA-seq were conducted for WT TT2 and J1. RNA-seq was also conducted for GLN-KO, GLN-KD, Klhdc4-KD, GLN-PB cells. And ChIP-seq was also performed for GLN-PB cells.

first: X

last: Zhou

first: A

last: Lee

first: D


title: Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture [ChIP-Seq]

city: Boston

first: Hye Ji

last: Cha

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

summary: Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.

overall_design:
Cells were crosslinked and nuclei were prepared for ChIP-seq experiments.

Please note that the records were updated with the ESC_*_input_* samples (GSM5687584-GSM5687590) on Nov 11, 2021.

first: Hye

first: Tianxin

last: Liu


title: Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture [RNA-Seq]

overall_design: mRNA expression profiles of control and Matr3 KO in MEL and mouse ES cells during differentiation

first: Qian

last: Zhu


title: Lower brown adipose tissue activity is associated with non-alcoholic fatty liver disease but not changes in the gut microbiota

city: Hamilton

first: Katherine

last: Morrison

address: 1280 Main street west

country: Canada

institute: McMaster

summary: In rodents, brown adipose tissue (BAT) contributes to whole body energy expenditure and low BAT activity is related to hepatic fat accumulation, partially attributable to the gut microbiome. Little is known of these relationships in humans. In adults (n=60), we assessed hepatic fat and cold-stimulated BAT activity utilizing magnetic resonance imaging and the gut microbiome with 16S sequencing. We transplanted gnotobiotic mice with feces from humans to assess the transferability of BAT activity and NAFLD through the microbiome. Individuals with NAFLD (n=29) had lower BAT activity than those without and BAT activity was inversely related to hepatic fat. Although the fecal microbiome was different in those with NAFLD, no differences were observed in relation to BAT activity and neither of these phenotypic traits were transmissible through fecal transplant to gnotobiotic mice. Thus, low BAT activity is associated with hepatic steatosis but this is not mediated through the gut microbiota.

sample_organism:
feces metagenome
human feces metagenome

platform_organism:
feces metagenome
human feces metagenome

overall_design: 60 stool samples from human adults. For the microbial transfer to mice; we used 9 NAFLD-/H-BAT + and 13 NAFLD+/L-BAT-.

first: Basma

last: Ahmed

first: Frank

last: Ong

first: Nicole

last: Barra

first: Denis

last: Blondin

first: Elizabeth

last: Gunn

middle: M

last: Oreskovich

first: Jake

last: Szamosi

first: Saad

last: Syed

first: Emily

last: Hutchings

first: Norman

middle: B

last: Konyer

first: Nina

last: Singh

first: Julian

last: Yabut

first: Eric

last: Desjardins

first: Fernando

middle: F

last: Anhê

first: Kevin

last: Foley

first: Alison

last: Holloway

first: Michael

last: Noseworthy

first: Francois

last: Haman

first: Andre

last: Carpentier

last: Surette

first: Jonathan

last: Schertzer

first: Zubin

last: Punthakee

first: Gregory

last: Steinberg


title: RNA-Seq of S.pistillata samples exposed to a 6-months darkness

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

institute: IRCAN

summary: Telomere DNA length is a complex trait controlled both by multiple loci and environmental factors. Even though the use of telomere DNA length measurement, as a method of assessing stress accumulation and predicting how this will influence survival, is currently being studied in numerous human cohort studies, the importance of telomere length for stress response in ecological studies remains at its infancy. Here, we investigated the telomere changes occurring in the symbiotic coral Stylophora pistillata that has experienced a continuous darkness over 6 months. This stress condition led to the loss of its symbionts, as what is also observed when bleaching occurs in the field at a large-scale due to climate changes and anthropogenic activities, threatening the worldwide reef ecosystem. We found that the continuous darkness condition was associated to telomere DNA length shortening and a downregulation of the expression of the telomere-associated protein POT2. These results pave the way for future studies on the role of telomere in coral stress response and the importance of telomere dysregulation in endangered coral species

overall_design: RNA-Seq performed on S.pistillata branch samples exposed to darkness during 6 months or in control condition

first: Alice

last: Rouan

last: Gilson


title: Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture [ATAC-Seq]

first: Hye Ji

last: Cha

overall_design: ATAC-seq experiments were performed using 50,000 MEL cells to assess chromatin accessibility.

first: Hye


city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Bacteria use a variety of mechanisms, such as two‐component regulatory systems (TCSs), to rapidly sense and respond to distinct conditions and signals in their host organisms. For example, a type III secretion system (T3SS) is the key determinant of the virulence of the model plant pathogen Pseudomonas syringae and contains the TCS RhpRS as a key regulator. However, the signal sensed by RhpRS remains unknown. We found that RhpRS directly senses plant-generated polyphenols and responds by switching off P. syringae T3SS via crosstalk with alternative histidine kinases. Through a chemical screen, we identified three natural polyphenols (tannic acid, 1,2,3,4,6-pentagalloylglucose and epigallocatechin gallate) that induced the expression of the rhpRS operon in a RhpS-dependent manner.

overall_design:
RNA-seq for polyphenols treated Pseudomonas syringae and microbiota analysis for Arabidopsis thaliana

Both 'Psph-wt-MM*' and 'PSPH-WT-MM*' are wild-type Pseudomonas savastanoi pv. phaseolicola 1448A strain that grown in minimal media but belong to different sequencing batches. The *MM* and *mock samples are also the same cases, they are all wild-type stain cultured in minimal media.

In the submitted RNA-seq data, Psph-wt-MM  is the control group for L13-NAR500-MM;
PSPH-WT-mock is the control group for  PSPH-WT-EGCG-10;
PSPH-WT-MM is the wild type sample for rhpS mutant and rhpS/3550/3736/5115

last: Deng


title: Transcriptional changes associated with endoplasmic reticulum stress in the eye imaginal disc of Drosophila melanogaster

city: New York

first: Brian

middle: Scott

last: Brown

address: 540 1st Avenue, SKI 5-2

department: Department of Cell Biology

institute: NYU School of Medicine

summary: We obtained transcriptional profiles of third instar eye imaginal disc nuclei with or without endoplasmic reticulum stress using next generation sequencing (NGS). We employed an isolation of nuclei tagged in specific cell type (INTACT) protocol (Ma and Weake, J. of Vis. Exp., 2014) to label nuclear membranes of GMR-GAL4-expressing cells with EGFP. The experimental group also expressed a mutant allele of the membrane visual protein rhodopsin (Rh-1(G69D)), which is known to cause endoplasmic reticulum stress and initiate Unfolded Protein Response (UPR) signaling. The goal of this study was to characterize the transcriptional changes associated with endoplasmic reticulum stress responses in a commonly used platform, the eye imaginal disc.

overall_design: Comparison of isolated nuclear transcriptomes from third instar control eye imaginal discs and third instar eye imaginal discs overexpressing the misfolded protein Rh-1(G69D), a potent inducer of endoplasmic stress

first: Hyung

last: Ryoo


title: Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture [Hi-C]

overall_design: Hi-C experiments were performed using 50,000 MEL cells during differentiation

first: Özgün

last: Uyan


title: Structural variation at the ZNF558 locus controls a gene regulatory network in human brain development

status: Public on Sep 19 2021

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

summary: The human forebrain has expanded in size and complexitycompared to that of chimpanzeedespite limited changesinprotein-coding genes, suggesting that gene regulation is an importantdriver of brain evolution. Here we identify a KRAB-ZFPtranscription factor, ZNF558, that isexpressed in human but not chimpanzee forebrain neural progenitor cells. ZNF558 evolved asa suppressor of LINE-1 transposons but has been co-opted to regulate the mitophagy geneSPATA18, supporting a link between mitochondrial homeostasis andcorticalexpansion. Theunusual on-off switchforZNF558expression resides in a downstream variable number tandemrepeat (VNTR) that is contracted in humans relative to chimpanzee.Our data reveal the brain-specific co-option of a transposon-controllingKRAB-ZFPand how a human-specificregulatory network is established by acis-acting structural genome variation. Thisrepresentsapreviouslyundescribedgenetic mechanisminthe evolution of the human brain.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
In order to silence the transcription of ZNF558 we used the catalytically inactive Cas9 (deadCas9) fused to the transcriptional repressor KRAB. Single guide sequences were designed to recognize DNA regions just down-stream of the transcription start site (TSS) according to the GPP Portal (Broad Institute). The guides were inserted into a deadCas9-KRAB-T2A-GFP lentiviral backbone containing both the guide RNA under the U6 promoter and dead-Cas9-KRAB and GFP under the Ubiquitin C promoter (pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP, a gift from Charles Gersbach, Addgene plasmid #71237 RRID:Addgene_71237). The guides were inserted into the backbone using annealed oligos and the BsmBI cloning site. Lentiviruses were produced as described below yielding titers between 4.9E+08 and 9.3E+09. Control virus with a gRNA sequence not present in the human genome (LacZ) was also produced and used in all experiments. All lentiviral vectors were used with an MOI between 5 and 20. (GSM5525367-GSM5525378)

H6 and H48 are different cell lines. They are HS1 and HS2 (mentioned in the paper), respectively.

bulk and single-cell RNA-seq and CUT&RUN

first: Pia

middle: A

last: Johansson

first: Per

last: Brattås

first: Christopher

middle: H

last: Douse

first: PingHsun

last: Hsieh

first: Julien

last: Pontis

first: Daniela

last: Grassi

first: Raquel

last: Garza

first: Marie

last: Jonsson

first: Diahann

last: Atacho

first: Karolina

last: Pircs

first: Feride

last: Eren

first: Yogita

last: Sharma

first: Jenny

first: Didier

last: Trono

first: Evan

last: Eichler


title: Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia [variation]

city: MInneapolis

first: Michael

last: Farrar

state: MN

address: 2101 6th Street SE

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: The transcription factors EBF1 and PAX5 are frequently mutated in B cell acute lymphoblastic leukemia (B-ALL). We demonstrate that Pax5+/- x Ebf1+/- compound heterozygous mice develop leukemia with high penetrance. Similar results were seen in Pax5+/- x Ikzf1+/- and Ebf1+/- x Ikzf1+/- mice for B-ALL, or in Tcf7+/- x Ikzf1+/- mice for T cell leukemia. To identify genetic defects that cooperate with Pax5 and Ebf1 compound heterozygosity to initiate leukemia, we carried out a Sleeping Beauty transposon screen. This screen identified a number of cooperating partners including gain-of-function mutations in Stat5 (~65%) and Jak1 (~68%), as well as loss-of-function mutations in Cblb (61%) and Myb (32%). These findings highlight the key role of JAK/STAT5 signaling in cooperating with Pax5 and Ebf1 compound haploinsufficiency to drive B cell transformation. Moreover, these studies pointed to unexpected roles for loss of function mutations in Cblb and Myb in B cell transformation. Subsequent RNA-Seq studies on WT, Pax5+/-, Ebf1+/-, Pax5+/- x Ebf1+/- pre-leukemic, Pax5+/- x Ebf1+/- leukemic cells and Pax5+/- x Ebf1+/- Sleeping Beauty leukemic cells demonstrated upregulation of a PDK1>SGK3>MYC pathway; treatment of Pax5+/- x Ebf1+/- leukemias with PDK1 specific inhibitors blocked their proliferation in vitro. Finally, we identified conserved transcriptional variation in a subset of genes between human leukemias and our mouse B-ALL models. Thus, compound haploinsufficiency for B cell transcription factors likely plays a critical role in transformation of human B cells and suggest that newly developed PDK1 inhibitors may be effective for treating patients characterized by such defects.

overall_design: Progenitor B cells were extracted from three groups of wild-type mice and pooled (three WT replicates). Leukemic B cells were extracted from Pax5 x Ebf1 mice with leukemia (five replicates from five individual mice).

first: Lynn

last: Heltemes-Harris

first: Sarah

last: Munro


title: Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia [RNA-seq]

overall_design: Pooled mice replicates were sequenced for the progenitor B cells and leukemic B cells. Sleeping Beauty mutagenesis was applied to 31 individual mice and leukemic B cells from these mice were sequenced in separate libraries.


title: Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia

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

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of bone marrow samples from Fsp1-Cre;Col1a1flox/flox mice and WT mice

status: Public on Sep 18 2021

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: We employed genetic mouse model (Fsp1-Cre;Col1a1flox/flox) to delete Col1a1 (type I collagen) specifically in Fsp1-expressing cells in comparison with control WT mice (Cre-negative;Col1a1flox/flox). Single-cell RNA-sequencing analyses were performed on unfractionated live cell mixtures from bone marrow samples from Fsp1-Cre;Col1a1flox/flox mice and WT mice, to investigate the impact of Fsp1-cell-specific Col1 deletion on bone marrow microenvironment.

overall_design: Unfractionated live cell mixtures from bone marrow samples of Fsp1-Cre;Col1a1flox/flox mice and WT mice were analyzed by 10x single-cell RNA-sequencing

first: Raghu

last: Kalluri


title: Transcriptomic responses of the kidney to development of and recovery from acute decompensated heart failure (ADHF)

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

country: New Zealand

institute: University of Otago, Christchurch

summary: We report changes in kidney gene expression in response to development of, and recovery from, ADHF using an ovine model of rapid cardiac pacing (220 beats per minute).

overall_design: We  obtained kidney biopsies prior to cardiac pacing (day 0), after development of ADHF (day 14) and at the end of the 25-day (non-pacing) recovery period from 6 Coopworth ewes (5 x Baseline, 6 x HF and 5 x Recovery serial samples).  To maximise statistical power, the serial samples were supplemented with kidney samples collected post-mortem from animals sacrificed before, during or after the same pacing protocol. This provided a total of 14 x Baseline, 13 x Heart Failure and 8 x Recovery samples for RNA-Seq analysis.

first: Miriam

last: Rademaker

middle: P

first: Leigh

middle: J

last: Ellmers

first: Suetonia

middle: C

last: Palmer

first: Trent

last: Davidson

first: Prisca

last: Mbikou

first: Nicola

last: Scott

first: Elizabeth

last: Permina

first: Christopher

last: Charles

first: Zoltan

last: Endre

first: A

last: Richards


title: Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus

city: Irvine

first: Timothy

last: Downing

address: Samueli School of Engineering, University of California, Irvine

department: Dept. of Biomedical Engineering

institute: University of California, Irvine

summary: We performed reduced representation bisulfite sequencing (RRBS) from mouse dorsal hippocampus – which is necessary for the formation and consolidation of specific types of memories – in young and aging mice of both sexes to determine age-dependent changes in methylation across genomic contexts. Overall, our findings demonstrate that methylation levels within the dorsal hippocampus are divergent between sexes during aging in genomic features correlating to mRNA functionality, transcription factor binding sites - with hypomethylated regions correlating with transcription factors involved in plasticity, and gene regulatory elements.

overall_design: DNA methylation analysis, including across context DMRs and histone modifications, of young and aging dorsal hippocampal mouse tissue

first: Carlene

last: Chinn

first: Honglei

last: Ren

first: Julien

last: Morival

first: Qing

last: Nie

first: Marcelo

last: Wood


title: Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture

first: Hye Ji

last: Cha

state: MA


title: RNA-seq of isogenic NPC1 mutant iPSC-derived microglia like cells

city: palo alto

first: John

last: Pluvinage

address: 3801 Miranda Ave Rm D3-131

institute: Stanford

summary: Expression data comparing the effect of I1061T NPC1 mutation and anti-CD22 treatment in iPSC-derived microglia like cells treated with NPC patient CSF.

overall_design: WT or I1061T mutant iPSC-derived microglia-like cells were treated with NPC patient CSF and isotype or anti-CD22 antibodies for 24 hours prior to bulk RNA extraction


title: Targeting Nuclear β-catenin as therapy for post-myeloproliferative neoplasm secondary AML

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: Transformation of post-myeloproliferative neoplasms into secondary (s) AML exhibit poor clinical outcome. In addition to increased JAK-STAT and PI3K-AKT signaling, post-MPN sAML blast progenitor cells (BPCs) demonstrate increased nuclear β-catenin levels and TCF7L2 (TCF4) transcriptional activity. Knockdown of β-catenin or treatment with BC2059 that disrupts binding of β-catenin to TBL1X (TBL1) depleted nuclear β-catenin levels. This induced apoptosis of not only JAKi-sensitive but also JAKi-persister/resistant post-MPN sAML BPCs, associated with attenuation of TCF4 transcriptional targets MYC, BCL-2 and Survivin. Co-targeting of β-catenin and JAK1/2 inhibitor ruxolitinib (rux) synergistically induced lethality in post-MPN sAML BPCs and improved survival of mice engrafted with human sAML BPCs. Notably, co-treatment with BET protein degrader ARV-771 and BC2059 also synergistically induced apoptosis and improved survival of mice engrafted with JAKi-sensitive or JAKi-persister/resistant post-MPN sAML cells. These preclinical findings highlight potentially promising anti-post-MPN sAML activity of combination of β-catenin and BETP antagonists against post-MPN sAML BPCs.

overall_design: Patient derived CD34+ secondary AML blast progenitor cells  from a patient were treated as biologic replicates (n=2) with the Beta Catenin antagonist BC2059 at a concentrations of 200 nM for 8 hours. Untreated control cells (n=2) were also analyzed.

middle: N

first: Warren

last: Fiskus


title: Extracellular ectonucleotidases are differentially regulated in murine tissues and human polymorphonuclear leukocytes during sepsis and inflammation

first: George

last: Hasko

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

summary: In the present studies we identified NTPDase8 a top downregulated gene in the liver of mice submitted to the cecal ligation-induced sepsis. Immunohistochemical analysis confirmed the decrease on NTPDase8 expression at the protein level. In vitro mechanistic studies using HepG2 hepatoma cells demonstrated that IL-6 but not TNF, IL-1b, bacteria or lipopolysaccharide are able to suppress NTPDase8 gene expression.

overall_design: RNAseq analysis of mice liver tissue in both sham and CLP (cecal ligation and puncture) sepsis model

first: Clarissa

last: Haas

first: Marianna

last: Lovászi

first: György

last: Haskó


title: The synthetic triterpenoid RTA-408 limits radiation damage to normal tissue

status: Public on Sep 17 2021

city: Philadelphia

last: Linnenbach

state: NJ

address: 233 S 10th Streert

institute: Thomas Jefferson University

summary:
Objective/Hypothesis: To assess the efficacy and mechanism of action of a novel approach to mitigate acute and chronic radiation toxicity in a validated animal model. We propose that synthetic triterpenoid RTA-408, an Nrf2 activator, activates additional protective pathways which stabilize soft tissue during radiation, thereby reducing necrosis and improves surgical outcomes in a subsequently created axial rotational flap.   Methods: Experimental animal study utilizing Sprague-Dawley rats were divided into 3 cohorts: (i) radiation + DMSO (inert vehicle), (ii) radiation + RTA-408 (therapeutic drug), and (iii) no radiation + DMSO. Two main groups of rats were utilized in these experiments: (i) rotational flap experiment (n=40) and (ii) transcriptome analysis (n=9). In the first experiment all animals in the radiation cohorts underwent 40 Gy of radiation to the soft tissue of the abdomen. Then all three cohorts underwent surgery with construction of an inferior epigastric axial rotational flap, which was performed 30 days after resolution of acute injury from radiation in the radiation groups. Percentage of flap necrosis, the primary endpoint, was calculated by standardized measurement of tissue necrosis by blinded observers and vascular density measured by CD31 staining. In a second experiment, an additional three cohorts, with identical treatment as described above underwent serial punch biopsies of the abdominal skin before, during, and after radiation and drug/vehicle control treatment. Transcriptome analysis utilizing gene set enrichment analysis and digital PCR were performed at the various timepoints.
Results: In the first experiment, 40 rats were divided into the three groups and underwent treatment accordingly. The average flap necrosis was 20% (95% CI, 16-45%) in the radiation control group, 3% (95% CI, 0-11%) in the non-irradiated control, and 3% (95% CI, 0.2-10%) in the radiation group treated with RTA-408. Vascular density was preserved in the treatment group as compared to the radiated control. Nine rats were included in the second experiment, and transcriptome analyses in the treatment group revealed robust activation of antioxidant pathways with induced expression of genes associated with hypoxia and adipogenesis/angiogenesis.   Conclusions: Administration of RTA-408 during radiation treatment in a rat model resulted in transcriptome changes which appear to mitigate the toxic effects of radiation, preserving capillary networks and improving flap survival and tissue healing after subsequent surgery. Such reductions in toxicity may have broad implications for functional outcomes and salvage surgery following therapeutic irradiation.

overall_design: Affymetrix gene chips (rat Clariom S) were used to measure genome-wide gene expression in irradiated rat skin, pretreated with either the drug RTA408 or vehicle control.

first: Alban

first: Adam

last: Luginbuhl


title: Identification of genes involved in class switch recombination by genome-wide CRISPR/Cas9 knock-out screen

city: Illkirch

first: Bernardo

last: Reina-San-Martin

address: 1, Rue Laurent Fries

institute: IGBMC- CNRS UMR 7104 - Inserm U 1258

summary: This screen aims to identify genes involved in class switch recombination (CSR), a process that allows B cells to change the isotype they express from IgM/IgD to IgG, IgA or IgE. For that purpose, the murine B cell line CH12 stably expressing Cas9 was used. This cell line can be induced to undergo CSR from IgM to IgA very efficiently in vitro when cultured with TGF-b, IL-4 and an anti-CD40 antibody. CH12Cas9 cells were transduced with the second-generation mouse Brie (mBrie) retroviral gRNA library (pMX-mBrie) and selected with puromycin for two weeks to allow for the Cas9-mediated generation of knockouts. Cells were then stimulated to undergo CSR for 72h. Those which failed to undergo CSR (which remained IgM+) or that succeed (which became IgA+) were sorted using magnetic beads. Genes, whose loss-of-function affect the efficiency of CSR, were identified by looking at gRNA enrichment in the IgM+ versus IgA+ populations through deep sequencing.

overall_design: Comparison of gRNAs enrichment between IgM+ and IgA+ populations by high-throughput sequencing

first: Mélanie

last: Rogier

first: Isabelle

last: Robert

first: Aurore

last: Frey


title: Cellular Origins of EGFR-driven Lung Cancer Cells Determines Sensitivity to Therapy

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: The purpose of this research is to study the cellular origins of EGFR-mutant lung cancers and their responses to therapies. We discovered that activation of EGFR T790M/L858R mutation in lung epithelial cells can drive lung cancers with alveolar or bronchiolar features, which can be originated from alveolar type 2 (AT2) cells or bronchioalveolar stem cells (BASCs), but not basal cells or club cells of the trachea. Crucially, the tumoroids with different cell-of-origins or epigenetic states had distinct drug vulnerabilities.

overall_design: RNA-sequencing profiles of murine lung organoids with or without EGFR T790M/L858R mutations before ex vivo transplantation, and EGFR T790M/L858R tumor organoids after ex vivo transplantation.

first: Jinpeng

last: Liu

first: Chi

last: Wang

first: Christine

last: Brainson


title: RNAs regulated by MEC-8 in C. elegnas touch receptor neurons

city: Riverside

middle: David

last: Norris

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: GFP-labeled touch receptor neurons from C. elegans were dissociated then sorted into Trizol (10,000+ cells per replicate) followed by polyA-enrichment and RNA-seq

overall_design: polyA-enriched RNA-seq from sorted GFP+ touch neurons from either wild-type or mec-8(e398) mutant C. elegans


title: scRNAseq comparison of iPSC-derived retinal organoids from Control and LCA7 patients

city: San Francisco

first: Deepak

last: Lamba

state: California

address: 35 Medical Center Way

department: Ophthalmology

institute: University of California, San Francisco

summary: To comprehensively capture changes in retinal transcriptome for the LCA7 organoids compared to control, we performed single cell RNA-sequencing (scRNAseq) using the 10X Genomics platform. Retinal organoids at D150 of differentiation were dissociated for scRNAseq analysis. scRNAseq data revealed significant dysregulation of specific photoreceptor genes between control and LCA7 organoids, as well as mutation-specific differences in various genes, including CRX, RCVRN, ARR3, and AIPL1.

overall_design: Comparison of iPSC-derived retinal organoids from 1 Control and 2 LCA7 patients with two different mutations: K99Q and T155ins4

first: Kathleen

last: Chirco

first: Shereen

last: Chew

first: Anthony

last: Moore

first: Jacque

last: Duncan


title: Highly Immunogenic Cancer Cells Require Activation of the WNT Pathway for Immunological Escape

city: Saint Louis

first: Robert

middle: D

last: Schreiber

address: 425 South Euclid

institute: Washington University in St. Louis

summary: PD-1 blockade therapy exerts antitumor effects by restoring the infiltration of tumor antigen-specific CD8+ T cells. While neoantigens arising from gene alterations in cancer cells comprise critical tumor antigens in antitumor immunity, a subset of non-small-cell lung cancers (NSCLCs) harboring substantial tumor mutation burden (TMB) lack CD8+ T cells in the tumor microenvironment (TME), resulting in resistance to PD-1 blockade therapy. This resistance is an urgent issue, so the mechanism(s) mediating impaired antitumor immunity in highly mutated NSCLCs need to be explored. Here, we show that activation of the WNT/b-catenin signaling pathway contributes to the development of a noninflamed TME in tumors with high TMB. NSCLCs that lack immune cell infiltration into the TME despite high TMB preferentially upregulate the WNT/b-catenin pathway. Immunological assays revealed that those patients harbored neoantigen-specific CD8+ T cells in the peripheral blood but not in the TME, suggesting impaired T cell infiltration into the TME due to the activation of WNT/b-catenin signaling. In our animal model, the accumulation of gene mutations in cancer cells increased CD8+ T cell infiltration into the TME, slowing tumor growth. However, further accumulation of gene mutations blunted antitumor immunity by excluding CD8+ T cells from tumors in a WNT/b-catenin signaling-dependent manner. Combined treatment with PD-1 blockade and WNT/b-catenin signaling inhibitors induced far stronger antitumor immunity than either treatment alone. We propose a mechanism-oriented combination therapy concept in the cancer immunotherapy field, i.e., the combination of immune checkpoint inhibitors with drugs that target specific molecules in cancer cell-intrinsic oncogenic signaling pathways involved in immune escape.

overall_design: Non-small cell lung cancer (NSCLC) samples from twenty-two patients were analyzed with RNA sequencing.

first: Yoshiko

last: Takeuchi

first: Tokiyoshi

last: Tanegashima

first: Eiichi

last: Sato

first: Takuma

last: Irie

first: Atsuo

last: Sai

first: Kota

last: Itahashi

first: Shogo

last: Kumagai

first: Yasuko

last: Tada

first: Yosuke

last: Togashi

first: Shohei

last: Koyama

first: Esra

last: Akbay

first: Takahiro

last: Karasaki

first: Keisuke

last: Kataoka

first: Soichiro

last: Funaki

first: Yasushi

last: Shintani

first: Izumi

last: Nagatomo

first: Hiroshi

last: Kida

first: Genichiro

last: Ishii

first: Tomohiro

last: Miyoshi

first: Keiju

last: Aokage

first: Kazuhiro

last: Kakimi

first: Seishi

last: Ogawa

first: Meinoshin

last: Okumura

first: Masatoshi

last: Eto

first: Atsushi

last: Kumanogoh

first: Masahiro

last: Tsuboi

first: Hiroyoshi

last: Nishikawa


title: RNAseq data comparing GFP, wildtype USP21 and enzyme-dead USP21 overexpressing iKPC PDAC cells with KRAS* expression (on dox) and KRAS* extinction (off dox)

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

summary: USP21 promotes PDAC tumor cells to bypass KRAS* dependency. To dissect the molecular mechanism, we conducted RNA-seq analysis comparing iKPC cancer cells overexpressing GFP, wildtype USP21 and enzyme-dead USP21 at day 3 after KRAS* extinction. KRAS*-expressing iKPC cells with GFP overexpression are positive control.

overall_design: Three independent iKPC PDAC cell lines (iKPC-1, iKPC-3 and iKPC-5) were used for the study. Cells were cultured in Matrigel.

first: Terrence

last: Wu

first: Jianhua

last: Zhang


title: Therapeutic radiation exposure of the abdomen during childhood induces chronic adipose tissue dysfunction

first: Paul

last: Cohen

address: 1230 York Ave

institute: The Rockefeller University

summary: Childhood cancer survivors who received abdominal radiotherapy (RT) or total body irradiation (TBI) are at increased risk for cardiometabolic disease, but the underlying mechanisms are unknown. We hypothesize that RT-induced adipose tissue dysfunction contributes to the development of cardiometabolic disease in the expanding population of childhood cancer survivors. We performed bulk RNA-sequencing of abdominal subcutaneous adipose tissue from adult childhood cancer survivors previously exposed to TBI, abdominal RT, or chemotherapy alone, alongside a group of healthy controls. We find that irradiated adipose tissue is characterized by a gene expression signature indicative of a complex macrophage expansion, which is also associated with dysregulated adipokine secretion. The full cohort is 30 subjects; however, 3 participants (2 in CHM group, 1 in CTL group) declined to share their sequencing data in a public database.

overall_design: Observational cohort with 4 groups: CTL (healthy controls); CHM (chemotherapy only); ABM (chemo+abdominal radiation); TBI (chemo+total body irradiation).

first: Danielle

last: Friedman

first: Xiaojing

last: Huang


title: Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries

city: Dallas

first: Michael

last: Buszczak

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center


title: Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma

city: Stanford

first: Magdalena

last: Matusiak

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

summary: Anti-PD-1 immunotherapies have transformed cancer treatment, but the determinants of clinical response are largely unknown. We performed CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions of advanced cutaneous T cell lymphoma (CTCL) from 14 patients enrolled in a clinical trial of pembrolizumab therapy. Clinical response was not associated with the frequency of tumor-infiltrating T cell subsets, but rather with striking differences in the spatial organization and functional immune state of the tumor microenvironment (TME). After treatment, pembrolizumab responders had a localized enrichment of tumor and CD4+ T cells, which coincided with immune activation and cytotoxic PD-1+ CD4+ T cells. In contrast, non-responders had a localized enrichment of Tregs pre- and post-treatment, consistent with a persistently immunosuppressed TME and exhausted PD-1+ CD4+ T cells. Integrating these findings by computing the physical distances between PD-1+ CD4+ T cells, tumor cells, and Tregs revealed a spatial biomarker predictive of pembrolizumab response. Finally, the chemokine CXCL13 was upregulated in tumor cells in responders post-treatment, suggesting that chemoattraction of PD-1+ CD4+ T cells towards tumor cells facilitates a positive outcome. Together, these data show that T cell topography reflects the balance of effector and suppressive activity within the TME and predicts clinical response to PD-1 blockade in CTCL.

overall_design: We Laser Capture Microdisected regions containing approximately 1000 cells from FFPE-tissue of CTCL lesions from responders and non responders before and after treatment with pembrolizumab.

first: Darci

last: Phillips

first: Belén

last: Rivero Gutierrez

first: Salil

middle: S

last: Bhate

first: Graham

middle: L

last: Barlow

first: Sizun

last: Jiang

first: Janos

last: Demeter

first: Kimberly

last: Smythe

first: Robert

last: Pierce

first: Steven

last: Fling

first: Nirasha

last: Ramchurren

first: Martin

last: Cheever

first: Yury

last: Goltsev

last: West

last: Khodadoust

first: Youn

last: Kim

first: Christian

last: Schürch

first: Garry

last: Nolan


title: Sequencing of RNA and footprints of wildtype and RpS5b mutant Drosophila ovaries [RNA-seq]

first: Michael

last: Buszczak

summary: Emerging evidence suggests that ribosome heterogeneity may have important functional consequences in the translation of specific mRNAs within different cell types and under various conditions. Ribosome heterogeneity comes in many forms including post-translational modification of ribosome proteins (RPs), lack of specific RPs, and different RP paralogs incorporation. The Drosophila genome encodes for two RPS5 paralogs, RpS5a and RpS5b. While RpS5a is expressed ubiquitously, RpS5b exhibits enriched expression in the reproductive system. Deletion of RpS5b results in female sterility marked by developmental arrest of egg chambers at stages 7-8 and posterior follicle cell (PFC) hyperplasia. Both phenotypes are caused by defects in the germline and over-expression of RpS5a can compensate it. RpS5b mutant display increased rRNA transcription and RP production, accompanied by increased protein synthesis. Loss of RpS5b leads to microtubule-based defects and mislocalization of several factors, leading failure of Notch pathway activation in PFCs. Together, our results indicate that germ cell specific expression of RpS5b promotes proper egg chamber development by regulating both ribosome homeostasis and protein trafficking during mid-oogenesis.

overall_design: RNA-seq and footprint-seq experiment to compare gene expression as well as ribosome distribution between wildtype and the mutant ovaries.

first: Seoyeon

last: Jang


title: Gene expression of Dcir-/- dendritic cells (DCs) after antigen stimuulation

status: Public on Sep 16 2021

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

country: Japan

institute: Tohoku Medicine and Pharmaceutical University

summary: Purpose: DCIR is an inhibitory type of C-type  lectin receptor that regulates DC functions. This study aimed to find the genes that could be regulated through DCIR.  Method: Splenic DCs from WT and Dcir-/- mice were colutured with T cells that express specific TCR for MOG35-55 for 3 days in the presence of MOG peptide. CD11c+ cells were collected by an auto MACS. RNA profiles were generated by deep sequencing, in triplicate, using DNBSEQ-G400.  Results: We detected xxx gense that were higher expression in Dcir-/- DCs, compared with WT DCs,  with a fold change ≥1.5 and p value <0.05.  Conclusion: Our data showed that Dcir deficiency in DCs changed the gene expression pattern, compared to WT DCs, in the coculture system of T cells. DCIR regulates the expression of DC genes that are associated with the functions of DCs.

overall_design: mRNA profiles of WT and Dcir-/- DCs for 3 days culture in the presence of myelin oligodendrocyte glycoprotein (MOG)

first: Kenji

last: Shimizu