title: Study of variants associated with Fuchs corneal endothelial dystrophy cases without expansion of CTG18.1 repeats

status: Public on Apr 30 2023

city: Moscow

first: Liubov

last: Skorodumova

address: Malaya Pirogovskaya st., 1A

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

summary: Fuchs' endothelial corneal dystrophy (FECD) is an inherited bilateral eye disease associated with a reduction in the density and functionality of the corneal endothelium. FECD is a genetic disease with autosomal-dominant inheritance. Genetic variants in the TCF4 gene have the most direct association with sporadic late-onset FECD in Caucasian patients. Association of the intronic single-nucleotide polymorphism (SNP) rs613872 in TCF4 gene with FECD was discovered in the Genome-Wide Association Study (GWAS) performed by Baratz et al. (2010; doi: 10.1056/NEJMoa1007064).The most specific genetic marker of the late-onset FECD also in TCF4 gene -  the CTG18.1 expansion of trinucleotide repeats was discovered by Wieben et al. (2012; doi: 10.1371/journal.pone.0049083). Expansion of the CTG18.1 trinucleotide repeats is detected in approximately 70% of FECD patients of European descent populations and considered to be causal for FECD.  Later the additional bigger GWAS on 1404 FECD cases and 2564 controls was conducted by Afshari with coauthors (2017; doi: 10.1038/ncomms14898).  However, there was no information on the CTG18.1 expansion status available for the whole set of participants. Participants of our set were genotyped for CTG181.1 expansion. We used our set to mark the haplotype associated with the CTG181.1 expanded allele.

overall_design: The overall set included 31 sample. There are two groups divided by condition and the CTG18.1 expansion status: patients with Fuchs endothelial corneal dystrophy without CTG18.1 expansion (n = 26) and control group with CTG18.1 expansion (n = 5). All of the patients from the Fuchs endothelial corneal dystrophy group were Caucasian.

first: L

middle: O

middle: N

last: Iulmetova


title: Comprehensive RNA-Chromatin Interactome Reveals Global and Specific Regulatory Functions by Long Non-Coding RNAs

city: Farmington

first: Oscar

middle: J.

last: Luo

state: CT

address: 10 Discovery Dr

country: USA

institute: The Jackson Laboratory for Genomic Medicine

summary: Long non-coding RNAs (lncRNAs) are an emerging class of regulatory molecules with a potentially broad-range of epigenomic regulatory functions. These functions are likely mediated by lncRNA-chromatin interactions either directly or indirectly through protein intermediates. Thus, comprehensive genomic mapping of all lncRNA targets describing the ‘RNA-chromatin interactome’ are critical for inferring lncRNA functions. Current methodologies for investigating lncRNA-chromatin interaction are one-RNA-at-a-time, and most inferred lncRNA functions were based on indirect “guilt-by-association”. To address these limitations, we devised an unbiased genome-wide strategy to identify all RNA interactions with chromatin by paired-end-tag sequencing (RICh-PET). We comprehensively characterized a human RNA-chromatin interactome and uncovered complex RNA-chromatin networks with many showing long-distance interactions predominantly at gene promoters. Further analysis revealed both global and specific transcriptional regulation by lncRNAs to genes involved in cancer biology, demonstrating the capacity of RICh-PET to concomitantly identify thousands of lncRNAs and chromatin targets in the human genome, thus significantly advancing the understanding of lncRNA functions.

overall_design: Approximately 10^8 HeLa S3 cells were subjected to dual-crosslinking with 1% formaldehyde and 1.5 mM EGS. Cells were harvested and lysed. Complexes of lncRNA-chromatin with protein were sheared to fragments of approximately 500 bp, which then were biotinylated with EZlink Iodoacetyl-PEG2-Biotin (IPB). The streptavidin beads-bound lncRNA-chromatin-protein complexes were subjected to RICh-PET library construction. The DNA fragments present in streptavidin beads-bound chromatin were end-repaired using T4 DNA polymerase. The chromatin complexes were split into two aliquots, followed by the addition of RNA linkers with different barcode sets modified with biotin and containing flanking MmeI restriction sites, RNA linker “R1” (tube1) and RNA linker “R2” (tube2). Linkers to the RNA end were annealed, first-strand cDNA was synthesized, and relative DNA linkers “D1” (tube 1) and DNA linker “D2” (tube 2) were ligated. The two tubes were mixed together for proximity ligation. Chromatin-associated RNA fragments with linkers were subjected to second-strand cDNA synthesis. The cDNA-DNA PETs were extracted from the ligation products by MmeI digestion. Released biotinylated PETs were purified by streptavidin-coated magnetic beads, ligated to adaptors, and scaled up by PCR. Gel-purified amplicons of PET templates were sequenced using an Illumina® HiSeq 2500 with paired-end sequencing.

middle: J

first: Meizhen

last: Zheng

first: Guoliang

last: Li


title: Modulation of lncRNA links endothelial glycocalyx to vascular dysfunction of tyrosine kinase inhibitors.

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Characterization of cell cycle phase specific chromatin accessibility using ATAC seq after FOXD3 depletion

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ATAC seq of inducible FOXD3 KO cells after cell cycle phase sorting to determine impact of FOXD3 loss on chromatin accessibility.

overall_design: FOXD3 depletion was induced by tamoxifen (4HT) addition.

first: Deniz

last: Gökbuget

first: Kevin

middle: X

last: Chen


title: Bidirectional changes in postmitotic H3K27me3 distributions underlie cerebellar granule neuron maturation dynamics [RNA-seq DIV3]

status: Public on Apr 28 2023

city: Durham

first: Anne

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

summary: The functional and transcriptional maturation of neurons is a prolonged process that extends well beyond mitotic exit and terminal fate commitment of progenitors. The differentiation of cerebellar granule neurons (CGNs) in the postnatal mouse cerebellum provides a useful model to identify chromatin mechanisms that orchestrate temporal changes in transcription as postmitotic CGNs mature. Here we report that CGN maturation is associated with dynamic changes in the genomic distribution of histone H3 lysine 27 trimethylation (H3K27me3), a modification best known for its role in repressing alternative fates during cell specification. H3K27me3 is gained rapidly in newly postmitotic CGNs at progenitor-expressed genes that are repressed in neurons. H3K27me3 is lost more gradually at the promoters of a subset of neuronal genes that are transcriptionally induced upon CGN maturation. The loss of H3K27me3 is facilitated by the lysine demethylase KDM6B, and genes that are induced in maturing CGNs show impaired expression in the cerebellum of conditional KDM6B knockout mice. Genes that lose H3K27me3 gain H3K27 acetylation and binding of the pro-maturation ZIC1/2 transcription factors, suggesting that developmental loss of H3K27me3 may be required to permit the onset of transcriptional maturation. Interestingly, pharmacological inhibition of the H3K27 methyltransferase EZH2 in early postmitotic CGNs not only blocked the repression of progenitor genes but also impaired the induction of mature CGN genes. These data show that regulation of H3K27me3 functions in developing postmitotic neurons beyond the period of cell fate commitment to regulate the dynamics of gene expression programs that underlie functional neuronal maturation.

overall_design: Cerebellum treated with DMSO or GSK-126, at DIV3.

first: Vijyendra

last: Ramesh

first: Fang

last: Liu

first: Melyssa

last: Minto

first: Urann

last: Chan


title: Nascent RNA sequencing of FOXD3 KO and WT mouse ESCs

summary: We performed nascent RNA sequencing of inducible FOXD3 KO cells with and without synchronization to determine primary response genes.

overall_design: FOXD3 depletion was induced by tamoxifen (4HT) addition and compared to solvent treated cells or OCT4-depleted cells.


title: Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

summary: Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in these species represents an opportunity to explore underutilized network aggregation approaches that highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets belonging to three different tissue conditions (leaf, berry and ‘all organs’). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied GCNs to study several TF gene families, showing its capacity of detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC and multiple secondary metabolism pathway reactions. Specifically, using TF gene- and pathway-centered network analyses, we ascertained the previously demonstrated role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing novel insights into its role as a potential regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino-acid pathways. This network was validated using DNA Affinity Purification Sequencing data, demonstrating that co-expression networks of activational transcription factors can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.

overall_design: Identification of binding sites for MYBPA1 transcription factor in Vitis vinifera by direct sequencing of affinity purified genomic DNA fragments.

first: José

middle: T

first: Luis

last: Orduña


title: Transcriptome profiling of erf4 seeds in Arabidopsis thaliana

city: Shenzhen

first: Xi

address: No.97in Buxin road, Dapeng district, Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

summary: Seeds establish dormancy for survival under severe conditions and break it for renascence under suitable ones. Here We identify a fate switch constituted by MKK3-MPK7 and ERF4 responsible for the transition of seeds state from dormancy to germination. We show that the MKK3-MPK7 module is activated by dormancy-breaking factors, affects and relies on the expression of some EXPAs to control seed dormancy. Furthermore, we identify a direct downstream substrate of this module, ERF4, which can suppress the expression of these EXPAs by directly binding to the GCC box in their exon region. The activated MKK3-MPK7 module phosphorylates ERF4 and leads to its rapid degradation, thereby releasing its inhibitory effect on the expression of these EXPAs. Our work identifies a signaling chain integrated by protein phosphorylation, degradation, and gene transcription, dependent on which the germination promoters within the embryonic nucleus are sensing and activated by the germination signals from the ambient conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dry and imbibed seeds of wildtype Col-0 and mutant erf4-1.

first: Qiujia

first: Yong

last: Xiang


title: IRE1 inhibitor [RNA-seq]

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

summary: The role of the unfolded protein response (UPR) in the cellular innate response to RSV infection is not fully understood.  To better the genomic targets for the IRE1-XBP1 pathway, RNA seq was conducted on RSV-infected small airway cells in the absence or presence of RSV infection and in the absence or presence of a selective IRE1a RNAse inhibitor.  We identified expression changes in ~3.2K genes; of these, 279 required IRE1 and were enriched in IL-10 signaling and cytokine signaling pathways.  These data indicate that IRE1a-XBP1s regulates genes important in epithelial mesenchymal transition, hexosamine biosynthesis and anti-viral signaling.

overall_design: hSAECs were cultured.  4 replicates were mock infected with sucrose cushion buffer alone.  Another 8 were infected with sucrose-purified RSV Long strain at a multiplicity of infection (MOI) of 1.0 for 24 h prior to harvest.  Four of the RSV infected plates were treated with a selective IRE1α RNAse inhibitor, kinase-inhibiting RNase attenuator (KIRA)-8 added directly to the culture medium at a concentration of 10 microMolar.  Total RNA was extracted and subjected to short read illumina sequencing.

middle: R

first: Dianhua

last: Qiao


title: Differential gene regulation by a synthetic vitamin D receptor ligand and active vitamin D in human cells

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

country: Japan

institute: Research Institute of Innovative Medicine

summary: Vitamin D (VD) exerts a wide variety of biological functions including calcemic activity. VD nutritional status is closely associated with the onset and development of chronic diseases. To develop a VD analog with the desired VD activity but without calcemic activity, we screened synthetic VDR antagonists. We identified DLAM-2b  as a VDR ligand in a competitive VDR binding assay for 1α,25(OH)2 vitamin D3 (1,25D3), and DLAM-2b  showed an antagonistic effect on 1,25D3-induced cell differentiation in HL60 cells. In a luciferase reporter assay in which human VDR was exogenously expressed in cultured COS1 cells, DLAM-2b acted as a transcriptional antagonist. Consistently, DLAM-2b had an antagonistic effect on the 1,25D3-induced expression of a known VD target gene (CYP24A1), and VDR-bound DLAM-2b was recruited to an endogenous VD response element in chromatin in human keratinocytes (HaCaT) and human colon cancer cells (HCT116) endogenously expressing VDR. In an ATAC-seq assay, the effects of 1,25D3 and DLAM-2b on chromatin reorganization were undetectable in HCT116 cells, while the effect of an androgen receptor (AR) antagonist (bicalutamide) was confirmed in prostate cancer cells (LNCaP) expressing endogenous AR. However, whole genome analysis using RNA-seq and ATAC-seq revealed differential gene expression profiles regulated by DLAM-2b versus 1,25D3. The upregulated and downregulated genes only partially overlapped between cells treated with 1,25D3 and those treated with DLAM-2b. Thus, the present findings illustrate a novel VDR ligand with gene regulatory activity differing from that of 1,25D3.

overall_design: Examination of 3 different method in 1 cell types.

first: Miho

last: Iwaki

first: Yoshiaki

last: Kanemoto

first: Kazuo

last: Nagasawa

first: Shigeaki

last: Kato


title: Twist1 regulates stem cell properties in mesenchymal stem cells

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

summary: To investigate the function TWIST1 in the regulation of stemness in mesenchymal stem cell, we established human mesenchymal stem cell in TWIST1-overexpression.

overall_design: Comparative gene expression profile analysis of NET-CAGE seq data for human mesenchymal stem cell and its TWIST1 overexpression cell line.

first: Kensuke

last: Toriumi

first: Tatsufumi

last: Mori

first: Joe

last: Hasei

first: Takeshi

last: Teramura


title: RNA seq to determine differential gene expression in pgph-2 oe C.elegans animals and the subset of HLH-30-dependent genes on normal growth and excess glucose conditions.

city: Tucson

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

summary: Metabolic stress caused by excess nutrients accelerates aging. We recently demonstrated that the newly-discovered enzyme glycerol-3-phosphate phosphatase (G3PP; gene Pgp), which operates an evolutionarily conserved glycerol shunt that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol, counters metabolic stress and promotes healthy aging in C. elegans. However, the mechanism whereby G3PP activation extends healthspan and lifespan, particularly under glucotoxicity, remained unknown. We demonstrated that G3PP (PGPH-2) overexpression activates three key longevity factors, AMPK, the TFEB homolog HLH-30, and autophagy, and is an attractive target for age-related metabolic disorders linked to excess nutrients. This transcriptomics analysis was designed to determine genes that are differentially regulated in pgph-2 oe animals in comparison to wild-type animals on normal and excess glucose conditions. To determine the role of HLH-30 in the regulation of gene expression, we also used pgph-2 oe; hlh-30 and hlh-30 mutant animals and found a signature mediated by pgph-2 oe and HLH-30-dependent.

overall_design: Synchronized young adult WT, pgph-2 o/e, pgph-2 o/e; hlh-30 and hlh-30 animals and grown on normal growth medium or plates supplemented with 2% glucose are harvested. Total RNA is extracted using trizol and purified with RNA purification kit and subjected to seq analysis.

first: Elite

last: Possik

first: Marc

last: Prentki


title: Transcriptional profiling of regional intestinal tissue from mice with and without Apc deficiency

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: A profile of gene expression differences along the length of the mouse intestine, in the presence and absence of functional Apc.

overall_design: Expression data from intestine at the noted locations with and without Apc deficiency.

first: Michael

last: Hodder

first: Owen

last: Sansom


title: HER2∆16 Engages ENPP1 To Promote an Immune Cold Microenvironment in Breast Cancer [tumor]

city: Montreal

first: Sherif

middle: Samer

last: Attalla

state: Quebec

address: 1160 Ave. Pine W

department: Goodman Cancer Institute

country: Canada

institute: McGill

summary: The tumor immune microenvironment (TIME) is a critical determinant of therapeutic response. However, the mechanisms regulating its modulation are not fully understood. HER2D16, an oncogenic splice variant of the human epidermal growth factor receptor (HER2), has been implicated in breast cancer and other tumor types as a driver of tumorigenesis and metastasis. Nevertheless, the underlying mechanisms of HER2Δ16-mediated oncogenicity remain poorly understood. Here, we show that HER2∆16 expression is not exclusive to the clinically HER2+ subtype and is associated with a poor clinical outcome in breast cancer. To understand how HER2 variants modulate the tumor microenvironment, we generated transgenic mouse models expressing either proto-oncogenic HER2 or HER2D16 in the mammary epithelium. We found that HER2∆16 tumors are immune cold, characterized by low immune infiltrate and an altered cytokine profile. Using an epithelial cell surface proteomic approach, we identified ENPP1 as a functional regulator of the immune cold microenvironment. We generated a knock-in model of HER2Δ16 under the endogenous promoter to understand the role of ENPP1 in aggressive HER2+ breast cancer. Knockdown of ENPP1 in HER2Δ16-derived tumor cells resulted in decreased tumor growth that was correlated with increased T-cell infiltration. These findings suggest that HER2Δ16-dependent ENPP1 activation is associated with aggressive HER2+ breast cancer through its immune modulatory function. Our study provides a better understanding of the mechanisms underlying HER2Δ16-mediated oncogenicity and highlights ENPP1 as a potential therapeutic target in aggressive HER2+ breast cancer.

overall_design: End point tumors harvested and flash frozen. RNA was extracted and sequenced

first: Attalla

last: Sherif

first: Boucher

last: Jonathan

first: Proud

last: Hailey

first: Taifour

last: Tarek

first: Zuo

last: Dongmei

first: Sangiun-Gendreau

last: Virginie

first: Ling

last: Chen

first: Johnson

last: Gabriella

first: Li

last: Vincent

first: Luo

last: Robin

first: Kuasne

last: Hellen

first: Papavasiliou

last: Vasilios

first: Walsh

last: Logan

first: Barok

last: Mark

first: Joensuu

last: Heikki

first: Park

last: Morag

first: Roux

last: Philippe

first: Muller

last: William


title: Modulation of lncRNA links endothelial glycocalyx to vascular dysfunction of tyrosine kinase inhibitors [dataset 2]

first: Jordan

last: Jousma

summary: Aims: Novel cancer therapies leading to increased survivorship of cancer patients have been negated by a concomitant rise in cancer therapies-related cardiovascular toxicities. Sunitinib, a first line multi receptor tyrosine kinase inhibitor (TKI), has been reported to cause vascular dysfunction although the initiating mechanisms contributing to this side effect remain unknown. Long non-coding RNAs (lncRNAs) are emerging regulators of biological processes in endothelial cells (ECs); however, their roles in cancer therapies-related vascular toxicities remain underexplored.    Methods and Results: We performed lncRNA expression profiling to identify potential lncRNAs that are dysregulated in human induced pluripotent stem cells-derived ECs (iPSC-ECs) treated with sunitinib. We show that the lncRNA hyaluronan synthase 2 antisense 1 (HAS2-AS1) is significantly diminished in sunitinib-treated iPSC-ECs. Sunitinib was found to downregulate HAS2-AS1 by an epigenetic mechanism involving hypermethylation. Depletion of HAS2-AS1 recapitulated sunitinib-induced detrimental effects on iPSC-ECs, whereas CRISPR-mediated activation of HAS2-AS1 reversed sunitinib-induced dysfunction. We confirm that HAS2-AS1 stabilizes the expression of its sense gene HAS2 via an RNA/mRNA heteroduplex formation. Knockdown of HAS2-AS1 led to reduced synthesis of hyaluronic acid (HA) and upregulation of ADAMTS5, an enzyme involved in extracellular matrix degradation, resulting in disruption of the endothelial glycocalyx which is critical for ECs. In vivo, sunitinib-treated mice showed reduced coronary flow reserve, accompanied by a reduction in has2os and degradation of the endothelial glycocalyx. Finally, we identify that treatment with high molecular-weight HA can prevent the deleterious effects of sunitinib both in vitro and in vivo by preserving the endothelial glycocalyx.    Conclusions: Our findings highlight the importance of lncRNA-mediated regulation of the endothelial glycocalyx as an important determinant of sunitinib-induced vascular toxicity and reveal potential novel therapeutic avenues to attenuate sunitinib-induced vascular dysfunction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three lines of hiPSC-EC  treated with either siControl or siHAS2-AS1

first: Sarath Babu

last: Nukala

first: Sang-Ging

last: Ong


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [4C]

status: Public on Apr 29 2023

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops. In addition to insulation of euchromatin from heterochromatin, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in human cancer, resulting in deregulation of global gene expression by altered methylated genomic states. In contrast to these studies, we here describe that inactivation of CTCF can drives subtle and local genomic effects that elevates oncogene expression levels from driving chromosomal rearrangements. For T cell acute lymphoblastic leukemia (T-ALL), heterozygous CTCF deletions or inactivating mutations are predominantly found in nearly 50 percent of t(5;14)(q35;q32.2) rearranged patients that couples the TLX3 oncogene in the vicinity of the BCL11B enhancer. This unique entity has been associated with γδ-lineage development. Functional CTCF loss results in diminished expression of the αβ-lineage commitment factor BCL11B from the non-rearranged allele, but unexpectedly drives higher levels of the TLX3 oncogene from the translocated allele. In line, Ctcf conditional knockout mice have reduced numbers of αβ T cells but increased numbers of γδ T cells, a phenotype identical to that of Bcl11b knockout mice and implying that CTCF is directly involved in the regulation of the BCL11B enhancer. We demonstrate that most TLX3-rearranged patients with heterozygous CTCF aberrations preserved single intervening CTCF bindings sites in the translocation breakpoint areas located in between the BCL11B enhancer and the TLX3 oncogene. These intervening CTCF sites insulate TLX3 from the enhancer by forming competitive loops with TLX3 regulatory sequences. Using reverse genetics, we provide evidence that heterozygous inactivation of CTCF diminishes competitive loop formation in favor of high-affinity TLX3 promoter loops to BCL11B enhancer sequences formed among multiple convergent CTCF binding sites. This boosts oncogene expression levels and leukemia burden in T-ALL patients.

overall_design: 4C experiment where interacting-loops of BCL11B and TLX3 has been studied in bulk and single cell clones from HPB-ALL have been studied

first: Jules

middle: P

last: Meijerink

first: Willem

middle: K

last: Smits

first: Carlo

last: Vermeulen


title: Characterization of active chromatin marks by CUT&Tag after FOXD3 depletion

first: Robert

last: Blelloch

summary: We performed CUT&Tag of inducible FOXD3 KO cells with or without cell cycle phase sorting to determine impact of FOXD3 loss of active chromatin marks.

overall_design: FOXD3 depletion was induced by tamoxifen (4HT) addition and compared to solvent treated cells.

first: Deniz

last: Gökbuget

first: Ryan

middle: M

last: Boileau


title: RNA-Seq data for murine BM Tx transduced with different sgRNA combinations [RNA-seq]

city: Hannover

first: Dorit

last: Borchert

address: Carl-Neuberg-Str. 1

department: Pediatric Hematology and Oncology

country: Germany

institute: Hannover Medical School

summary: To elucidate the mutational interplay of Ezh2, Runx1 and Bcor we transplanted mice transplanted with LSKs transduced with sgRNAs in all combinations and observed them for development of myeloid leukemia and subsequent expression analysis of whole bone marrow by RNA-Seq.

overall_design: LSK cells expressing SpCas9 were transduced with sgRNA combinations and transplanted into irradiated C57Bl/6J mice. BM was harvested after development of a leukemia or after 6 months and used for RNA extraction.

first: Dirk

last: Heckl


title: Chemically synthesized guide RNAs can direct CRISPR-CasRx cleavage of circRNAs with high efficiency and specificity

city: AARHUS C

first: Karim

last: Rahimi

address: C.F. Møllers Allé 3

country: Denmark

institute: Aarhus University

summary: In this study, we demonstrate that CRISPR/RfxCas13d (CasRx)-mediated circRNA depletion is, for the circRNAs studied, more efficient than Argonaute 2-dependent short hairpin RNA (agoshRNA)-mediated depletion and with fewer off-target effects on the linear host RNAs. We also designed and optimally used synthetic guide RNAs (syn-gRNAs) in combination with CasRx to efficienctly deplete circRNA ciRS-7. None of the knockdown strategies tested (pre-gRNA, gRNA, syn-gRNA and agoshRNA) showed any significant off-target effects at the transcriptomics level. Differential expression analysis was performed for each KD setup versus non-targeting control (three biological replicates of each). In conclusion, CasRx-mediated circRNA knockdown using both vector-based and syn-gRNA strategies is a useful tool for future studies on circRNA functions.

overall_design: Off-targeting assay of four different KD approaches (pre-gRNA, gRNA, syn-gRNA, and agoshRNA) upon ciRS-7 depletion in SH-SY5Y cells used here could lead to more general off-target effects.  We subjected samples from each ciRS-7 KD and the corresponding NTC controls   (pre-gRNA, gRNA, syn-gRNA, and agoshRNA) to mRNA sequencing, generating 30 to 35 million reads per sample. Differential expression analysis was performed for each KD setup versus NTC using DESeq2.

first: Maria

middle: S

last: Andersen

first: Sabine

last: Seeler

first: Thomas

middle: B

last: Hansen

first: Jørgen

last: Kjems


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [CTCF_ChIPseq]

overall_design: In order to observe if there is more or less looping when CCCTC-binding factor (CTCF) is deleted within T-ALL patients, ChIPseq is performed. CTCF and Cohesin (SMC3) were used to detect binding positions for patients and HPB-ALL. HPB-ALL was used to re-introduce CTCF to restore wild type status


title: Transcriptom profiling of a novel CD8+ T-cell subset with a polyamine metabolism signature (Tpam)  during TCR-mediated ex vivo activation (bulk RNA-seq)

city: Prague

first: Veronika

last: Cimermanova

address: Videnska 1083

department: lab of adaptive immunity

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: The aim of this study was to investigate transcriptomic changes during T-cell activation of a novel T-cell subset (Tpam) in a comparison to conventional CD8+ T cells

overall_design: Cells were isolated from spleens and lymph nodes of C57BL/6J mice. Tpam and conventional CD8+ T cells were sorted (Aria) out of CD8+ T-cell pool, based on CD137(41BB) marker, which defined Tpam cells (41BB+) and conventional CD8+ T cells (41BB-). Sorted cells were either directly submitted for RNA extraction (for samples before activation, time 0h) or were ex vivo activated by Dynabeads Mouse T-Activator CD3/CD28 for two time points: time 24h and time 72h, for TCR post-activation samples, followed by the RNA extraction. Samples are in biological triplicates. In total, 18 samples were sequenced.

first: Ondrej

last: Stepanek

last: Niederlova


title: Effect of PI3Kgamma inhibition on inflammation in a mouse model of COVID-19

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

summary: SARS-CoV-2 infections induce aberrant pulmonary and systemic inflammation, vascular leak, coagulation and fatal organ damage. To identify therapeutic strategies to suppress COVID-19-associated inflammation, we sequenced lung tissue from sham infected mice and mice infected with SARS-CoV-2 that were treated with the cancer therapeutic IPI-549 (eganelisib) or vehicle. IPI-549 suppressed signatuers of pulmonary inflammation and reduced signatures of lung damage. These studies demonstrate the essential role of myeloid cells and PI3Kγ in SARS-CoV-2 inflammatory disease and support the use of myeloid cell inhibitors such as IPI-549 to suppress inflammation and promote survival in pulmonary infections like SARS-CoV-2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of mice infected with Sars-Cov-2 and treated with either Vehicle or IPI549 (clinical inhibitor of PI3Kγ)

last: Shepard

first: Anghesom

last: Ghebremedhin


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [Array CGH]

first: Rico

last: Hagelaar

type: Genome variation profiling by genome tiling array

overall_design: Copy number variance was checked using 2x 400k, 105K and 44K arrayCGH microarrays for 94 patient samples

first: Jules

last: Meijerink

last: Smits

last: Vermeulen


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [BeadChip Methylation]

overall_design: Genome wide DNA methylation of CTCF wild type vs CTCF deleted/mutated patients.

first: Willem

first: Carlo


title: HER2∆16 Engages ENPP1 To Promote an Immune Cold Microenvironment in Breast Cancer [cell line]

first: Sherif

last: Attalla

overall_design: RNA extracted from cultured cell lines

first: Attalla

last: Sherif

first: Boucher

last: Jonathan

first: Proud

last: Hailey

first: Taifour

last: Tarek

first: Zuo

last: Dongmei

first: Sangiun-Gendreau

last: Virginie

first: Ling

last: Chen

first: Johnson

last: Gabriella

first: Li

last: Vincent

first: Luo

last: Robin

first: Kuasne

last: Hellen

first: Papavasiliou

last: Vasilios

first: Walsh

last: Logan

first: Barok

last: Mark

first: Joensuu

last: Heikki

first: Park

last: Morag

first: Roux

last: Philippe

first: Muller

last: William


title: RIPK3 negatively regulates the (CXCL4+TLR8)-induced IFN response while promoting NLRP3 inflammasome activation in human monocytes

city: New York

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: To investigate the function of RIPK3 in regulation of IFN response and inflammatory response in human monocytes stimulated with CXCL4 and TLR8, We blocks (CXCL4 + TLR8)-induced pyroptosis and RIPK3 activation using necrosulfonamide (NSA, 5 µM) and GSK'872 (10 µM) and measure gene expression genome-wide with RNA-seq.

overall_design: Human monocytes was pretreated with NSA itself or NSA+GSK'872 and then stimulated with CXCL4 (10 µg)and TLR8 ligand ORN8L (20 µg) for 6 h.

first: Chao

last: Yang

first: Lionel

last: Ivashkiv


title: Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

first: Rico

last: Hagelaar

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

overall_design: Refer to individual Series


title: The OGT/HIF-2α axis promotes the progression of clear cell renal cell carcinoma and its targetable vulnerability to ferroptosis

city: Shanghai

first: Zhou

state: Shanghai

address: 270 Donan Road

institute: Fudan University

summary: O-GlcNAc transferase (OGT) has been reported to participate in the development of various cancers, but its role in clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, we found that OGT was upregulated in ccRCC compared with paired nontumor renal tissues and was associated with worse survival. Moreover, OGT promoted the proliferation, clone formation, and invasive abilities of VHL-mutated ccRCC cells. Mechanistically, OGT promoted the expression of hypoxia-inducible factor-2α (HIF-2α) (the main driver of the clear cell phenotype) by repressing ubiquitin‒proteasome system-mediated degradation. Interestingly, the OGT/HIF-2α axis confers ccRCC sensitivity to ferroptosis, rendering it vulnerable. In conclusion, OGT promotes the progression of VHL-mutated ccRCC by inhibiting the degradation of HIF-2α. On the other hand, the OGT/HIF-2α axis renders ccRCC vulnerable to ferroptosis, suggesting that ferroptosis inducers are a promising therapy for patients with upregulated OGT and mutated VHL ccRCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for OGT overexpressed ccRCC cells.


title: Differential expression profiles and functional prediction of tRNA-derived small RNAs in plasma of patients with aortic dissection during deep hypothermic circulatory arrest

city: wenhzou

first: liang

last: zhang

address: wenhzou

institute: wenzhou medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: The purpose of this study was to detect the expression profile of tsRNA during deep hypothermia circulatory arrest, and to find possible regulatory factors according to the changes in its expression level, in the hope of providing an effective organ protection strategy for this process.Three blood samples were collected from a central veins line into ethylenediaminetetraacetic acid (EDTA) tubes as follows: T1 (before starting circulatory arrest), T2 (15 min after initiation of DHCA), T3 (after declamping the left common carotid artery and before rewarming). A total of 286 commonly expressed tsRNAs were identified in the T1 and T2 groups, 68 tsRNAs specifically expressed in the T1 group, and 44 tsRNAs specifically expressed in the T2 group. A total of 290 commonly expressed tsRNAs were identified in the T2 and T3 groups, 64 tsRNAs specifically expressed in the T2 group, and 43 tsRNAs specifically expressed in the T3 group. Next, four tsRNAs were selected to be verified by qRT-PCR. In summary, this study innovatively proposed the correlation between the deep hypothermic circulatory arrest process and the expression profile of tsRNA, and evaluated the expression level and regulation mode of tsRNA. A preliminary exploration of its potential biological role in the process of deep hypothermic circulatory arrest has been carried out, which can provide a better basis and a more comprehensive explanation for the organ protection mechanism of deep hypothermic circulatory arrest. And in further research, we are expected to achieve targeted protection of organs by overexpressing or inhibiting the corresponding tsRNA.

overall_design: Detection of human plasma samples at different time points during deep hypothermia circulatory arrest

first: Liang

last: Zhang

first: Han

last: Xu

first: Jue

last: Wang


title: Transcriptional profiling of Liver tissue from mice with bcatenin and Myc mutations

first: Kathryn

last: Gilroy

summary: The effect of combinations Apc, Bcatenin and Myc mutation on mouse liver was examined with RNAseq at two time points.

overall_design: Expression data from liver with the noted mutations at the noted time points.

first: Alexander

last: Raven

first: Owen

last: Sansom


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest [RNA-seq]

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identified 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.

overall_design: RNA expression profiling of cranial neural crest cell subpopulations (PA2 and PA3 at E10.5, Pinna at E12.5 and E14.5) of wildtype and HIRE1 knockout genotypes using RNA-seq.

first: Sandra

last: Keßler

first: Maryline

last: Minoux

first: Onkar

last: Joshi

first: Yousra

last: Ben Zouari

first: Sebastien

last: Ducret

first: Fiona

last: Ross

first: Nathalie

last: Vilain

first: Adwait

last: Salvi

first: Joachim

last: Wolff

first: Hubertus

last: Kohler

first: Michael

last: Stadler

last: Rijli


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest [PCHi-C]

overall_design: promoter capture Hi-C for different subpopulations of cranial neural crest cells at E10.5, E12.5 and E14.5


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest  [ATAC-seq]

overall_design: Analysis of chromatin accessibility in PA2 and Pinna cells at embryonic timepoints E10.5, E12.5 and E14.5


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest [ChIP-seq]

overall_design: Chromatin ImmunoPrecipitation DNA-Sequencing for the histone modifications H3K4me2, H3K27ac and H3K27me3 and for CTCF in murine E10.5, E12.5 and E14.5 cranial neural crest cells


title: Long-term exposure to decabromodiphenyl ether promotes the proliferation and tumorigenesis of papillary thyroid carcinoma by inhibiting TRß

city: Jinan

first: Xinpei

last: Wang

address: #44 Wenhua West Road

institute: Shandong University

summary: To further decipher the mechanism by which long-term and environment dose exposure to BDE209 promotes thyroid cancer, we performed RNA-seq analysis in Nthy-ori 3-1 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nthy-ori 3-1 cells between the BDE209 group (treated with 2.5 μM BDE209 for 27 days) and the control group (treated with the same volume of DMSO for 27 days).

first: Zhiyan

last: Liu


title: Transcriptomic regulations underlying pair-bond formation and maintenance in the socially monogamous male and female prairie vole

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

summary:
Background: The ability to form enduring social bonds is characteristic of human nature and as a result, impairments in social affiliation are central features of severe neuropsychiatric disorders including autism spectrum disorders and schizophrenia. Due to its ability to form long-term pair-bonds, the socially monogamous prairie vole (Microtus ochrogaster) has emerged as an excellent model to study the neurobiology of social attachment. Despite the enduring nature of the bond, however, surprisingly few genes have been implicated in the pair-bonding process in either sex.
Results: Using RNA-sequencing, we aimed at identifying the transcriptomic regulations in the nucleus accumbens (NAc) underlying the formation and maintenance of a pair-bond in male and female prairie voles and found sex-specific response patterns despite similar behavioral indicators of pair-bond establishment. Indeed, 24 hrs of cohabitation with an opposite-sex partner induced widespread transcriptomic changes that remained sustained to some extent in females after 3 weeks, but returned to baseline before a second set of regulations in males. This led to a highly sexually-biased NAc transcriptome in the later phase of the bond related to processes such as neurotransmission, protein turnover, and DNA transcription. In particular, we found sex-specific alterations of mitochondrial dynamics following cohabitation, with a shift towards fission in males.
Conclusions: In addition to identifying the genes, networks, and pathways involved in the pair-bonding process in the NAc, our work illustrates the vast extent of sex differences in the molecular mechanisms underlying pair-bonding in prairie voles, and paves the way to further our understanding of the complex social bonding process.

overall_design: A total of 46 prairie voles were used: 16 were paired with a same-sex littermate for 3 weeks (6 males, 10 females), or with an opposite-sex partner for 24 hrs (6 males, 10 female) or 3 weeks (5 males, 6 females).

first: Florian

last: Duclot

first: Lindsay

last: Sailer

first: Panagiotis

last: Koutakis

first: Zuoxin


title: ChIP-seq of in vitro differentiated naïve and Th9 cells

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary:
To investigate changes in chromatin accessibility over time, we differentiated Th9 cells in vitro from naïve T cells from human and murine sources, and followed them over an extended time course, during which they gained and then lost capacity for IL-9 production
We then performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me1, K3K4me3, and H3K27Ac in cells from 2 different human donors and from 2 mice at 4 time points.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Peaks for various histone marks normalized to input

first: Aran

last: Son


title: RNA-seq of in vitro differentiated naïve and Th9 cells

summary:
To investigate changes in gene expression over time, we differentiated Th9 cells in vitro from naïve T cells from human and murine sources, and followed them over an extended time course, during which they gained and then lost capacity for IL-9 production
We then performed gene expression profiling analysis using data obtained from RNA-seq in cells from 2 different human donors and from 2 mice at 4 time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for d0 (naïve), d3, d4. and d8 Th9 cells (mouse) or d0 (naïve), d5, d8, and d15 Th9 cells (human)


title: Sex modulates genome regulatory system in heart failure in humans

status: Public on Apr 27 2023

city: Chicago

first: Igor

last: Efimov

address: 303 E Superior St

institute: Northwestern University

summary: Heart failure and other cardiomyopathies have distinct presentations in males versus females that are often overlooked, leading to ineffective treatment, and contributing to the growing mortality from heart diseases. Understanding the differences in the pathogenesis of heart disease in males and females can guide early diagnostics and sex-specific therapy. Thus, there is a pressing need to investigate the sex-specificity of promoter and enhancer activity in the pathogenesis of heart failure. Here, using cap analysis of gene expression we characterize the sex-specific activity of transcriptional regulatory elements in 17 male and 14 female healthy and failing hearts. We show that differentially expressed transcribed regulatory elements between two sexes are spread throughout the entire genome in healthy and failing atria and ventricles, and are related to immune system, metabolic, cardiomyocyte function, and developmental pathways. Moreover, we found 720 genes with sex-dependent promoter switching of which 40 switched dominant promoters. Among those was CREM, a transcription factor, with a short repressive dominant isoform exclusive for males. CREM is related to extensive β-adrenergic receptor stimulation that leads to elevated arrhythmic activity, hypertrophy and heart dysfunction. Furthermore, we identified metabolic pathways being more responsible for female aging and developmental pathways for male aging. We also showed sex-specific aging patterns, such as age-specific promoter usage of 1,100 genes that behaved differently depending on sex, including UCKL1 and HAND2 linked to uridine metabolism and cardiac development, respectively.

overall_design: RNA-Seq of healthy human donor heart samples from left atria, right atria, left ventricles, and right ventricles.

first: Anna

last: Gams

first: Ruslan

last: Deviatiiarov

first: Ivan

middle: V

last: Kulakovskiy

first: Andrey

last: Buyan

first: Ramesh

last: Singh

first: Palak

last: Shah

first: Tatiana

last: Tatarinova

first: Oleg

last: Gusev


title: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [cell mixtures scRNA-seq]

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

summary: RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-Seq and snRNA-Seq, scnRNA-Seq for short), can help characterize the composition of tissues and reveal cells that influence key healthy and disease functions. However, the use of these technologies is challenging because of their relatively high costs and exacting sample collection requirements. Computational deconvolution methods that infer the composition of RNA-Seq-profiled samples using scnRNA-Seq-characterized cell types can expand the benefit of these technologies, but their effectiveness remains controversial. We produced the first systematic evaluation of deconvolution methods on datasets with either known compositions or based on concurrent RNA-Seq and scnRNA-Seq profiles. Our analyses revealed biases that are common to scnRNA-Seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-Seq and scnRNA-Seq profiles can help improve the accuracy of both scnRNA-Seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), combined RNA-Seq transformation and a dampened weighted least squares deconvolution approach to consistently outperform other methods in predicting the composition of cell mixtures and tissue samples. Moreover, our analysis suggested that only SQUID could identify outcomes-predictive cancer cell subtypes in pediatric acute myeloid leukemia and neuroblastoma datasets.

overall_design: We developed a solid tumor model that includes multiple solid-tumor cell types, immune cells, and lower-abundance stem cells. Following this model, we established in vitro cell mixtures that are composed of varying proportions of cells from 3 breast cancer lines (T47D, BT474, MCF7), monocytes (Thp1), lymphocytes (Jurkat), and stem cells (hMSC). Mixture composition was recorded based on input cell counts. Cells each 6 mixture were profiled by single-cell RNA-seq (n=6).


title: Alteration of gene expressions in RCC cell lines co-cultured with HGECs with down-regulated INSR

city: Tokushima city

first: Kei

last: Daizumoto

address: 3-18-15, Kuramoto-cho

institute: Tokushima University Graduate School of Biomedical Sciences.

summary: RCC cell lines (786-O cell line and Caki-1 cell line)were co-cultured with human renal glomerular endothelial cells (HGECs) treated with si-RNA of INSR (HGEC-siINSR). Gene expression alteration was analyzed using microarray.

overall_design: 786-O cell line and Caki-1 cell line were co-cultured with HGECs with down-regulated INSR. Small interfering RNA oligonucleotides were used to knock down INSR in HGEC. Non-silencing RNA duplex was used as a negative control. Transfection with 10 nM of small interfering RNA of INSR to HGECs was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) with the forward transfection method. Seventy-two hours after transfection, HGECs were seeded into 6-well ThinCert™ cell culture inserts, and 2.5 ml of Caki-1 cell suspension containing 8x104 cells/ml in CS-C Complete Medium was placed into a 6-well plate. The inserts were placed in each well of the 6-well plate, and co-cultures were maintained for 24 h.

first: Hideaki

last: Horikawa

first: Masayuki

last: Takahashi


title: ATAC-seq, ChIP-seq and RNA-seq of in vitro differentiated naïve, Th1, and Th9 cells


title: ATAC-seq of in vitro differentiated naïve, Th1, and Th9 cells

summary: To investigate changes in chromatin accessibility over time, we differentiated Th9 cells in vitro from naïve T cells from human and murine sources, and followed them over an extended time course, during which they gained and then lost capacity for IL-9 production

overall_design:
We then performed Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) on cells from 2 different human donors and from 2 mice at 4 time points. In a separate experiments, we performed ATAC-seq on in vitro differentiated Th1 cells from human donors, which were sorted based on CXCR3 and CCR4 expression
Peaks called relative to background, using MACS1.4


title: Transcriptional profiling of multiple tissues from mice with and without Apc deficiency

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: The effect of whole body Apc deficiency on multiple mouse tissues was examined with RNAseq.

overall_design: Expression data from the noted tissues with and without Apc deficiency.

first: Alexander

last: Raven

first: Owen

last: Sansom


title: Uridylation is a genomic feature of encapsidated GFLV RNAs [Purified virions]

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary: Using 3' RACE-seq method, we measured uridylation frequencies of GFLV RNAs (K30 and B844 isolates) for total RNA of C. quinoa infected plants or for purified RNA from GFLV virions.

overall_design: 3’ RACE-seq method was used to measure poly(A) tail sizes and analyze uridylation levels. This protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

first: Anne-Caroline

last: Joly

first: Hélène

last: Zuber


title: RNA uridylation percentages for virus of the Secoviridae family

summary: Using 3' RACE-seq method, we analyzed global 3’ terminal RNA uridylation profiles of Secovirus RNAs.

sample_organism:
Nicotiana benthamiana
Vitis vinifera
Chenopodium quinoa

first: Shahinez

last: Garcia


title: Expression data of Drosophila malignant tumors of distinct genetic orgins

city: new haven

first: Tian

last: Xu

state: CONNECTICUT

address: 295 congress ave

department: Genetics

institute: Yale school of medicine

summary:
To explore whether Drosophila malignant tumors share a common molecular basis for their malignancy, we examined common gene expression changes associated with these tumors.
We performed a complementary DNA (cDNA) microarray experiment to systematically investigate gene expression profiles of tumors derived from four different genotypes (RasV12scrib-, RasV12baz-, RasV12cdc42- and RafGOFscrib-) in comparison to those of eye-antennal discs containing wild-type clones.

overall_design: Large Drosophila malignant tumors were induced from clones of cells in the larval eye-antenna imaginal discs by defined genetic mutations (RasV12scrib-, RasV12baz-, RasV12cdc42- and RafGOFscrib-). Tumors and wild-type controls from 3rd instar larvae were collected for RNA extraction and hybridization on customized microarrays. Biological replicates: 4 replicates per genotype.

first: Wu

last: Ming

first: Dong

last: Yongli

first: Xu

last: Tian


title: Propranolol inhibit tumor growth through reducing T cell exhaustion

city: Nanjing

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

institute: China Pharmaceutical University

summary: Recently, targeting or reinvigorating exhausted T cells have become the focus of cancer immunotherapy. Propranolol, a non-selection β1 and β2 adrenergic receptor blocker, or in combination with other drug, can inhibit the development of various tumors. Additionally, β2-adrenergic receptor (ADRB2) signaling suppresses the effector function of CD8+ T cell. However, whether propranolol plays an anti-tumor role by directly inhibiting T cell exhaustion remains unclear. In this study, we found that Propranolol significantly inhibited the development of AOM/DSS-induced colorectal cancer, and reduced the exhaustion of infiltrating T cell in colorectal cancer tissues. The anti-tumor effect of propranolol was further determined by CT26, B16F10, and MC38 subcutaneous tumor models in vivo. Cell viability analysis showed that Propranolol concentration below 40 μM had no effect on the viability of CT26 colorectal cancer cells. We also found that propranolol treatment did not inhibit the growth of tumors in BALB/c nude mice. The above results indicated that Propranolol relied on T cells to exert its anti-tumor effects. Bioinformatics analysis highlighted that ADRB2 was positive correlated with T cell exhaustion signature in colon adenocarcinoma, pancreatic adenocarcinoma, testicular germ cell tumors, and glioblastoma multiforme patients using the website of GEPIA. Accordingly, Propranolol directly inhibited T cells exhaustion, and increased IFN-γ secretion of CD4+ and CD8+ T cells in vitro. Collectively, propranolol plays anti-tumor role by directly inhibiting T cell exhaustion.

overall_design: CT26 subcutaneous tumors mRNA profiles of Control and Propranolol tretment mice were generated by deep sequencing, in duplicate.

first: Yong

last: yang

first: Yanting

last: Lin


title: Serum miRNA as Potential Biomarkers for ovarian cancer

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Serum samples were obtained from patients with ovarian cancer (OC; n=64) and noncancerous control (n=4) for microarray. We found that four miRNAs were significantly high-expression level in OC relative to the controls.

overall_design: The aim of this study was to examine whether serum microRNAs is useful as a biomarker for ovarian cancer (OC).

first: Takuma

last: Fujii

first: Rina

last: Kawahara


title: Uridylation is a genomic feature of encapsidated GFLV RNAs [GFLV]

summary: To determine whether the single 3’ terminal uridine of the positive strand is encoded and whether this feature is shared by the negative strand, we attempted to map the 5’ and 3’ ends of the minus strand for both GFLV RNA1 and RNA2.

overall_design: Using 3' and 5' RACE-seq method, we sequenced 3’ and 5' extremities of plus and minus strands of GFLV RNAs (GT isolate).


title: Long-Term Persistence of Fetal Hepatocyte Gene Expression and Histone Modification Signatures Following Transplantation to Adult Liver

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: Introduction: Hepatic cell transplantation offers an alternative to orthotopic liver transplantation for chronic liver disease. We previously demonstrated that fetal rat hepatocytes durably persist and proliferate when transplanted to an injured adult liver. To identify mechanisms underlying fetal hepatocyte repopulation, we profiled gene expression and histone post-translational modifications (hPTM) of post-transplantation fetal colonies and surrounding liver, as well as those of primary fetal and adult hepatocytes.   Methods: Using the DPPIV rat model, we transplanted and traced fetal hepatocytes into adult hosts. At 10 months after transplantation, we used laser capture microscopy to isolate fetal-derived colonies and surrounding adult host tissue. RNA and histones were extracted from laser captured tissue and isolated hepatocytes for RNA-seq and quantitation of hPTM.   Results: Principal component analysis of RNA-seq results discriminated between fetal-derived colonies and surrounding adult host tissue. We identified 953 differentially expressed genes, many of which were significantly overexpressed in pre-transplant fetal hepatocytes relative to adult hepatocytes. This gene set included a disproportionate number of genes encoding ion transmembrane transporters. Proteomic analyses identified 13 distinct marks on Histone H3 whose relative abundance differed significantly between fetal-derived colonies and adult host tissue. Of these 13 marks, 11 had abundance profiles similar to those of fetal hepatocytes.  Conclusions: A distinct gene expression and epigenetic profile seen in pre-transplant fetal cells is retained for at least 10 months following transplantation. Ontological and pathway analysis indicates activation of ion transporters, which may relate to the growth advantage of transplanted fetal cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pre-transplant sorted fetal and adult hepatocytes, as well as post-transplant fetal-derived colony tissue and surrounding adult host tissue.

first: Anders

middle: W

last: Ohman

first: Megan

middle: G

last: Heaney

first: Joan

last: Boylan

first: John

middle: C

last: Santiago

first: Juliette

middle: A

last: Morris

first: Jeannie

last: Camarillo

first: Neil

middle: L

last: Kelleher

first: Philip

last: Gruppuso


title: Vitis riparia shoot tip transcriptome in response to long and short photoperiod.

city: Brookings

first: Anne

middle: Y

last: Fennell

state: South Dakota

address: North Campus Drive

department: Department of Plant Science

institute: South Dakota State University

summary: Winter season with reduced day length (photoperiod); led to the growth cessation, dormancy induction and cold acclimation in woody perennial plants. To develop an understanding of the photoperiod signal transduction in Vitis riparia; shoot tip transcriptome profiling was performed under differential photoperiod treatments (long (LD, 15h) and short day (SD, 13h)) for 7 or 21 days after shoots reached 10 nodes (LD7, SD7, LD21 or SD21).

overall_design: Three biological replicates of LD and SD shoot tip RNA were sequenced and analysed.

first: Shuchi

last: Smita

first: Michael

last: Robben


title: Loss of proximal tubular Kruppel-like factor 15 (KLF15) exacerbates kidney injury through loss of fatty acid oxidation

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

department: Department of Medicine

institute: Stony Brook University

summary: KLF15 has a critical role in other kidney cell types, but its role in mediating proximal tubular (PT) fatty acid oxidation (FAO) in AKI has not been determined.  PT-specific KLF15 knockdown (Klf15PTKO) and control Klf15fl/fl mice were treated with multiple low doses of the PT-specific DNA-damaging agent aristolochic acid I (AAI) and RNA-sequencing of kidney cortex undertaken. Klf15PTKO exhibited worse kidney injury than Klf15fl/fl mice after AAI treatment. Immune system and integrin signaling pathways were significantly upregulated in Klf15PTKO versus Klf15fl/fl mice. Metabolic pathways, specifically FAO, were significantly downregulated in Klf15PTKO versus Klf15fl/fl mice, including PPARalpha signaling.

overall_design: Kidney cortex mRNA profiles were generated in Klf15fl/fl and Klf15PTKO mice treated with DMSO or AAI for 2 weeks or AAI for 2 weeks followed by 2 weeks remodeling time using RNA-sequencing.

first: Sian

middle: E

last: Piret


title: Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

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

overall_design: Refer to individual Series


title: Involvement of Arabidopsis TUTases in viral RNA uridylation

first: Dominique

last: Gagliardi

summary: Using 3' RACE-seq method, we analyzed the impact of URT1 and/or HESO1 inactivation on the uridylation of GFLV, TuMV and TCV RNAs in Arabidopsis.

first: Anne-Caroline

last: Joly

first: Hélène

last: Zuber


title: Cluster thinning effect on Cabernet Sauvignon berry ripening

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

summary: The impact of yield on fruit and wine quality has been studied extensively; vine response to increased yield is well known, but responsible mechanisms – including the regulation of pathways responsible for color, aroma and mouthfeel – have not been characterized at the level of genetic regulation. To examine the impact of crop load on transcriptomic and metabolomic changes during grape berry maturation vines from two cluster thinning treatments (50% or 75% of clusters removed following fruit set) were compared to control vines (no cluster thinning).  Treatments were applied to mature Cabernet Sauvignon grapevines over three consecutive vintages. Agronomic parameters, including yield per vine and the yield to pruning weight ratio, as well as fruit and wine composition, were determined at harvest.  Fruit transcriptomic and metabolomic changes were measured in berry samples collected from each treatment at 7 to 10 day intervals from fruit set to harvest. The patterns of berry development by weight, sugar accumulation, and malic acid degradation indicated that vines responded differentially to crop load reduction by accelerating berry maturation progress. RNA-Seq analysis, and untargeted GC-MS and UHPLC-QTOF-MS -based metabolomic approaches were used. The indication of the acceleration of maturation transcriptional programs and of metabolite accumulation in the treated vines was suggested by multivariate analyses. To identify the transcriptional key triggers of this response we applied a two-regression step statistical approach which identified genes modulated over development dependent on the crop load. Comparing vintages we were able to estimate the environmental influence on the crop load treatments among years. The application of this multifaceted approach allowed the construction of robust models describing the impact of crop load on the genetic regulation of grape maturation.

overall_design: Cluster thinning treaments were applied removing 50% or 75% of clusters following fruit set. Grape berries were collected at ten-day intervals in 2012, and weekly in 2013 and 2014 beginning at fruit set until harvest (24.5 °Brix) at the same time of day (8:00 am). Samples were collected in randomized 6-vine block designs along nine rows (3 rows/treatment plus control). Each sample entailed the collection of 26 clusters from each vine block. 60 berries, selected from 6 isolated clusters randomly selected from the vine blocks, were ground under liquid nitrogen. Seeds were removed in the grinding process. Frozen powder was aliquoted in 100mg and 400 mg samples for metabolite and RNA extractions respectively. Transcriptomic and metabolomic approaches were used to monitor the expression of all grapevine genes and to elucidate grape berry metabolome during development.

first: Chandra

last: Richter

first: Sara

last: Zenoni

first: Giovanni

last: Tornielli

first: Nicola

last: Vitulo

first: Silvia

last: Dal Santo

first: Nick

last: Dokoozlian

first: Mario

last: Pezzotti


title: Transcriptional response of HIV-infected CD4 memory T cells to co-culture with TCR activated CD8 T cells.

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The persistence of HIV infection under ART is due to a reservoir of latently infected cells that harbor replication-competent virus and evade immune recognition. Defining the mechanisms responsible for the establishment and maintenance of HIV latency is crucial to achieve HIV eradication or functional cure. Previous studies demonstrated a non-cytotoxic CD8+ T-cells mediated inhibition of virus replication during untreated HIV/SIV infection and inhibition of virus production under ART; however, the mechanisms responsible for this antiviral effect remained poorly understood.  In our primary cell-based in vitro latency model we demonstrated that co-culture with CD8+ T-cells promotes changes in metabolic and cell survival pathways in HIV-infected memory CD4+ T-cells that may negatively regulate HIV expression and ultimately promote the establishment of latency. Modulation of this CD8-mediated activity may represent a tool to disrupt HIV latency and reservoir persistence in ART-treated individuals.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from HIV naïve healthy donors. From each donor memory CD4+ T cells were enriched and infected with HIV, and CD8+ T cells were selected and TCR-activated. RNA was extracted from HIV infected memory CD4+ T cells were that were mono-cultured and co-cultured with TCR-activated CD8+ T cells.

first: Lavinia

last: Franchitti

first: Ashish

last: Sharma

first: Talia

last: Mota

first: Hong

last: Wang

first: Abigail

last: Willemse

first: Jared

last: Weiler

first: Rafick

last: Sékaly

first: Steve

last: Bosinger

first: Mirko

last: Paiardini

first: R

last: Jones

first: Guido

last: Silvestri

first: Deanna

last: Kulpa

first: Simona

last: Mutascio


title: Single-cell RNA-sequencing of blood and tonsillar CD4+ CD57+ and CD57- T cells

city: Canberra

first: Yuwei

last: Hao

address: Level 6, Building 10, The Canberra Hospital, Yamba Drive,

country: Australia

institute: JCSMR of ANU

summary: Gene-environment interactions are implicated in immunopathology, but few specific mechanisms have been identified. We defined two terminal-differentiation pathways for human CD4+ T cells each marked by CD57. Rare blood CD57+ CD4+ T cells marked by TCF1 downregulation (Thcyt) adopt a cytotoxic and terminal-effector transcriptome. By contrast, human CD57+ GC-Tfh cells exhibit a transcriptome of the precursor exhausted T cells marked by TCF7, TOX and ID3 and constitutive expression of CTLA4, which collectively confer resistance to becoming cytotoxic. By clarifying human CD4+ T cell terminal differentiation, we have revealed how CTLA4 mitigates the risk of maladaptive cytotoxicity during infection.

overall_design: CD57+ CD4+ T cells (7AAD- CD19- CD3+ CD4+ CD8- CD57+) and CD57- CD4+ T cells (7AAD- CD19- CD3+ CD4+ CD8- CD57-) from tonsil and blood samples of a child were FACS-purified into 1.5-ml Eppendorf tubes with FACS buffer. Single cell gene expression and VDJ libraries were prepared by Biomolecular Resource Facility at ANU using Chromium Next GEM Single Cell 5' Kit v2 Dual Index and Single Cell Human TCR Amplification Kit (10x Genomics) according to the manufacturer’s instructions. The library was sequenced in S1 flow cell with 2 x 50 bp paired-end reads by NovaSeq 6000 sequencer (Illumina). The 10X Cell Ranger package (10X Genomics, v6.0.1) was used to process data and align to human genome (GRCh38-2020-A).

first: Zhi-Ping

last: Feng

first: Matthew

last: Cook


title: Imbalanced gut microbiota drives nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model

city: Madison

first: Vanessa

last: Leone

state: WI

address: 1933 Observatory Dr.

institute: University of Wisconsin-Madison

summary: This study employed low and high-fat purified diets containing two levels of added dietary cholesterol in conventionally raised, specific-pathogen free (SPF) mice harboring a full microbial community as compared to germ-free (GF) mice raised in complete absence of gut microbes on disease outcomes. It was hypothesized that FF-diets would lead to an earlier onset of gut dysbiosis, corresponding with elevated biomarkers of NAFLD and NASH. In the present study, we aimed to dissect the role of FF diet induced gut dysbiosis in order to mechanistically identify the underlying mechanism that influences gut-liver crosstalk between specific diet-induced bacterial populations and hepatic tissue to drive NAFLD/NASH onset and progression

overall_design: Germ-free and SPF mice were fed one of four purified diets for either 8 or 24 weeks and saccrificed. NAFLD/NASH progression was evaluated via histology and biochemical analyses and concomitant changes in gut microbiota was assessed via 16S rRNA gene amplicon sequencing and shotgun metagenomics.

last: Fei

first: Sawako

last: Miyoshi

first: Jake

last: Hermanson

first: Maximilian

last: Hawkins

first: Jun

first: William

last: Charlton

first: Bingqing

last: Xie

first: Mark

last: D'Sousa

first: Dinanth

last: Sulakhe

first: Eugene

last: Chang

first: Michael


title: Atlas of lymphangiogenesis

city: Melbourne

first: Tyrone

last: Chen

state: VIC

address: 305 Grattan St

department: Bioinformatics Core (RRID: SCR_025901); Organogenesis and Cancer Program

institute: Peter MacCallum Cancer Centre


title: Transcriptome of mouse E12 neocortex

city: Los Angeles

first: Liang

state: CA

address: 1050 Childs Way

institute: University of Southern California

summary: Transcriptome of mouse E12 neocortex

overall_design: Mouse neocortices were dissected from a pregnant female (E12). RNA was extracted immediately using TRIzol. RNA libraries were generated using Illumina True-seq RNA library preparation kit.

first: Sika

last: Zheng


title: Atlas of lymphangiogenesis [scATAC-Seq]

summary: During development, lymphatic vasculature forms as a second and distinct network that derives from embryonic blood vessels. Transdifferentiation of venous endothelial cells into specified lymphatic endothelial cells (LECs) is the first step in this process. Transdifferentiation and specification of LEC fate requires Prox1, but how Prox1 regulates transdifferentiation and differentiation is not fully understood. We present a single cell transcriptomic atlas of lymphangiogenesis spanning four key developmental stages that reveals new markers and functional regulators of lymphatic development. We extend this to comprehensively profile single cell transcriptomic and chromatin changes controlled by Prox1 using zygotic prox1a mutants, which form lymphatics that then dedifferentiate. Combining this with single cell analysis of Prox1-null, double prox1a/prox1b maternal zygotic mutants, we reveal in depth the role of Prox1 in control of LEC fate specification and differentiation.  This resource reveals dual and progressive functions for Prox1, blocking blood vascular and hematopoietic fate while simultaneously up-regulating a small number of early acting genes that include tspan18a/b and lgals3a/b which are essential for lymphangiogenesis. This embryonic developmental resource will serve as a baseline to better understand both developmental and pathological lymphangiogenesis in the future. [Citations in sample metadata correspond to reference numbers in the associated publication.]

overall_design: Single cell ATAC profiles of endothelial cells from developing zebrafish at 4dpf in Zprox-/- mutant and matched WT siblings. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan_lab/browse/2022_Grimm_Mason_et_al_PROX1_NatCellBiol/

first: Lin

last: Grimm

first: Elizabeth

last: Mason

first: Neil

middle: I

last: Bower

first: Kazuhide

last: Okuda

first: Oliver

last: Yu

first: Stefanie

last: Dudczig

first: Scott

last: Paterson

first: Anne

last: Senabouth

first: Joseph

last: Powell

first: Kelly

last: Smith

first: Natasha

last: Harvey

first: Kaska

last: Koltowska

first: Benjamin

last: Hogan


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (scATAC-seq)

status: Public on Apr 26 2023

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: We recently demonstrated the chemical reprogramming of human somatic cells to pluripotent stem cells, which provides a fundamentally new approach for cell fate manipulation. However, the utility of this chemical approach is currently hampered by the slow kinetics. Here, by screening for new small-molecule boosters and systematically optimizing the original chemical reprogramming condition, we have established a robust, chemically defined protocol. With this new protocol, the entire chemical reprogramming process is remarkably accelerated, reducing the time needed from ~50 days to a minimum of 16 days. Moreover, this new protocol enables highly reproducible and efficient generation of human pluripotent stem cells from all 17 tested donors with a reprogramming efficiency of up to 31%. Our method provides a unique and powerful strategy for human cell fate manipulation and pluripotent stem cell manufacturing for cell-based therapeutic applications.

overall_design: To dissect the molecular mechanism of human chemical reprogramming, human somatic cells and cells at different time points throughout chemical reprogramming process were analyzed by single cell ATAC-seq.

first: Shijia

last: Liuyang

first: Guan

last: Wang

first: Yanglu

first: Huanjing

last: He

first: Jinlin

first: Hongkui

last: Deng


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (scRNA-seq)

overall_design: To dissect the molecular mechanism of human chemical reprogramming, human somatic cells and cells at different time points throughout chemical reprogramming process were analyzed by single cell RNA-seq.


title: Identification of evolutionary mechanisms of myelomatous effusion by single-cell RNA sequencing

first: Zhegnxu

last: Sun

address: Guangzhou Road 300

institute: Jiangsu Province Hospital

summary: Myelomatous effusion (ME) is a rare manifestion of extramedullary multiple myeloma (MM) with limited therapeutic options and poor outcomes. To investigate the evolutionary mechanisms of ME, we used single-cell RNA sequencing to assess the transcriptomes of bone marrow, peripheral blood, and pleural effusion/ascites from three patients with ME.

overall_design:
We performed single-cell RNA sequencing of bone marrow, peripheral blood, and pleural effusion/ascites samples from three patients with ME to investigate the evolutionary mechanisms of ME.
NOTE FROM SUBMITTER: We cannot submit the raw data files due to patient privacy concern.

first: Zhengxu

first: Jiamei

last: Ji

first: Jianyong

last: Li

first: Xiaoyan

last: Qu


title: Gene expression profiling of HL-1 cells with lncRNA ZNF593-AS  overexpression under palmitic acid stimulation

city: Wuhan

first: rong

last: xie

state: Hubei

address: Jiefang Ave.

institute: Huazhong university of science and technology

summary: The aim of this study is to investigate molecular mechanisms underlying the function of lncRNA ZNF593-AS in cardiomyocyte under palmitic acid stimulation in vitro.

overall_design: HL-1 cells were transfected with vector or ZNF593-AS under the stimulation of palmitic acid. RNA-seq using Illimina platform was than performed.

first: Rong

last: Xie

first: Jiahui

last: Fan


title: mRNA-sequencing of thyroid cancer cell lines

city: Dallas

first: David

last: McFadden

state: Texas

address: 5323 Harry Hines Blvd, K3.219

department: Departments of Internal Medicine and Biochemistry

institute: UT Southwestern Medical Center

summary: A metabolic hallmark of cancer identified by Warburg is the increased consumption of glucose and secretion of lactate, even in the presence of oxygen. Although many tumors exhibit increased glycolytic activity, most forms of cancer rely on mitochondrial respiration for tumor growth. We report here that Hürthle cell carcinoma of the thyroid (HTC) models harboring mitochondrial DNA-encoded defects in complex I of the mitochondrial electron transport chain exhibit impaired respiration and alterations in glucose metabolism. CRISPR-Cas9 pooled screening identified glycolytic enzymes as selectively essential in complex I-mutant HTC cells. We demonstrate in cultured cells and a PDX model that small molecule inhibitors of lactate dehydrogenase selectively induce an ATP crisis and cell death in HTC. This work demonstrates that complex I loss exposes fermentation as a therapeutic target in HTC and has implications for other tumors bearing mutations that irreversibly damage mitochondrial respiration.

overall_design: mRNA-sequencing was performed on thyroid cancer cell lines to assess the expression of LDH genes

first: Anderson

last: Frank

first: Jiwoong

last: Kim

first: Yang


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming (CUT&TAG)

first: Yulin

overall_design: To characterize human chemically induced pluripotent stem cells (hCiPSCs), hCiPSCs were analyzed and compared to human somatic cells and human embryonic stem cells (hES) by CUT&TAG.

first: Shijia

first: Guan


title: Pooled CRISPR-Cas9 screens for metabolic liabilities in Hurthle cell carcinoma

overall_design: Genome-wide and targeted pooled CRISPR-Cas9 knockout screens were performed in thyroid cancer cell lines to identify Hurthle cell carcinoma-specific metabolic vulnerabilities


title: Atlas of lymphangiogenesis [scRNA-Seq]

first: Tyrone

last: Chen

overall_design: Single cell RNA profiles of endothelial cells from wild type developing zebrafish across 4 stages of development (40hpf, 3dpf, 4dpf, 5dpf), Zprox-/- mutant and matched WT siblings at 4dpf, and MZprox-/- mutant and matched WT siblings at 40hpf. All code associated with this data and publication are publicly available under an open source software license at: https://atlassian.petermac.org.au/bitbucket/users/tyrone.chen/repos/hogan_lab/browse/2022_Grimm_Mason_et_al_PROX1_NatCellBiol/

first: Lin

last: Grimm

first: Elizabeth

last: Mason

first: Neil

last: Bower

first: Kazuhide

last: Okuda

first: Oliver

last: Yu

first: Stefanie

last: Dudczig

first: Scott

last: Paterson

first: Anne

last: Senabouth

first: Joseph

last: Powell

first: Kelly

last: Smith

first: Natasha

last: Harvey

first: Kaska

last: Koltowska

first: Benjamin


title: Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming

first: Yulin

last: Lyu


title: Isolated astrocytes from young BMAL1aKO and wildtype mice

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary:
Purpose: The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function, but also leads to a unique cell-autonomous activation phenotype. We have undertaken RNAsequencing of isolated astrocytes from young wildtype and BMAL1 astrocyte-specific knockout mice (Bmal1fl/fl, ALDH1L1-CreERT2, termed BMAL1 aKO) to uncover changes to gene expression as a result of BMAL1 disruption in astrocytes.
Methods: BMAL1 aKO mice and wildtype littermates were given tamoxifen at 2 months of age and harvested around 7 months of age and brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads. RNA was extracted in Trizol reagent and sent for sequencing. Samples from BMAL1 aKO and wildtype astrocytes were compared and flowthrough samples were compared to astrocytes to confirm cell-type purity.
Results: BMAL1 aKO results in both up- and down-regulation of many astrocyte genes. GO pathway analysis points to lysosomal pathways as dysregulated by knockout of BMAL1 in astrocytes. While astrocytes are enriched by our isolation methods, there is some degree of contamination from neurons and oligodendrocytes.
Conclusions: While our astrocyte isolation method has some caveats in terms of purity, BMAL1 aKO appears to dysregulate lysosomal pathways, which will be investigated by further experiments.

overall_design: 3 wildtype astrocyte samples compared to 5 BMAL1 aKO astrocyte samples, 4 flowthrough samples of 2 wildtype and 2 BMAL1 aKO brains each.

first: Celia

last: McKee

first: Erik

last: Musiek


title: ATAC-seq of sotorasib-resistant H23 and H358 cells treated with TEAD inhibitor GNE-7883

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

overall_design: ATAC-Seq

first: Kamakoti

middle: P

last: Bhat

first: Xin

last: Ye

first: Musa

last: Ahmed


title: RNA-seq of HCC1576 and OVCAR8 cells treated with TEAD inhibitor GNE-7883

overall_design: RNA-Seq

first: Xiaosai

last: Yao

first: Thijs

last: Hagenbeek

first: Anwesha

last: Dey


title: ATAC-seq of H226 cells treated with TEAD inhibitor GNE-7883

summary: ATAC-seq of H226 cells treated with TEAD inhibitor GNE-7884


title: Sex differences in the effects of caloric restriction (CR) on hepatic gene expression in mice

city: Edinburgh

first: William

last: Cawthorn

address: 47 Little France Crescent

department: University/BHF Centre for Cardiovascular Science

institute: The University of Edinburgh

summary: The effects of caloric restriction (CR) on glucose homeostasis and metabolic function differ between males and females. To investigate if hepatic function contributes to these sex differences, we collected liver samples from male and female C57BL/6NCrl mice that were fed ad libitum (AL) or underwent caloric restriction (CR; receiving 70% of daily AL intake) from 9-13 weeks of age. Livers were then analysed by bulk RNA-seq.

overall_design: The goal of this study was to determine how caloric restriction (CR) influences the hepatic transcriptome and if this differs between males and females. The experiment included five ad libitum (AL)-fed females, six CR females, six AL males and five CR males. Mice were fed AL or CR from 9-13 weeks of age. To minimise effects resulting from differences in fasting duration, mice in both the AL and CR groups were fasted for ~8 hours prior to necropsy and liver sampling.

first: Yoshiko

last: Ikushima

first: Hiroshi

last: Kobayashi

first: Kuan-Chan

last: Chen


title: Effect of high fat diet on gene expression in pancreatic islet associated macrophages

city: Oxford

first: Cecilia

last: Lindren

address: Old Road Campus

department: Big Data Institute

institute: University of Oxford

summary: We have exploited islet-associated macrophages (IAMs) as a model of resident macrophage function, focusing on more physiological conditions than the commonly used extremes of M1 (inflammation) versus M2 (tissue-remodelling) polarization. Under steady-state, murine IAMs are metabolically poised between aerobic glycolysis and oxidative phosphorylation, and thereby exert a brake on glucose-stimulated insulin secretion (GSIS). This is underpinned by epigenetic remodelling via the metabolically-regulated histone demethylase Kdm5a. Conversely, GSIS is enhanced by engaging Axl receptors on IAMs, or by augmenting their oxidation of glucose. Following high-fat feeding, efferocytosis is stimulated in IAMs in conjunction with Mertk and Tgfb receptor signalling. This impairs GSIS and potentially contributes to b-cell failure in pre-diabetes. Thus, IAMs serve as relays in many more settings than currently appreciated, fine-tuning insulin secretion in response to dynamic changes in the external environment. Intervening in this nexus might represent a means of preserving b-cell function during metabolic disease.

overall_design: Mice were maintained from 8 weeks of age for an additional 8 weeks on either standard chow diet (10.88 kJ/g; 8% fat, 21% protein, and 71% carbohydrate) or a high fat diet (19.67kJ/g; 45% fat, 20% protein, 35% carbohydrate). RNA was extracted from CD11b+, F4/80+ cells prepared from pancreatic islets isolated from C57BL/6J. A total of 4 replicates per diet condition were analysed, each comprising extracts pooled from two mice.

first: Trevor

last: Biden

first: Liam

last: O'Reilly

first: Saskia

last: Reibe


title: Differentially expressed mRNAs in lungs between hypoxic human umbilical cord mesenchymal stromal cell-derived extracellular vesicles (Hypo-EVs)-INH-treated mice and OVA-induced asthma mice

city: Zhenjiang

first: Xiaowei

last: Xu

address: No.438, Jiefang Road, Jingkou District, Zhenjiang City, Jiangsu Province

institute: Jiangsu University

summary:
To better understand the molecular processes of nebulized Hypo-Evs on asthma intervention, OVA-induced chronic asthma model were established (OVA group), and a therapeutic regimen was instigated by inhaling Hypo-EVs four times (Hypo-EVs group) .
Then a global RNA sequencing of mouse lung from the OVA and Hypo-EVs groups was performed.

overall_design: Comparative gene expression profiling analysis of mouse lung from the OVA and Hypo-EVs groups.

first: Liyang

last: Dong


title: The basolateral amygdala-anterior cingulate pathway contributes to depression-like behaviors and comorbidity with chronic pain behaviors in male mice

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

summary: While depression and chronic pain are frequently comorbid, underlying neuronal circuits, and their relevance for the understanding of psychopathology, remain poorly defined. Here we show in mice that hyperactivity of the neuronal pathway linking the basolateral amygdala to the anterior cingulate cortex is essential for chronic pain-induced depression. In naive male mice, we demonstrate that activation of this pathway is sufficient to trigger depressive-like behaviors, as well as transcriptomic alterations that recapitulate core molecular features of depression in the human brain. These alterations notably impact gene modules related to myelination and the oligodendrocyte lineage. Among these, we show that Sema4a, a hub gene significantly upregulated in both male mice and humans in the context of altered mood, is necessary for the emergence of depressive-like behaviors. Overall, these results place the BLA-ACC pathway at the core of pain and depression comorbidity, and unravel the role of impaired myelination and Sema4a in mood control.

overall_design: 23 samples were generated to analyze gene expression changes induced in mice that received 9 optogenetic stimulations of the BLA-ACC neuronal pathway (stim, n=10), as compared to controls (ctrl, n=12)

first: Ipek

last: Yalcin

first: Léa

last: Becker


title: Dissolution of RNA condensates by the embryonic stem cell protein L1TD1 [CLIP-seq]

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: L1TD1 is a cytoplasmic RNA-binding protein that is specifically expressed in pluripotent stem cells and, unlike its mouse paralogue, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known domesticated gene from a LINE-1 (L1) retroelement, the functional legacy from its ancestral protein, ORF1p of L1, and the novelty are so far unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs, localizes to high-density ribonucleoprotein (RNP) condensates, and increases L1 retrotransposition. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatments of neurodegenerative diseases caused by disturbed stress granule dynamics.

overall_design: CLIP-seq of endogenous L1TD1 and G3BP2 by using anti-L1TD1 antibody (Sigma-Aldrich, HPA030064), anti-G3BP2 antibody (Bethyl, A302-040A) and IgG controls.


title: Isolated astrocytes from aged BMAL1aKO and wildtype mice

first: Eric

last: Tycksen

summary:
Purpose: The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function, but also leads to a unique cell-autonomous activation phenotype. We have undertaken RNAsequencing of isolated astrocytes from aged wildtype and BMAL1 astrocyte-specific knockout mice (Bmal1fl/fl, ALDH1L1-CreERT2, termed BMAL1 aKO) to uncover changes to gene expression as a result of BMAL1 disruption in astrocytes and to confirm those changes persist during aging.
Methods: BMAL1 aKO mice and wildtype littermates were given tamoxifen at 2 months of age and harvested around 20 months of age and brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads. RNA was extracted in Trizol reagent and sent for sequencing. Samples from BMAL1 aKO and wildtype astrocytes were compared and flowthrough samples were compared to astrocytes to confirm cell-type purity.
Results: BMAL1 aKO results in both up- and down-regulation of many astrocyte genes. GO pathway analysis points to lysosomal pathways as dysregulated by knockout of BMAL1 in astrocytes. While astrocytes are enriched by our isolation methods, there is some degree of contamination from neurons and oligodendrocytes.
Conclusions: While our astrocyte isolation method has some caveats in terms of purity, BMAL1 aKO appears to dysregulate lysosomal pathways, which will be investigated by further experiments.

overall_design: 4 wildtype astrocyte samples compared to 4 BMAL1 aKO astrocyte samples, 4 flowthrough samples of 2 wildtype and 2 BMAL1 aKO brains each.

first: Celia

last: McKee

first: Erik

last: Musiek


title: Cyclic GMP-AMP synthase and interferon activation diminish MEF2C-mediated cognitive resilience

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

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

overall_design: Refer to individual Series


title: Cyclic GMP-AMP synthase and interferon activation diminish MEF2C-mediated cognitive resilience IV

summary: Pharmacological inhibition of cGAS with TDI-6570 protected against the synaptic loss and cognitive deficits in P301S tauopathy model, likely via enhancing MEF2C transcriptional network and associated cognitive resilience

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus with and without P301S Tau and TDI-6570 treatment.

first: Joe

last: Udeochu

first: Sadaf

last: Amin

first: Yige

last: Huang

last: Fan

first: Eileen

middle: R

last: Torres

first: Gillian

middle: K

last: Carling

first: Bangyan

last: Liu

first: Hugo

last: McGurran

first: Guillermo

last: Coronas-Samano

first: Grant

last: Kauwe

first: Gergey

last: Mousa

first: Man

last: Wong

first: Pearly

last: Ye

first: Ravi

last: Nagiri

first: Iris

last: Lo

first: Julia

last: Holtzman

first: Carlo

last: Corona

first: Allan

last: Yarahmady

first: Sue-Ann

last: Mok

first: Michael

middle: T

last: Gill

first: Ravikiran

last: Raju

first: Shiaoching

last: Gong

first: Wenjie

last: Luo

first: Mingrui

last: Zhao

first: Tara

last: Tracy

first: Rajiv

last: Ratan

first: Li-Huei

last: Tsai

first: Subhash

last: Sinha


title: scRNA-seq data for H-23 and H-358 cells traced under using customized barcode

first: Marc

last: Hafner

summary: We barcoded clones with specific sequences and split the pools of cells into different sample that were treated with DMSO, single agent Sotorasib (AMG-510) or combination of Sotorasib and TEAD inhibitor (G'7883) for different duration. We performed this experiment for two cell lines (H-23 and H-358) independently.

overall_design: NCI-H358 and NCI-H23 cell lines were barcoded with TraCe-seq barcoding libraries and expanded in culture to establish the starting TraCe-seq cell populations. A fraction of the starting populations were profiled by single cell RNA-sequencing (scRNA-seq) to capture the relative clonal abundance and transcriptional profile of each barcoded clones right before drug treatment. In parallel, the rest of the cells were treated with sotorasib alone or in combination with GNE-7883 until resistant clones emerged under sotorasib single agent treatment. We conducted scRNA-seq profiling to capture acute responses to the treatment at 72h post treatment as well as after resistance has emerged to capture adaptive changes. These time points were chosen to allow us capture the differential transcriptional responses in the resistant versus sensitive clones, and compare the responses to sotorasib single agent versus sotorasib + GNE-7883 combination at individual clone and single cell level.

first: Xin

first: Michal

last: Kabza


title: Cyclic GMP-AMP synthase and interferon activation diminish MEF2C-mediated cognitive resilience III

first: Li

last: Gan

summary: To induce chronic IFN-I activation, we injected wildtype and Ifnar1–/– mice with five treatments of DMXAA, a STING agonist, followed by snRNA-seq analysis of hippocampal tissues. In wildtype mice, we showed that microglia had the strongest IFN response to STING activation of all cell types. Ablation of interferon alpha and beta receptor 1 (IFNAR1) abolished microglial IFN-I response and suppression of neuronal MEF2C transcriptional network

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus of WT and Ifnar1 KO mice with or without DMXAA treatment.

first: Joe

last: Udeochu

first: Sadaf

last: Amin

first: Yige

last: Huang

last: Fan

first: Eileen

last: Torres

first: Gillian

last: Carling

first: Bangyan

last: Liu

first: Hugo

last: McGurran

first: Guillermo

last: Coronas-Samano

first: Grant

last: Kauwe

first: Gergey

last: Mousa

first: Man

last: Wong

first: Pearly

last: Ye

first: Ravi

last: Nagiri

first: Iris

middle: M