title: EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform to identify cancer-specific epigenetic vulnerabilities

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

summary: Dysregulation of the epigenome due to alterations in chromatin modifier proteins commonly contribute to malignant transformation. To interrogate the roles of epigenetic modifiers in cancer cells, we generated an epigenome-wide CRISPR-Cas9 knockout library (EPIKOL) that targets a wide-range of epigenetic modifiers and their cofactors. We conducted eight screens in two different cancer types and showed that EPIKOL performs with high efficiency in terms of sgRNA distribution and depletion of essential genes. We discovered novel epigenetic modifiers that regulate triple-negative breast cancer and prostate cancer cell fitness. We confirmed the growth-regulatory functions of individual candidates, including SS18L2 and members of the NSL complex (KANSL2, KANSL3, KAT8) in triple negative breast cancer cells. Overall, we show that EPIKOL, a focused sgRNA library targeting approximately 800 genes, can reveal epigenetic modifiers that are essential for cancer cell fitness under in vitro and in vivo conditions and enable identification of novel anti-cancer targets. Due to its comprehensive epigenome-wide targets and relatively high number of sgRNAs per gene, EPIKOL will facilitate studies examining functional roles of epigenetic modifiers in a wide range of contexts, such as screens in primary cells, patient-derived xenografts as well as in vivo models.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Epigenome-focused CRISPR/Cas9 Screens to identify genes whose mutations cause fitness defects in prostate and triple-negative breast cancer. 4 cells lines per cancer type were screened. For each screen, initial and final timepoint samples were collected and sequenced as triplicates. For in vivo screen, initial pellet from MDA-MB-231 cells were collected and triplicate tumors were collected and sequenced for week2 and week4 after implantation. To understand transcriptomic changes upon SS18L2 knockout, cells infected with either NT1 or SS18L2 guide carrying viruses were collected as triplicates on day 6 post-transduction.

first: Ozlem

last: Yedier-Bayram

first: Bengul

last: Gokbayrak

first: Alisan

last: Kayabolen

first: Ali

last: Aksu

first: Ayse

first: Ahmet

last: Cingöz

first: Ezgi

middle: Y

last: Kala

first: Goktug

last: Karabiyik

first: Rauf

last: Günsay

first: Beril

last: Esin

first: Tunc

last: Morova

first: Firat

last: Uyulur

first: Hamzah

last: Syed

first: Martin

last: Philpott

first: Sonia

last: Kung

first: Nathan

last: Lack

first: Tamer

last: Onder

first: Tugba

last: Bagci-Onder


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [bulk RNA-seq]

status: Public on Aug 22 2022

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

type: Expression profiling by high throughput sequencing

summary: Regulatory T (Treg) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Here, we show that Treg cells in the tumor microenvironment (TME) of human lung cancers harbor a completely different open chromatin profile compared to effector T cells and peripheral Treg cells. The integrative sequencing analyses revealed that BATF, IRF4, NF-κb, and NR4A were important transcription factors for Treg cell differentiation in the TME. Particularly, BATF was identified as a key regulator, which leveraged Treg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of Treg cells in the TME. BATF deficiency in Treg cells remarkably inhibited tumor growth and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. Our results propose the specific chromatin remodeling and differentiation program of Treg cells in the TME, which can be applied in the development of Treg cell-targeted therapies.

overall_design: bulk RNA-seq about T cell subsets (Treg cells, Tconv cells and CD8+ T cells)

first: Kota

last: Itahashi

first: Takuma

last: Irie


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [scRNA-seq]

overall_design: scRNA-seq about Treg cells


title: Novel lymphocytic choriomeningitis virus strain sustains abundant exhausted progenitor CD8 T cells without systemic viremia

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Department of Microbiology and Immunology

country: USA

institute: University of Minnesota

summary: Lymphocytic choriomeningitis virus (LCMV) is the prototypic arenavirus and a natural mouse pathogen. LCMV Armstrong, an acutely resolved strain, and LCMV Clone 13, a mutant that establishes chronic infection, have provided contrasting infection models that continue to inform the fundamental biology of T cell differentiation, regulation of exhaustion, and response to checkpoint blockade. Here, we report the isolation and characterization of LCMV Minnesota (LCMV-MN), which was naturally transmitted to laboratory mice upon cohousing with pet shop mice and shares 80-95% amino acid homology with previously characterized LCMV strains. Infection of laboratory mice with purified LCMV-MN resulted in viral persistence that was intermediate between LCMV Armstrong and Clone 13, with widely disseminated viral replication and viremia that was controlled within 15-30 days, unless CD4 T cells were depleted prior to infection. LCMV-MN responding CD8+ T cells biased differentiation towards the recently described PD1+ CXCR5+ Tim-3lo stem-like CD8+ T cell population (also referred to as T exhausted progenitors, Tpex) that effectuates responses to PD-1 blockade checkpoint inhibition, a therapy that rejuvenates responses against chronic infections and cancer. This subset resembled previously characterized PD1+ TCF1+ stem-like CD8+ T cells by transcriptional, phenotypic, and functional assays, yet was atypically abundant. LCMV-MN may provide a tool to better understand the breadth of immune responses in different settings of chronic antigen stimulation as well as the ontogeny of T exhausted progenitors and the regulation of responsiveness to PD-1 blockade.

overall_design: To investigate the transcriptional programs of LCMV-MN induced H-2Db/gp33-tetramer positive Slamf6+/Tim3- and Slamf6-/Tim3+ CD8 T subsets, we sorted them from the spleen and LNs 30 days after infection and performed RNAsequencing.

first: Lalit

middle: K

last: Beura

first: Milcah

middle: C

last: Scott

first: Mark

middle: J

last: Pierson

first: Vineet

last: Joag

first: Sathi

last: Wijeyesinghe

first: Matthew

middle: R

last: Semler

first: Clare

middle: F

last: Quarnstrom

first: Kathleen

last: Busman-Sahay

first: Jacob

middle: D

last: Estes

first: Sara

middle: E

last: Hamilton

first: Vaiva

last: Vezys

middle: H

last: O’Connor


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [bulk ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: bulk ATAC-seq about T cell subsets (Treg cells, Tconv cells and CD8+ T cells) and T-cell leukemia/lymphoma (ATLL) cell lines.


title: Strong basal/tonic TCR signals are associated with transcriptional and epigenetic changes in naive CD4+ T cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

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

overall_design: Refer to individual Series


title: Strong basal/tonic TCR signals are associated with chromatin accessibility changes in naive CD4+ T cells

summary: Naïve T cells constantly experience TCR signals in response to self-peptides presented by MHC (pMHC) in vivo. The intensity of these basal or tonic TCR signals can be indirectly read out by expression of surrogate markers of tonic TCR signaling, including the Nur77-GFP transgene and Ly6c. The strength of tonic TCR signaling varies broadly across the naïve CD4+ T cell population and is correlated with functional heterogeneity.Cells that experience the most basal TCR signaling (Nur77-GFP hi, Ly6c lo) are hyporesponsive to peptide-MHC stimulation. Here we examine whether tonic TCR stimulation is associated with differences in chromatin accessibility.

overall_design: Naïve, CD4 T cells (FoxP3-RFP negative, CD44lo, CD4+) from spleens plus lymph nodes from untreated mice were sorted  into four populations based on the expression of Nur77-GFP and Ly6c. Sorted cells were either Nur77-GFPlo Ly6c+ (Population A), Nur77-GFP intermediate Ly6c+ (Population B), Nur77-GFP intermediate Ly6c- (Population C) or Nur77-GFP hi Ly6c- (Population D). We made biological duplicates for Population A samples, and biological  triplicate samples for Populations B, C, and D. A total of 11 samples.

first: W

middle: M

last: Zinzow-Kramer

first: J

last: Eggert

first: C

first: B

middle: B

last: Au-Yeung


title: Extrinsic factors facilitate neurogenesis in a human induced pluripotent stem cell-derived model of the dentate gyrus

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

summary: Modeling development and maturation of the human hippocampus in culture is  crucial to elucidate the physiological and pathological mechanisms of its  neurogenesis. We established human hippocampal cell cultures by means of  controlled neuralization of human induced pluripotent stem cells (hiPSCs). The  timely re-activation of WNT signaling in hiPSCs, which were previously driven  toward a dorsal telencephalic identity by the combined inhibition of WNT, BMP and  TGF-β signaling, produced neural progenitors with a gene expression signature  typical of human embryonic dentate gyrus (DG) cells. Key markers of neurogenesis  resulted downstream of the NOTCH and WNT pathway and were upregulated in  these progenitors. Notably, we found that, in addition to continuous WNT signaling,  a specific laminin isoform is crucial to prolonging DG stem state and to extend DG  progenitor proliferation for over 200 days in vitro. In fact, transition from laminin  511 to mouse laminin inhibited cell proliferation and promoted the differentiation of  DG cells. Interestingly, global gene expression profiles of early and late progenitor  cells and neurons suggest that a niche of laminin 511 and WNT signaling is  sufficient to maintain a cell population enriched in DG progenitor cells and neurons.  Finally, the xenograft of human DG progenitors into the DG of adult  immunosuppressed host mice produced efficient integration of neurons, which  innervated CA3 layer cells with an area covered by synapses similar to the area  covered by endogenous hippocampal neuron synapses. Our observations indicate  that neurons produced in the established culture niche resemble bona-fide human  DG neurons.

overall_design: Three replicates per sample, corresponding to two subsequent time points of hiPSC in vitro differentiation in the presence of different signaling agonists.

first: Keagan

last: Dunville

first: Federico

last: Cremisi


title: Nascent Transcriptome of AP and VP from Xenopus laevis Embryos at 5-9 hpf (stage 7-9)

city: Philadelphia

last: Good

state: PA

address: Room 1140, 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: To characterize the spatial patterns of zygtoic transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). The animal pole (AP, ~ 1/3 at the top region of embryo) and the vegetal pole (VP,~ 1/3 at the bottom region of embryo) regions were dissected and used for total RNA isolation. To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the nascent transcripts. All libraries were sequenced on illumina NextSeq 500.

overall_design: Two experiments were conducted. In the first experiment, the AP and VP regions from three clutches of embryos at 5-9 hpf (three biological replicates) were used for sequecing the nascent transcripts. In the second experiment, the AP and VP regions from one clutch of embryos at 6-9 hpf (one biological replicate, two technical replicates) were used for sequencing the nascent transcripts.

first: Hui

last: Chen


title: Timing of Germ Layer Initiation Linked to Spatially Patterned Onset of Genome Activation


title: Strong basal/tonic TCR signals are associated with gene expression changes in naive CD4+ T cells

summary: Naïve T cells constantly experience TCR signals in response to self-peptides presented by MHC (pMHC) in vivo. The intensity of these basal or tonic TCR signals can be indirectly read out by expression of surrogate markers of tonic TCR signaling, including the Nur77-GFP transgene and Ly6c. The strength of tonic TCR signaling varies broadly across the naïve CD4+ T cell population and is correlated with functional heterogeneity.Cells that experience the most basal TCR signaling (Nur77-GFP hi, Ly6c lo) are hyporesponsive to peptide-MHC stimulation. Here we examine whether tonic TCR stimulation is associated with differences in mRNA expression.

overall_design: Naïve, CD4 T cells (FoxP3-RFP negative, CD44lo, CD4+) were sorted from mouse spleens plus lymph nodes into four populations based on the expression of Nur77-GFP and Ly6c. Cells were sorted directly into RLT buffer. Sorted cells were either Nur77-GFPlo Ly6c+ (population A), Nur77-GFP intermediate Ly6c+ (population B), Nur77-GFP intermediate Ly6c- (population C) or Nur77-GFP hi Ly6c- (population D). We made biological triplicate samples for a total of 12 samples (4 populations x 3 replicates).


title: Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

summary: To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.

overall_design: Two replicates of embryos from one clutch were treated with CHX from 5 hpf to 7.5 hpf. EU labeled nascent RNAs from both replicates of control and CHX-arrested embryos were sequenced.


title: Total and Nascent Transcriptome of Xenopus laevis Embryos at 5-9 hpf (stage 7-9)

summary: To characterize the nascent transcriptome during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the total RNA ('All'), nascent transcripts ('Bead') and the flowthrough after purification of nascent transcripts ('FL'), respectively. To categorize maternal-zygotic (MZ) genes and zygotic-only (Z) genes, total RNAs from eggs were isolated for constructing libraries. All libraries were sequenced on illumina NextSeq 500.

overall_design: Two experiments were conducted. In the first experiment, two clutches of embryos at 5-9 hpf (two biological replicates) were used for sequecing 'All' (total RNA), 'Bead' (nascent transcripts) and FL (flowthrough RNAs), repsecitvely. In the second experiment, two clutches of embryos at 5-9 hpf (two biological replicates) were used for sequecing 'Bead' (nascent transcripts) and FL (flowthrough RNAs), repsecitvely, two clutches of unfertilized eggs (teo biilogical replicates) were used for sequencing 'All' (total RNA), and two clutches of embryos at 5 hpf (two biological replicates) were used for sequecing 'All' (total RNA).


title: APOE4 cell-specific mechanisms underlying cerebrovascular disorder precede neuronal and synaptic dysfunction and cognitive deficits in mice

city: Los Angeles

first: Berislav

last: Zlokovic

state: CA

address: 1501 San Pablo Street

department: Zilkha Neurogenetic Institute

institute: University of Southern California

summary: We performed single-nucleus RNA-sequencing of the cortex of APOE3 and APOE4 knock-in (KI)flox/flox mice to investigate the effects of human APOE4 gene on cell-specific signaling mechanisms at the BBB and in the brain.

overall_design: 10X single-nucleus RNA-Seq profiling of mouse cortex

first: Giuseppe

last: Barisano

first: Miles

last: Gilliam

first: Fan

last: Gao

middle: V


title: RNA data of MKN45 tumours treated with ERY974 and/or capecitabine in huNOG mice

status: Public on Aug 21 2022

city: Kajiwara

first: YUJI

last: SANO

state: Kamakura

institute: Chugai Pharmaceutical Co., Ltd

summary:
We found that ERY974 shows only moderate antitumor efficacy in MKN45 non-inflamed tumor in huNOG mice. We also observed that ERY974 + capecitabine increases antitumour efficacy in non-inflamed MKN45 tumours.
To identify a mechanism of combination effect, we compared RNA expression of MKN45 tumors treated with ERY974, capecitabine, or combination.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumors treated with ERY974, capecitabine, or combination in huNOG model.

first: Yuji

last: Sano

first: Yukari

last: Nishito

first: Yumiko

last: Azuma

first: Yasuko

last: Kinoshita

first: Toshiaki

last: Tsunenari

first: Takahiro

last: Ishiguro


title: Regulation of chemosensitivity in pancreatic cancer cells

city: Houston

first: Yulin

last: Li

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary: We performed RNA-seq to investigate gene expression changes in pancreatic cancer cells following chemotherapeutic drug treatment. We identify a reversible senescence state among the drug-tolerant persister cells.

overall_design: RNA-seq was performed in MIA PaCa-2 cells in biological triplicates under normal culture conditions and under various conditions of drug treatment (Torin 1 and gemcitabine).

first: Yuanhui

last: Liu

first: Nancy

middle: G

last: Azizian

first: Delaney

last: Sullivan


title: Myeloid-derived Itaconate Suppresses Cytotoxic CD8+ 1 T Cells and Promotes Tumor Growth

status: Public on Aug 20 2022

city: Charlestown

first: Da

last: Teng

state: MA

address: Building 149, 13th Street

institute: Massachusetts General Hospital

summary: To investigate the effect of itaconate on CD4+ T cells, we treated the purified splenic CD4+ T cells with NaCl or itaconate, and then performed the gene expression profilling analysis using data from RNA-seq of 2 different treatment cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NaCl (Ctrl) or itaconate (ITA) treatment of mouse splenic CD4+ T cells

first: Tengjia

last: Jiang

first: Lei

last: Gu


title: Transcriptional profiling by RNA-seq in siDDX5 Rh30 rhabdomyosarcoma cells

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood characterized by the inability to exit the proliferative myoblast-like stage. Here, we identified the DEAD box RNA helicase 5 (DDX5) as a potential therapeutic target to inhibit alveolar rhabdomyosarcoma (ARMS) growth. We show that DDX5 is overexpressed in alveolar RMS cells, demonstrating that its depletion drastically decreases ARMS viability and slows tumor growth in xenograft models. Mechanistically, we provide evidence that DDX5 functions upstream the G9a/AKT survival signalling pathway, by modulating G9a protein stability

overall_design: mRNA profiles of Rhabdomyosarcoma cells with knock-down of DDX5, three biological replicates.

first: Alberto

last: Gualtieri

first: Chiara

last: Mozzetta


title: Liver fibrosis

status: Public on Aug 19 2022

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech


title: CDA-HFD induced NASH liver fibrosis

summary: To understand the fibrotic response in the CDA-HFD induced NASH fibrosis model, we performed RNA-seq on liver samples collected from mice fed with normal chow (week 0) or CDA-HFD chow (weeks 8 and 16).

overall_design: Wild type mice were fed either normal chow or CDA-HFD chow. Samples were collected after 8 weeks on normal chow (denoted week 0), 8 weeks on CDA-HFD, or 16 weeks on CDA-HFD.

first: Ryan

last: LaCanna

first: Jim

last: Jia

middle: A

first: Hans

last: Brightbill

first: Ning

last: Ding


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

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

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

overall_design: Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of selected factors was achieved either thorugh targeted degradation (auxin-degron system) or gene deletion. For degron experiments, corresponding control and treatment sample files are labeled DMSO and 3IAA (3-indolacetic acid), respectively. Control samples for deletion experiments are indicated in the Methods section of the accompanying manuscript. All experiments were done in three replicates (A,B,C).

first: Linda

last: Warfield

first: Lakshmi

last: Mahendrawada

first: Steven

last: Hahn


title: The DNA binding of R270C mutant form of p53 in mouse osteosarcoma AXT cells

city: Tokyo

first: Takatsune

last: Shimizu

address: 2-4-41, Ebara, Shinagawa-ku

department: Pathophysiology

institute: Hoshi University

summary: Mouse osteosarcoma AXT cells were established from bone marrow stromal cells of Ink4a / Arf-null mice by overexpressing human c-MYC (Oncogene 29: 5687-5699, 2010, Cancer Research 74: 6531-6541, 2014). AXT cells harbor R270C mutant form of p53 (equivalent to human R273C mutant). R270C mutant p53 did not show transcriptional activity nor exert critical roles in osteosarcoma progression in vivo. Therfore, we examined whether mutant p53 could bind to chromatin by ChIP-seq analysis using AXT cells. The ChIP-seq of H3K4me3 and H3K9me3 was also performed as the marker of transcriptional activation and repression, respectively.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for mouse p53 as well as the histone modifications H3K4me3 and H3K9me3 in AXT cells cultured in 10% FBS containing IMDM medium.


title: Extracellular Vesicle-Mediated Metastasis Suppressors NME1  and NME2 Modify Lipid Metabolism in Fibroblasts

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

summary: Our aim was to understand how  vesicular NME1 and NME2 released by breast cancer cells influence the tumour microenvironment.  As a model, we used human invasive breast carcinoma cells overexpressing NME1 or NME2, and first  analysed in detail the presence of both isoforms in EV subtypes by capillaryWestern immunoassay  (WES) and immunoelectron microscopy. Data obtained by both methods showed that NME1 was  present in medium-sized EVs or microvesicles, whereas NME2 was abundant in both microvesicles  and small-sized EVs or exosomes. Next, human skin-derived fibroblasts were treated with NME1 or  NME2 containing EVs, and subsequently mRNA expression changes in fibroblasts were examined.  RNAseq results showed that the expression of fatty acid and cholesterol metabolism-related genes  was decreased significantly in response to NME1 or NME2 containing EV treatment. We found that  FASN (fatty acid synthase) and ACSS2 (acyl-coenzyme A synthetase short-chain family member 2),  related to fatty acid synthesis and oxidation, were underexpressed in NME1/2-EV-treated fibroblasts.  Our data show an emerging link between NME-containing EVs and regulation of tumour metabolism.

overall_design: Transcriptomic analysis of patient-derived normal fibroblasts treated by NME1-EVs, NME2-EVs compared to control vector containing Evs (Co-EVs) derived from MDA-MB-231T triple negative breast carcinoma cells.

first: Barbara

last: Mátyási

first: Henriett

last: Butz

first: Mathieu

last: Boissan

first: Anna

last: Sebestyén

first: Krisztina

last: Takacs-Vellai


title: RNA data of NCI-H446 tumours treated with ERY974 and/or paclitaxel in huNOG mice.

first: YUJI

last: SANO

summary:
We found that ERY974 shows only moderate antitumor efficacy in NCI-H446 non-inflamed tumor in huNOG mice. We also observed that ERY974 + paclitaxel increases antitumour efficacy in non-inflamed NCI-H446 tumours.
To identify a mechanism of combination effect, we compared RNA expression of NCI-H446 tumors treated with ERY974, cisplatin, or combination.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumors treated with ERY974, paclitaxel, or combination in huNOG model.

first: Yuji

last: Sano

first: Yukari

last: Nishito

first: Yumiko

last: Azuma

first: Yasuko

last: Kinoshita

first: Toshiaki

last: Tsunenari

first: Takahiro

last: Ishiguro


title: KLF17 promotes human naive pluripotency through repressing MAPK3 and ZIC2

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

summary: Human naïve ESCs cultured in RSET medium  with KLF17 knockdown and human primed ESCs cultured in mTeSR with KLF17 overexpression were sequenced by poly(A)+RNA-seq.

overall_design: Human naïve ESCs cultured in RSET medium  with or without KLF17 knockdown and human primed ESCs cultured in mTeSR with or without KLF17 overexpression were sequenced by poly(A)+RNA-seq.

first: Shaohua

first: Jing

last: Hao

first: Ming

last: Shi


title: Carbon tetrachloride (CCl4) induced liver fibrosis

first: Jason

last: Vander Heiden

summary: To understand the fibrotic response in the CCl4 induced liver fibrosis model, we performed RNA-seq of liver samples from mice treated with oil or CCl4.

overall_design: Mice received intraperitoneal injection of either oil or CCl4 3 times per week for 6 weeks. The whole liver RNA was harvested via RNeasy kit (Qiagen). There were two groups, receiving either oil injection (n=6) or CCl4 injection (n=6).

first: Elsa

last: Ndiaye-Dulac

first: Alexander

last: Abbas

first: Ning

last: Ding


title: Transcriptional profiling by RNA-seq in shG9a Rh41 rhabdomyosarcoma cells

first: Valerio

last: Licursi

summary: Alveolar Rhabdomyosarcoma (ARMS) is the most aggressive subtype mainly caused by the expression of PAX3/7-FOXO1 oncoproteins Here, we show that G9a interacts with PAX3-FOXO1 and regulates its activity. In line with this, transcriptomic analysis by RNA-seq revealed that G9a depletion in RH41 cells induced transcriptional changes inversely correlated by those imposed by PAX3-FOXO1 expression. Overall, our results indicate that G9a promotes PAX3-FOXO1 stability, thus sustaining ARMS myoblastic state.

overall_design: mRNA profiles of Rhabdomyosarcoma cells with knock-down of G9a, four biological replicates.

first: Alberto

last: Gualtieri

first: Chiara

last: Mozzetta


title: Th2 single-cell heterogeneity and clonal interorgan distribution in helminth-infected mice

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

country: Germany

institute: University Clinic Erlangen

summary: Th2 cells provide effector functions in type 2 immune responses to helminths and allergens. Despite substantial knowledge about molecular mechanisms of Th2 cell differentiation, there is little information on Th2 cell heterogeneity and clonal distribution between organs mainly due to technical limitations. To address this issue, we performed combined single-cell transcriptome and TCR clonotype analysis on murine Th2 cells in mesenteric lymph nodes (MLN) and lung after infection with Nippostrongylus brasiliensis (Nb) as a model of human hookworm infection. We identified strong organ-specific expression profiles, but also found populations with conserved effector or migration signatures. A substantial MLN subpopulation with an interferon response signature suggests a role for interferon-signaling in Th2 cell differentiation or diversification. RNA-inferred developmental directions further implied proliferation as a hub for differentiation decisions. Although the TCR repertoire appeared to be highly heterogeneous, we identified expanded Th2 clones and CDR3 motifs. Clonal relatedness between distant organs confirmed the effective exchange of Th2 effector cells. However, locally expanded clones dominated the response, as the most expanded clones in MLN and lung did not overlap.  This new insight in Th2 cell subsets and clonal relatedness in distant organs demonstrates their heterogeneity and suggests that they serve distinct effector functions.

overall_design: We performed combined transcriptome and TCR clonotype analysis using the chromium 10xGenomics and Illumina single cell sequencing platform with Th2 cells isolated from lung and MLN of two IL-4eGFP reporter (4get) mice (Mohrs et al. Immunity 2001) that had been infected 10 days before with Nb. Th2 cells (CD4+IL-4eGFP+) were sorted from single cell suspensions of both organs and were directly subjected to scRNA library preparation. Additionally, we compared the transcriptional profile of the lung draining mediastinal LN and MLN in a second single cell sequencing run.

first: Natalie

last: Thuma

first: Arif

last: Ekici

first: Philipp

last: Kirchner

first: Daniel

last: Radtke


title: Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer

city: Uppsala

first: Longlong

last: Luo

address: Husargatan 3

department: Dermatology and Venereology, Department of Medical Sciences

country: Sweden

institute: Uppsala University

summary: Maintenance of adult tissues requires constant replacement of functional cells that are lost. How highly proliferative stem cell populations undergo differentiation to generate post-mitotic, terminal cell types is poorly understood. Here we combine intravital imaging with molecular insights to investigate how stem cell differentiation is orchestrated in the skin of living mice. We demonstrate that this journey, from initial gene expression changes to movement out of the stem cell compartment, occurs gradually and takes several days to complete. Differentiation-committed cells are capable of proliferating and generating progeny that complete the differentiation trajectory. These divisions are not required to amplify the pool of differentiating cells, but instead occur to protect density in the stem cell layer. Our results thus define epidermal differentiation as a multi-step process, with cell fate commitment temporally preceding the loss of proliferative capacity to satisfy distinct needs within the tissue.

overall_design: Epidermal cell suspensions were isolated from the dorsal skin of two 57-day-old Ivl-CreERT2/R26-tdTomato female mice. Two days prior to cell isolation, these mice were treated with Tamoxifen (10μg/g i.p.) to trace Ivl-expressing cells. Cells were FACS-isolated to traced and non-traced populations of live basal interfollicular epidermis cells (Sytox blue-neg/CD49f+/LY6A+/CD34-neg), which were both captured on a microfluidic Fluidigm C1 system.

first: Karl

last: Annusver

first: Maria

last: Kasper


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors [mouse bulk ATAC-seq]

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

institute: National Cancer Center

summary: Regulatory T (Treg) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Here, we show that Treg cells in the tumor microenvironment (TME) of human lung cancers harbor a completely different open chromatin profile compared to effector T cells and peripheral Treg cells. The integrative sequencing analyses revealed that BATF, IRF4, NF-κb, and NR4A were important transcription factors for Treg cell differentiation in the TME. Particularly, BATF was identified as a key regulator, which leveraged Treg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of Treg cells in the TME. BATF deficiency in Treg cells remarkably inhibited tumor growth and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. Our results propose the specific chromatin remodeling and differentiation program of Treg cells in the TME, which can be applied in the development of Treg cell-targeted therapies.

overall_design: bulk ATAC-seq about mouse tumor infiltrating T cells

first: Kota

last: Itahashi

first: Takuma

last: Irie


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner

status: Public on Aug 18 2022

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1, 53127 Bonn

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: Universitätsklinikum Bonn

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

overall_design: Refer to individual Series


title: Embryonic and neonatal waves generate distinct populations of hepatic ILC1s

city: Zollikerberg

first: Sonia

last: Tugues

address: 104 Forchstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: Group 1 innate lymphoid cells (ILCs) comprising circulating natural killer (cNK) cells and tissue-resident ILC1s are critical for host defense against pathogens and tumors. Despite a growing understanding of their role in homeostasis and disease, the ontogeny of group 1 ILCs remains largely unknown. Here, we used fate mapping and single-cell transcriptomics to comprehensively investigate the origin and turnover of group 1 ILCs. While cNK cells are continuously replaced throughout life, we uncovered tissue-dependent development and turnover of ILC1s. A first wave of ILC1s emerges during embryogenesis in the liver and transiently colonizes fetal tissues. After birth, a second wave quickly replaces ILC1s in most tissues apart from the liver, where they layer with embryonic ILC1s and persist until adulthood undergoing a unique developmental program. While embryonically-derived ILC1s give rise to a cytotoxic subset, the neonatal wave establishes a helper-like subset. Our findings uncover key ontogenic features of group 1 ILCs and their association with unique cellular identities and functions.

overall_design: 1) Embryonic, neonatal and adult hepatic group 1 innate lymphoid cells of WT and Hobit KO mice were obtained by Fluorescence-Activated Cell Sorting (FACS) and their gene expression analyzed by means of single-cell RNA sequencing (sc-RNA seq) using the 10X sequencing platform. 2) Neonatal and adult murine bone marrow was processed and analyzed by sc-RNA seq using the 10X sequencing platform to assess the developmental pathways leading to the hematopoiesis of group 1 innate lymphoid cells in mice.

first: Colin

last: Sparano

first: Darío

last: Solís-Sayago

first: Anjali

last: Vijaykumar

last: Rickenbach

first: Florian

last: Ingelfinger

first: Marijne

last: Vermeer

first: Gioana

last: Litscher

first: Caroline

last: Mussak

first: André

last: Fonseca

first: Maud

last: Mayoux

first: Christin

last: Friedrich

first: César

last: Nombela-Arrieta

first: Georg

last: Gasteiger

first: Burkhard

last: Becher


title: Gene expression data from Akkermansia perfusion trial

city: Örebro

first: Robert-Jan

last: Brummer

address: Södra Grev Rosengatan 42 A

department: School of Medical Sciences

institute: Örebro University

summary:
We studies the effect of Akkermansia perfusion on human by taking biopsies before and after perfusion and assess gene expression.
Affymetrix HuGene 1.1 ST arrays were used to assess whole biopsy gene expression profiles

overall_design: For each subject, biopsies were taken before perfusion (time=1), 2h after perfusion (time=2), and a week after perfusion (time=3). 7 subjects received Akkermansia perfusion (group=”Akk”), 3 subjects received placebo perfusion (group=”Plac”)

first: Ignacio

last: Rangel

first: Dirk

last: Repsilber

first: Michael

last: Muller

first: Guido

last: Hooiveld

first: Jarrko

last: Salojärvi


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner [2]

first: Rayk

last: Behrendt

summary: Loss of SAMHD1 causes chronic activaiton of the MDA5/MAVS dsRNA sensing pathway, only when cGAS/STING signaling is intact.

overall_design: Peritoneal macrophages from  mutant and control mice were isolated by FACS.  Total RNA was subjected to next generation mRNA sequencing.

first: Tina

last: Schumann

first: Andreas

last: Dahl

first: Mohamad

last: Mayo


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner [1]


title: Assessment of unique behavioral, morphological, and molecular alterations in the comparative developmental toxicity profiles of PFOA using the zebrafish model system

city: West Lafayette

first: Jennifer

last: Freeman

state: IN

address: 550 Stadium Mall Drive

department: School of Health Sciences

institute: Purdue University

summary: Perfluoroalkyl substances (PFAS) are a class of synthetic chemicals that are persistent in the environment. Due to concerns linked with longer chain PFAS, shorter chain chemicals were used as replacements, but developmental toxicity assessments of the shorter chain chemicals are limited. The aim of this study was to compare the developmental toxicity of three perfluoroalkyl acids (PFAAs): perfluorooctanoic acid (PFOA), composed of 8 carbon (C8), perfluorohexanoic acid (PFHxA, C6), and perfluorobutanoic acid (PFBA, C4) using the zebrafish (Danio rerio).  LC50s at 120 hour post fertilization (hpf) were determined to assess the potency of each PFAA by exposing developing zebrafish (1-120 hpf) to a range of concentrations. In sublethal assessments, zebrafish were exposed to 0, 4, 40, or 400 parts per billion (ppb; µg/L) of the PFAAs throughout embryonic development (1-72 hpf). Effects of the embryonic exposure on locomotor activities was completed with the visual motor response test at 120 hpf. At 72 hpf, morphological changes including total body length, head length, and head width were assessed. Additionally, transcriptomic profiles of PFOA, PFHxA, and PFBA were determined at 72 hpf to compare altered molecular and disease pathways. The LC50 ranking was PFOA > PFHxA > PFBA, which followed trend as expected based on chain length. PFOA caused hyperactivity and PFBA hypoactivity, while PFHxA did not change behavior. PFOA, PFHxA, and PFBA caused morphological and transcriptomic alterations that were unique for each chemical and were concentration dependent. Cancer was a top enriched disease for PFOA, while FXR/RXR activation was a top canonical pathway in all PFBA exposures. Overall, an embryonic exposure to PFOA, PFHxA, or PFBA resulted in morphological alterations in zebrafish eleuthero-embryos; however, only PFOA and PFBA induced neurobehavioral alterations. The transcriptomic profile of each chemical was unique indicating different toxicity mechanisms and were aligned with human adverse health outcomes supporting predictive value.

overall_design: We treated zebrafish embryos from approximately 1 hour post fertilization through 72 hours post fertilization (embryogenesis) with 0, 4, 40, or 40 ppb PFOA. Following the 72 hour exposure period, fish were processed for transcriptomic analysis.

first: Ola

last: Wasel

middle: L


title: Assessment of unique behavioral, morphological, and molecular alterations in the comparative developmental toxicity profiles of PFHxA using the zebrafish model system

overall_design: We treated zebrafish embryos from approximately 1 hour post fertilization through 72 hours post fertilization (embryogenesis) with 0, 4, 40, or 40 ppb PFHXA. Following the 72 hour exposure period, fish were processed for transcriptomic analysis.


title: Single-cell analysis of human fetal and post-natal γδ thymocytes reveals distinct functional programming.

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

summary: Developmental thymic waves of innate-like and adaptive-like gd T cells have been described, but the current understanding of γδ T cell development is mainly limited to mouse models. Here, we combined single cell (sc) RNA gene expression and sc γδ T cell receptor (TCR) sequencing on fetal and pediatric γδ thymocytes in order to understand the ontogeny of human γδ T cells. Mature fetal γδ thymocytes were committed to either a type 1, a type 3 or type 2-like effector fate, independent from γδ T cell subset type (Vγ9Vδ2 vs nonVγ9Vδ2), and were enriched for public CDR3 features upon maturation. Strikingly, type 1, type 3 and type 2 cells expressed different CDR3 sequences and followed distinct developmental trajectories. In contrast, the pediatric thymus generated only a small effector subset that was highly biased towards Vγ9Vδ2 TCR usage and showed a mixed type 1/type 3 effector profile. Thus, our combined dataset of gene expression and detailed TCR information at the single-cell level defines γδ thymocyte development in human and provides a resource for further study.

overall_design: ϒδT cells were sorted from fetal and pedriatic thymuses, followed by 5'-RNA single cell transcriptome and TCR sequening (10x genomics). In parallel, Vγ9+Vδ2+ and nonVγ9Vδ2 subsets were sorted from fetal and pediatric thymus samples followed by bulk RNA-seq and TCR-seq runs.

first: Guillem

last: Sanchez Sanchez

first: Maria

last: Papadopoulou

first: Abdulkader

last: Azouz

first: Yohannes

last: Tafesse

first: Archita

last: Mishra

first: Jerry

last: Chan

first: Yiping

last: Fan

first: Isoline

last: Verdebout

first: Silvana

last: Porco

first: Frédérick

last: Libert

first: Florent

last: Ginhoux

first: Bart

last: Vandekerckhove

first: Stanislas

last: Goriely


title: Linking transcriptomes with morphological and functional phenotypes in mammalian retinal ganglion cells

city: Guangzhou

first: Sheng

last: Liu

address: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: We characterize the transcriptomic, morphological and functional features of 472 high-quality RGCs using Patch-seq, providing functional and morphological annotation of many transcriptomic defined cell types of previously established RGC atlas.

overall_design: Retinal ganglion cells (RGCs) from mice were analyzed

first: Wanjing

last: Huang

first: Qiang

last: Xu

first: Jing

last: Su

first: Lei

last: Tang

first: Zhao-Zhe

last: Hao

first: Chuan

first: Ruifeng

first: Yuhui

last: Shen

first: Xuan

last: Sang

first: Nana

first: XiaoXiu

last: Tie

first: Zhichao

last: Miao

first: Xialin

first: Ying

first: Yizhi


title: KLF5 governs sphingolipid metabolism and barrier function of the skin

city: Houston

first: Yejing

last: Ge

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

summary: Stem cells are fundamental units of tissue remodeling, whose functions are dictated by lineage-specific transcription factors. Home to epidermal stem cells and their upward stratifying progenies, skin relies upon its secretory functions to form the outmost protective barrier, of which a transcriptional orchestrator has been elusive. KLF5 is a Krüppel-like transcription factor broadly involved in development and regeneration, whose lineage specificity, if any, remains unclear. Here we report KLF5 specifically marks the epidermis, and its deletion leads to skin barrier dysfunction in vivo. Lipid envelopes and secretory lamellar bodies are defective in KLF5-deficient skin, accompanied by preferential loss of complex sphingolipids. KLF5 binds to and transcriptionally regulates genes encoding rate-limiting sphingolipid metabolism enzymes. Remarkably, skin barrier defects elicited by KLF5 ablation can be rescued by dietary interventions. Finally, we found KLF5 is widely suppressed in human diseases with disrupted epidermal secretion, and its regulation of sphingolipid metabolism is conserved in human skin. Altogether, we establish KLF5 as a disease-relevant transcription factor governing sphingolipid metabolism and barrier function in the skin, likely representing a long-sought secretory lineage defining factor across tissue types.

overall_design: Skin epithelium of heterozygous (Het) and KLF5 KO E17.5 murine embryos were purified and assayed for their genome-wide transcripts (RNA-Seq). There are three replicates for Het and Klf5 KO RNA-seq respectively. H3K27ac and Klf5 ChIP-Seq were performed on skin epithelium of E17.5 murine embryos and HaCaT cells. ATAC-Seq was performed on the skin epithelium of E17.5 murine embryo.

last: Lyu


title: Immune landscape in patients at 6 month post hematopoietic stem cell transplantation

city: HEFEI

first: wang

last: hiuru

state: State...

address: NO 17 Lujiang ROAD , HEFEI

department: The First Affiliated Hospital of USTC

institute: USTC

summary: Cytomegalovirus infection is one of the most common and serious infections after hematopoietic stem cell transplantation. Here, we analyzed the gene expression of immune cells in peripheral blood mononuclear cells of six patients who experienced CMV infection after transplantation by single cell sequencing.

overall_design: High-dimensional single-cell RNA sequencing (10X Genomics) was used to profile the transcriptomes of total immune cells isolated from peripheral blood mononuclear cells obtained from six patients at 6 month post hematopoietic stem cell transplantation

first: Wang

last: Huiru

first: Liu

last: huilan


title: Assessment of unique behavioral, morphological, and molecular alterations in the comparative developmental toxicity profiles of PFBA using the zebrafish model system

first: Jennifer

last: Freeman

overall_design: We treated zebrafish embryos from approximately 1 hour post fertilization through 72 hours post fertilization (embryogenesis) with 0, 4, 40, or 40 ppb PFBA. Following the 72 hour exposure period, fish were processed for transcriptomic analysis.

first: Ola

last: Wasel


title: Transcriptomic and epigenetic investigation of Zika virus (ZIKV) infection in human monocyte-derived dendritic cells and other cell types

city: La Jolla

first: Aaron

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

summary: Dendritic cells are key targets for ZIKV infection. To identify host pathways manipulated by ZIKV in dendritic cells, we developed a system that enables characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring, uninfected primary human dendritic cells.

overall_design: We first applied RNA-seq of ZIKV infected and uninfected bystander human monocyte-derived dendritic cells (moDCs) exposed to an unmodified clinical strain of ZIKV to identify ZIKV-regulated transcripts. We then applied a new genomic method recently developed by our group to sequence capped short mRNAs (csRNA-seq) in these cells. In addition to defining mRNA start sites at base pair resolution, this method also identifies transcriptionally active enhancers. Analysis of ZIKV-activated enhancers and promoters defined by csRNA-seq in infected moDCs revealed substantial enrichment for motifs recognized by sterol regulatory element binding proteins (SREBPs). Using ChIP-seq assays, we confirmed that in moDCs, ZIKV increased recruitment of SREBPs to lipid gene promoters and increased nascent expression of these genes.

first: Christopher

last: Benner

first: Sujan

last: Shresta


title: Transcriptomes of adult sorted Epcam+ CD44- enterocytes from small intestine of wildtype and CmafLEC-KO mice

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

summary: Small intestinal villi are highly specialized structural and functional units uniquely adapted to the absorption of nutrients in higher vertebrates. Intestinal villus enterocytes are organized in spatially resolved “zones” dedicated to specialized tasks, such as anti-bacterial protection, and absorption of amino-acids, carbohydrates and lipids. However, the molecular mechanisms for the establishment and maintenance of villus intestinal epithelial zonation are incompletely understood. Here, we show that transcription factor C-Maf is highly expressed in mature lower and mid-villus small intestinal enterocytes, where it is induced in response to BMP signaling. In vivo depletion of C-Maf in the adult enterocytes perturbed the villus epithelial zonation transcriptional program and enhanced the expression of genes involved in carbohydrate metabolism and bile acid regulation and transport, while suppressing genes related to amino acid transport and lipid metabolism. Loss of C-Maf under homeostatic conditions had no effect on body weight due to compensatory small intestinal remodeling, accompanied by increased generation of tuft cells and goblet cell hyperplasia. However, upon challenge with anti-metabolite therapy, C-Maf inactivation impaired body weight recovery, resulting in reduced survival, due to delayed enterocyte maturation. Our results identify a novel role for C-Maf in maintaining the zonation program of differentiated intestinal epithelium, by balancing absorptive versus secretory cell differentiation in the small intestine, while highlighting the importance of coordination between stem/progenitor cell and enterocyte differentiation programs for intestinal regeneration.

overall_design: Methods:RNA QC, library preparations, and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were clustered on two lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

first: Alejandra

last: González-Loyola

first: Tatiana

last: Petrova


title: Integrated multiomics profiling identifies the differentiation program of regulatory T cells in human tumors

first: Hiroyoshi

last: Nishikawa

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center


title: Intestinal type 2 inflammation reprograms mesenteric adipose tissue and permanently alters its resident immune cell niche [bulk RNA]

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: In addition to adipocytes, adipose tissue (AT) is populated by mesenchymal stem cells (MSC) in stages of commitment to the adipocyte lineage, and immune cells which support homeostatic tissue function. How MSC and immune cells interact during infection is poorly understood. We found that during intestinal nematode infection, MSC in gut-associated AT (mFAT) exhibit a bias away from commitment to the adipocyte lineage towards a pluripotent progenitor state. During this time, MSC became metabolically active, and began secreting the alarmins IL-33 and TSLP, and extracellular matrix collagens. In parallel, mFAT became irreversibly populated by Th2 resident memory (Th2RM) cells, which make the tissue modulatory cytokines amphiregulin and TGFβ1. Secretion of these cytokines, and Th2RM activation and maintenance, was driven by IL-33 and TSLP and in turn MSC activation was induced by amphiregulin and TGFβ1. Our findings link Th2RM cells to reversible mFAT remodeling during intestinal infection and underscore the reciprocal dependence of stroma and resident immune cells for lasting tissue immunity.

overall_design: 3 mice for each condition (Control, single infection, recovery and secondary infection) were used.

first: Agnieska

last: Kabat

first: Alexandra

last: Hackl

first: David

last: Sanin

first: Patrice

last: Zeis

first: Katarzyna

last: Grzes

first: Ryan

last: Kyle

first: George

last: Caputa

first: Joy

last: Edwards-Hicks

first: Nisha

last: Rana

first: Angela

last: Castoldi

first: Matteo

last: Villa

first: Leentje

last: Dreesen

first: Jonathan

last: Curtis

first: Joseph

last: Urban

first: Dominic

last: Grun

first: Erika

last: Pearce

first: Edward


title: Transcriptome profiling of the lungs of K18-hACE2 mice infected with SARS-CoV-2 wild-type strain or beta variant

status: Public on Aug 17 2022

city: Daejeon

first: Dae-Gyun

last: Ahn

state: Daejeon

address: 141 Gajeong-ro, Yuseong-gu

department: Center for Convergent Research of Emerging Virus Infection (CEVI)

country: South Korea

institute: Korea Research Institute of Chemical Technology (KRICT)

summary:
Diverse severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged since the beginning of COVID-19 pandemic. We investigated the immunological and pathological characteristics of SARS-CoV-2 beta variant of concern (VOC) compared to the ancestral strain.
To investigate a broad spectrum of immunological responses and to determine the underlying mechanisms of differentially expressed cytokines, we analyzed the whole transcriptome of lung homogenates from SARS-CoV-2 ancestral strain- and beta variant-infected mice at 4 and 6 dpi.

overall_design: Uninfected controls (n=5), SARS-CoV-2 ancestral strain (n=5, 4 dpi), SARS-CoV-2 ancestral strain (n=5, 6 dpi), SARS-CoV-2 beta variant (B.1.351) (n=5, 4 dpi), SARS-CoV-2 beta (B.1.351) (n=5, 6 dpi)

first: Sunhee

last: Lee

first: Gun Young

last: Yoon

first: Su Jin

first: Seong-Jun

last: Kim


title: Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [RNA-seq]

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

institute: University of Perugia

summary: Chromothripsis is a mitotic catastrophe that arises from multiple double strand breaks and incorrect re-joining of one or a few chromosomes. We report on incidence, distribution, and features of chromothriptic events in T-cell acute lymphoblastic leukemias (T-ALL). SNP array was performed in 103 T-ALL (39 ETP/near ETP, 59 non-ETP, and 5 with unknown stage of differentiation), including 38 children and 65 adults. Chromothripsis was detected in 11.6% of all T-ALL and occurred only in adult cases with an immature phenotype (12/39 cases; 30%). It affected 1 to 4 chromosomes, and recurrently involved chromosomes 1, 6, 7, and 17. Abnormalities of genes typically associated with T-ALL were found at breakpoints of chromothripsis. In addition, it gave rise to new/rare alterations, such as, the SFPQ::ZFP36L2 fusion, reported in pediatric T-ALL, deletions of putative suppressors, such as IKZF2 and CSMD1, and amplification of the BCL2 gene. Compared to negative cases, chromothripsis positive T-ALL had a significantly higher level of MYCN expression, and a significant downregulation of RGCC, which is typically induced by TP53 in response to DNA damage. Furthermore we identified mutations and/or deletions of DNA repair/genome stability genes in all cases, and an association with NUP214 rearrangements in 33% of cases.

overall_design: mRNA profiles 25 T-ALL cases including 6 T-ALL cases chromotripsis positive and 19 T-ALL cases chromotrispis negative

first: Roberta

last: La Starza


title: Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [SNP]

summary: Chromothripsis is a mitotic catastrophe that arises from multiple double strand breaks and incorrect re-joining of one or a few chromosomes. We report on incidence, distribution, and features of chromothriptic events in T-cell acute lymphoblastic leukemias (T-ALL). Chromothripsis was detected in 11.6% of analyzed T-ALL and occurred only in adult cases with an immature phenotype (30%). It affected 1 to 4 chromosomes, and recurrently involved chromosomes 1, 6, 7, and 17. Abnormalities of genes typically associated with T-ALL were found at breakpoints of chromothripsis. In addition, it gave rise to new/rare alterations, such as, the SFPQ::ZFP36L2 fusion, reported in pediatric T-ALL, deletions of putative suppressors, such as IKZF2 and CSMD1, and amplification of the BCL2 gene. Compared to negative cases, chromothripsis positive T-ALL had a significantly higher level of MYCN expression, and a significant downregulation of RGCC, which is typically induced by TP53 in response to DNA damage. Furthermore we identified mutations and/or deletions of DNA repair/genome stability genes in all cases, and an association with NUP214 rearrangements in 33% of cases.

overall_design: Copy number analysis of 12 T-ALL cases chromotripsis positive by CytoScan HD Affymetrix platform

first: Valentina

last: Pierini


title: Intestinal type 2 inflammation reprograms mesenteric adipose tissue and permanently alters its resident immune cell niche

first: Immunometabolism

last: Department

overall_design: Refer to individual Series


title: Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults


title: Treatment of infected Syrian hamsters with FG-4592

city: Oxford

first: Peter

last: Wing

address: Old Road Campus, Roosevelt Drive,

country: United Kingdom

institute: University of Oxford

summary: An in vivo experiment to understand the impact of PHD inhibition on SARS-CoV-2 infection.

overall_design: Hamsters infected with SARS-CoV-2 received pre- or post-infection doses of the PHD inhibitor FG-4592.

first: Jane

last: McKeating


title: Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [gene expression]

overall_design: Gene expresion analysis was carried out on 68 T-ALL cases (cth+=11; cht-=57)


title: The HIF prolyl hydroxylase inhibitor FG-4592 reduces infectious SARS-CoV-2 and epithelial damage in a hamster COVID-19 model

sample_organism:
Homo sapiens
Mesocricetus auratus

platform_organism:
Homo sapiens
Mesocricetus auratus


title: The effect of trimethylamine N-oxide on the metabolism of visceral white adipose tissue in spontaneously hypertensive rat

first: guodong

last: he

address: zhongshan road No.102

institute: Guangdong Provincial People's Hospital

summary: Male SHRs and normotensive Wistar-Kyoto(WKY) rats were purchased from Vital River (Vital River Laboratory Animal Technology Co., Ltd, Beijing, China). Briefly, eightteen SHRs aged seven to eight weeks old were randomly assigned to one of three groups: water group (drinking tap water), water containing 333 mg/L or 1g/L TMAO group (TMAO, product number: T1362, Tokyo Chemical Industry, Japan). Six WKY rats of the same age were used as normotensive controls. In this study, WKY rats (n=6), SHR (n=6), and SHR treated with 1g/L TMAO (n=6) were uesd for experiments.

overall_design: Visceral white adipose tissue (vWAT) was sampled from the abdominal cavity. RNA of visceral white adipose tissue was isolated using the TRIzol reagent/chloroform isolation method. SMART technology (Clontech) was used to construct the RNA-seq libraries. RNA sequencing was performed using a illumine Nova-Seq 6000 System with the technical support of the Guangzhou Epibiotek Co., Ltd. The GENCODE database was used to annotate mRNAs. RNA reads were counted using featureCounts (http://bioinf.wehi.edu.au/featureCounts/). The FPKM method was employed to normalize gene expression counts for the sequence.

first: Guo-dong

last: He

first: Xiao-Cong

last: Liu

first: Xing-Hua

last: Hou

first: Ying-qing

last: Feng


title: Spatial transcriptomic analyses of distal colon cross-sections from mice fed high fiber and control diet

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: To perform a global analysis of high fiber diet-induced changes in gene expression in various compartments of the colonic microenvironment, we employed a spatial transcriptomic analysis using the 10X Genomics® platform. This technique allowed for visualization of gene expression in histological cross-sections of the distal colon with spatial information and therefore enabled detection of differentially expressed genes simultaneously in diverse cell types, together with information about their anatomical location in the tissue. Distal colon samples were processed using a Visium Spatial Gene Expression Slide & Reagent Kit (PN-1000184, 10X Genomics) as per the manufacturer’s instructions. Unbiased clustering divided the colon into four distinct zones: epithelium, lamina propria & submucosa, muscularis, and neuronal plexus, as visualized by hematoxylin and eosin (H&E) staining.

overall_design: Four samples from two control diet-fed mice and four samples from two high fiber diet-fed mice were used

first: Mohammad

last: Arifuzzaman

first: David

last: Artis


title: Longitudinal transcriptional profiling of CD8 cells in response to infection and vaccination across tissues

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To determine whether persistent antigen in AdNP immunized mice has any potential cell-intrinsic effects on the genetic program of lung TRM that result in their enhanced longevity, we compared the transcriptional profiles of influenza NP-specific lung TRM (CD8+ i.v. antibody- NP+ CD69+ CD103+), lung TRM that were CD69 single positive (CD8+ i.v. antibody- NP+ CD69+ CD103-) and splenic TEM (CD8+ CD62L- NP+) from mice either infected with x31 influenza or immunized with AdNP at 1-month (35 days post-infection (d.p.i.), x31 and AdNP) and 1-year (365 d.p.i., AdNP only) time points.

overall_design: Transcriptional profiling of 9 experimental groups with 2 samples per group.

first: C

first: J

last: Kohlmeier


title: Reciprocal regulation of Th2 and stroma cells remodels mesenteric adipose tissue in type 2 inflammation

summary: Adipose tissue (AT) contains mesenchymal stromal cells (MSC) in stages of commitment to becoming specialized tissue cells, including adipocytes and fibroblasts, and immune cells which support tissue homeostasis. How MSC and immune cells interact during infection is poorly understood. We show that during intestinal helminth infection MSC in mesenteric AT (mAT) become enriched in non-differentiated progenitor cells. This is accompanied by MSC-intrinsic metabolic reprogramming supporting increased secretion of extracellular matrix (ECM), IL-33, and TSLP. In parallel, Th2 resident memory (Th2RM) cells populate the mAT and persist after infection is resolved. These cells express Areg, TGFβ and IL-5, and are necessary to promote infection induced changes within mAT, including MSC reprogramming and tissue eosinophilia. In turn, IL-33 and TSLP from MSC facilitate Th2RM activation and maintenance. Our findings link Th2RM cells to mAT remodeling during intestinal infection, underscoring the reciprocal dependence of stroma and resident immune cells for lasting tissue immunity.

overall_design: Comprehensive single-cell atlas of CD45+ TCRb+ CD4+ T cells isolated form mesenteric fat, mesenteric lymph nodes and small intestine lamina propria from uninfected conditon and primary and secondary  infection with the intestinal nematode Heligmosomoides polygyrus bakeri (H. polygyrus)

first: Patrice

last: Zeis

first: Dominic

last: Grün


title: Genome wide maps of histone modifications in PRC2 isogenic human MPNST cells with or without DNA demethylating therapy (ChIP-Seq)

first: Ping

last: Chi

address: 417 East 68th Street

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Goals of this study were to determine the effect of PRC2 loss or DNA demethylating therapy (GSK862 and DAC) either alone or in combination on histone modifications.

overall_design: Analysis of 3 histone modifications (H3K27me3, H3K4me3, H3K27ac) in SUZ12 isogenic M3 MPNST cells treated with either Vehicle, GSK862, or DAC.

first: Amish

last: Patel


title: A role for HIFs in the SARS-CoV-2 life cycle

first: Peter

summary: Calu-3 cells were infected with SARS-CoV2, before being treated with 50uM FG-4592 for 24 hours. The impact of cuture conditions on both the host and viral transcriptome were determined by RNA-sequencing.

overall_design: mRNA expression profiles of SARS-CoV-2 infected Calu-3 cells cultured in the absence (control) or presence of 50uM FG-4592 for 24 hours.


title: Perturbation-informed signatures from crosswise integration of transcriptome and chromatin accessibility analyses predict susceptibility to candidate anticancer drugs

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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


title: Perturbation-informed signatures from crosswise integration of transcriptome and chromatin accessibility analyses predict susceptibility to candidate anticancer drugs [ATAC-Seq]

summary: Despite the tremendous advances in the use of omic-based technologies to serve the new paradigm of precision medicine, efforts are still required to expedite their routine use in drug discovery. In this work, we present a case study describing the use of multi-omics to push the development of 3-chloropiperidines (3-CePs), a new class of potential anticancer DNA alkylating agents. The combined analyses of transcriptome and chromatin accessibility efficiently identified proteostasis and DNA repair unbalances as the mechanisms underlying the tropism of 3-CePs against a pancreatic adenocarcinoma cell line. Further on, we implemented a new versatile strategy for the integration of RNA-seq and ATAC-seq information, which could be easily exported to accelerate and extend the separate analyses of omic layers. In addition, this platform offered a new anchor for the construction of a perturbation-informed basal signature able to efficiently predict cell lines sensitivity to 3-CePs and to further direct their development against specific tumor types. Overall, this approach offered a clinically-applicable pipeline to support both the early phases of drug discovery and the correct positioning of therapeutics in the medical practice.

overall_design: Chromatin accessibility profile (ATAC) of BxPC-3 and HCT-15 treated with 2 compounds of the 3-chloropiperidines class. The analysis was performed at 2 time-points including untreated control to investigate the dynamic effect of the new molecules.

first: Caterina

last: Carraro

first: Lorenzo

last: Bonaguro

first: Barbara

last: Gatto


title: Transcriptome of sorted ILC2s in mice fed high-fiber and control diet

summary: To determine the activation patterns of ILC2s and associated ILC2-intrinsic functional molecules triggered by the high fiber diet, we administered either a control or high fiber diet in WT mice and performed RNA sequencing of FACS-sorted ILC2s from mouse colons. RNAseq libraries were prepared from 1,000 sorted colonic lamina propria ILC2s (CD45+Lin-CD90.2+CD127+KLRG1+) by the Epigenomics Core at WCM using the Clontech SMARTer® Ultra® Low Input RNA Kit V4 (Clontech Laboratories). Libraries were sequenced on an Illumina HiSeq 2500, generating 50 bp single-end reads. Two samples from two control diet-fed WT SPF mice and two samples from two high fiber diet-fed WT SPF mice were used.

overall_design: 2 samples were used for each diet group, each sample representing one mouse.


title: Perturbation-informed signatures from crosswise integration of transcriptome and chromatin accessibility analyses predict susceptibility to candidate anticancer drugs [RNA-Seq]

overall_design: Trancriptomic profile of BxPC-3 and HCT-15 treated with 2 compounds of the 3-chloropiperidines class. The analysis was performed at 2 time-points including untreated control to investigate the dynamic effect of the new molecules.


title: Retinal microglia transition to a neurodegenerative MGnD phenotype in glaucoma.

status: Public on Aug 16 2022

city: Boston

first: Oleg

last: Butovsky

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: The apolipoprotein E4 (APOE4) allele is associated with an increased risk of Alzheimer’s disease and a decreased risk of glaucoma, but the underlying mechanisms remain poorly understood. Here we find that in two mouse glaucoma models and in human glaucomatous retinas, microglia transition to a neurodegenerative (MGnD) phenotype characterized by upregulation of Apoe and Lgals3 (Galectin-3). Mice in which Apoe was targeted in microglia or carrying the human APOE4 allele were protected from retinal ganglion cell (RGC) loss despite elevated intraocular pressure (IOP). Similar to Apoe–/– retinal microglia, APOE4 microglia did not upregulate MGnD genes, including Lgals3, following IOP elevation. Genetic and pharmacologic targeting of Galectin-3 ameliorated RGC degeneration, and Galectin-3 expression was attenuated in human APOE4 glaucoma samples. These results demonstrate that impaired activation of APOE4 microglia is protective in glaucoma, and that the APOE-Galectin-3 signaling pathway can be targeted to treat this blinding disease.

overall_design: Illumina NextSeq500 was used to investigate the molecular signature of FCRLS+ sorted retinal microglia isolated from different glaucoma disease models and genetic backgrounds.

first: Milica

last: Margeta


title: Apoe–/– retinal microglia remain homeostatic despite elevated IOP in the microbead glaucoma model.


title: Retinal microglia induce MGnD molecular signature in the DBA/2J glaucoma model


title: Retinal MGnD phenotype can be elicited by exposure to apoptotic neurons in vivo, and is dependent on Apoe.


title: GATA4 and GATA6 loss-of-expression is associated with extinction of the "classical" programme and poor outcome in pancreatic ductal adenocarcinoma

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

summary: GATA4 is the second most expressed GATA factor in the pancreas. GATA4 mRNA is enriched in classical, compared to basal-like pancreatic adenocarcinomas. We utilized CUT&RUN to profile genomic loci bound by GATA4 in PaTu8988S pancreatic adenocarcinoma cells.

overall_design: GATA4 Cut&Run on PaTu8988S cells

first: Mónica

middle: P

last: de Andrés

first: Francisco

middle: X

last: Real


title: Analysis of PRC2 isogenic human MPNST cells with or without DNA demethylating therapy

type: Methylation profiling by high throughput sequencing


title: LncEPAT-induced by EGFR inhibits USP16-mediated H2A deubiquitination

city: Richmond

first: Suyun

last: Huang

state: VA

address: 401 College Street

institute: Virginia Commonwealth University

summary: Depleting lncEPAT in GBM cells leads to altered cell-senescence related gene expression, and this phenotype can be reversed by USP16 further knock-down.

overall_design: We derived three stable GSC23 cell lines (shCtrl, lncEPAT-sh2 and lncEPAT-sh2+USP16-sh2), two replicates for each group. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications ubH2AK119 and RING1B in three cell lines. H3/H15 data are from shCtrl#1, H4/H16 data are from shCtrl replicate. H5/H17 data are from lncEPAT-sh2, H6/H18 data are from lncEPAT-sh2 replicate. H7/H19 data are from lncEPAT-sh2+USP16-sh2, H8/H20 data are from lncEPAT-sh2+USP16-sh2 replicate.

first: Linlin

last: Li

first: Yanjun

last: Wei

first: Yiwen

last: Chen


title: APOE4 retinal microglia remain homeostatic in glaucoma.


title: Myod and Myog ChIP-seq in quiescent and activated muscle stem cells (mouse)

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: We report here the genome-wide deposition of Myod and Myog in quiescent and activated muscle stem cells from wild-type mice.

overall_design: A floxed alleles expressing mito-Dendra2 was combined with the Pax7-Cre(ERT2) driver to induce recombination in the muscle stem cells of adult mice. Tibialis anterior muscles were injured with BaCl2 administration. Quiescent and activated muslce stem cells were purified 2 days post injury, three replicates.

first: Xun

last: Wang

first: Yuemeng

last: Jia


title: A Mitofusin2-Hif1alpha axis regulates the neonatal-to-adult transition in regenerating muscle


title: Gene expression in cornea of BALB/c and C57BL/6N mice

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

summary: Gene expression was quanitified in  4 naive corneas from BALB/c and 4 corneas from C57BL/6N mice without intervention by RNAseq of total RNA with the Ovation Kit for model organisms. To avoid false positive differential expression from better alignment of the reads from C57BL/6 mice to the reference representing a closely related strain while retaining the applicability of the standard reference genome annotation, two pseudogenomes were generated incorporating the known variants into the reference and aligning to the resulting genomes. BAM files were then converted with Lapels to the standard reference, which includes conversion of genome coordinates and adjusting CIGAR strings. Then expression quantification is possible with respect to the standard gene model (here Ensembl version 94) again.

overall_design: Gene expression by sequencing of total RNA fron cornea in two classical inbred mouse strains.

first: Thomas

last: Clahsen


title: H3K9me3 and H3K27me3 ChIP-seq in wild-type, Mfn2-/-, Vhl-/- and HIF1dPA regenerating myofibers.

summary: We report here the genome-wide deposition of H3K9me3 and H3K27me3 in wild-type, Mfn2-/-, Vhl-/- and HIF1dPA regenerating myofibers.

overall_design: Floxed alleles targeting knockout of Mfn2, Vhl, or expression of HIF1dPA were combined with the Pax7-Cre(ERT2) driver to induce recombination in the muscle stem cells of adult mice. Regenerating myofibers were harvested at 14 days post injury for analysis. Four genotypes were analyzed (wild-type, Mfn2-/-, Vhl-/- and HIF1dPA), with three replicates per genotype.


title: NFAT1 (NFATc2) ChIP-seq in wild-type and Mfn2-/- regenerating myofibers

summary: We report here the genome-wide deposition of NFAT1 (NFATc2) in wild-type and Mfn2-/- regenerating myofibers.

overall_design: A floxed Mfn2 alele was combined with the Pax7-Cre(ERT2) driver to induces Mfn2 deletion in the muscle stem cells of adult mice. Regenerating myofibers were harvested at 14 days post injury for analysis. Two genotypes were analyzed (wild-type and Mfn2-/-), with two replicates per genotype.


title: Genetic targeting or pharmacological inhibition of galectin-3 dampens microglia reactivity and delays retinal degeneration

status: Public on Aug 15 2022

city: Cologne

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

institute: University of Cologne

summary: Dysfunctional humoral and cellular innate immunity are key components in the development and progression of age-related macular degeneration (AMD). Specifically, chronically activated microglia and their disturbed regulatory system contribute to retinal degeneration. Galectin-3, a b-galactose binding protein, is a potent driver of macrophage and microglia activation and has been implicated in neuroinflammation, including neurodegenerative diseases of the brain. Here, we report that galectin-3 is strongly upregulated in reactive retinal microglia of AMD patients and in two related mouse models of retinal degeneration. Specific targeting of galectin-3 by genetic knockout or using the small-molecule inhibitor TD139 blocks microglia reactivity and protects from retinal damage in different models of light-induced retinal degeneration. These data define galectin-3 as potent driver of retinal degeneration and highlight the protein as a drug target for ocular immunomodulatory therapies.

overall_design: Global mRNA expression analysis of Balb/cJ mouse retinas in naive and light exposued mice with vehicle or TD139 treatment

first: T


title: EZH2 Catalytic Inhibition Prevents Urothelial Carcinoma Progression Through Immune Activation [ChIP-seq]

city: Chicago

first: Joshua

last: Meeks

state: Illinois

address: 302 E. Huron Street, Simpson Querrey Building, Room number: 7-500

department: Urology/BMG

institute: Northwestern University

summary: The long-term survival of advanced urothelial carcinoma (UCa) patients is limited due to an innate resistance to treatment. We identified elevated expression of the histone methyltransferase EZH2 as a hallmark of aggressive UCa, and therefore, hypothesized that EPZ-011989, a small molecule catalytic inhibitor of EZH2, might have anti-tumor effects in UCa. Here we show that in a carcinogen-induced mouse bladder cancer model, EZH2 inhibition results in reduced tumor progression, elevated tumor infiltrating T cells, increased pro-inflammatory cytokine secretion and MHC class II expression on UCa cells. Treatment of mice with EPZ011989 causes increased MHC class II expression on the urothelium, and was able to activate CD4+ T cells, which is completely abrogated with genetic ablation of the acquired immune system.  These findings support a unique role for EZH2 catalytic activity in mediating UCa immune evasion and, for the first time, prove the efficacy of EZH2 catalytic inhibitors in a UCa model, a finding that can potentially be expanded to humans with UCa.

overall_design: Chromatin immunoprecipitation sequencing (Chip-seq) for histone modification H3K27me3

first: Andrea

last: Piunti


title: EZH2 Catalytic Inhibition Prevents Urothelial Carcinoma Progression Through Immune Activation.

overall_design: Refer to individual Series


title: Integrated multi-omics approach revealed cellular senescence landscape

city: Beijing

first: Qiao

last: Song

address: No.45 Changchun Street

department: Department of Clinical laboratory

institute: Xuanwu Hospital, Capital Medical University

summary: Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq, and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements.

overall_design: Considering that human diploid 2BS fibroblasts are a widely used cell model to study cellular senescence and aging-related disorders, we employed growing 2BS cells and senescent 2BS cells as Replicative Cellular Senescence (RS) representatives to generate ATAC-seq libraries , which can sensitively measure high-resolution chromatin accessibility.  For each age stage, we obtained two independent ATAC-seq replicates.

first: Peichang

first: Chengyang

first: Liheng

last: Zhang

first: Guisheng

first: Yuli

last: Hou

first: Jing

last: Liu

first: Yaqi

first: Yuting

last: Cui


title: Chronic Activation of pDCs in Autoimmunity is linked to Dysregulated ER Stress and Metabolic Responses

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: Plasmacytoid dendritic cells (pDCs) chronically produce type I interferon (IFN-I) in multiple autoimmune diseases, such as systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). Here, we report that the IRE1α-XBP1 branch of the unfolded protein response (UPR) inhibits the production of IFN-α by TLR7- or TLR9-activated pDCs. In SSc patients, pDCs demonstrated reduced expression of UPR marker genes, which inversely correlated with the levels of IFN-I-stimulated genes. CXCL4, a chemokine that is elevated in SSc patients, downregulated IRE1α-XBP1-controlled genes and promoted IFN-α production by pDCs. Mechanistically, IRE1α-XBP1 activation rewired glycolysis to serine biosynthesis by inducing phosphoglycerate dehydrogenase (PHGDH) expression. This process reduced pyruvate access to the tricarboxylic acid (TCA) cycle and blunted mitochondrial ATP generation and cAMP signaling, which are essential for pDC IFN-I responses. Notably, PHGDH expression was reduced in pDCs from patients with SSc and SLE, and pharmacological blockade of TCA cycle reactions inhibited IFN-I responses in pDCs from these patients. Hence, modulating the IRE1α-XBP1-PHGDH axis may represent a hitherto unexplored strategy for alleviating chronic pDC activation in autoimmune disorders.

overall_design: Gene expression analysis of RNA-seq data from healthy human pDCs comparing response of pDCs to ER-stress inducing agents (Tunicamycin and Thapsigargin) and TLR9 activating ligands.

first: Vidyanath

last: Chaudhary

first: David

last: Oliver

first: Franck

last: Barrat


title: EZH2 Catalytic Inhibition Prevents Urothelial Carcinoma Progression Through Immune Activation [RNA-seq]

overall_design: RNA sequencing data for bladder cancer cell-lines treated with DMSO/EPZ0011989 and BBN mouse tumors from mice treated with either vehicle control or EPZ0011989


title: Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models.

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Chromosome 16p11.2 reciprocal genomic disorder due to recurrent copy number variants (CNVs) involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue, cell-type, and dosage specific, though more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2163 differentially expressed genes) and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated/loss-of-function constraint/FMRP gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, while single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Both neuronal ratios and gene expression changes in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption in 16p11.2 carriers that may contribute to changes in neurodevelopmental and cognitive function.  Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes, with relative impacts that are context-specific.

overall_design: bulk RNAseq based transcriptomic analyses of six tissues from 16p11.2 deletion and duplication as well as control mouse models; single cell RNAseq based transcriptomic analyses of human iPSC-derived 16p11.2 deletion and duplication as well as control organoids.

first: Derek

last: Tai

first: Parisa

last: Razaz

first: Dadi

last: Gao

first: Jennifer

first: Xander

last: Nuttle

first: Celine

last: de Esch

first: Ryan

last: Collins

first: Benjamin

last: Currall

first: Kathryn

last: O' Keefe

first: Nicholas

last: Burt

first: Rachita

last: Yadav

first: Lily

first: Kiana

last: Mohajeri

first: Tatsiana

last: Aneichyk

first: Ashok

last: Ragavendran

first: Alexei

last: Stortchevoi

first: Elisabetta

last: Morini

first: Weiyuan

last: Ma

first: Diane

last: Lucente

first: Alex

last: Hastie

first: Raymond

last: Kelleher

first: Roy

last: Perlis

first: Michael

last: Talkowski

first: James

last: Gusella


title: Establishing a reproducible approach to study cellular functions of plants cells with 3D bioprinting

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

institute: North Carolina State University

summary: Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. To investigate the cellular reprogramming underlying the initial cell divisions prior to microcallus formation, we collected RNA from isolated differentiated root cells immediately, 1, and 3 days after bioprinting. We showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli and of which the timing coincides with the induction of core cell cycle genes and regeneration-related genes. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.

overall_design: For the expression profiles, we collected RNA from bioprinted constructs and isolated cells (as a control) from meristematic and differentiated Arabidopsis thaliana root tissue.  We performed three independent experiments.

first: Maimouna

last: Abderamane Tahir

first: Ross

last: Sozzani


title: Neuregulin 4 suppresses NASH-associated liver cancer through restraining tumor-prone liver microenvironment

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

summary: The mammalian liver comprises heterogeneous cell types within its tissue microenvironment that respond to physiological cues and undergo pathophysiological reprogramming in disease states, such as nonalcoholic steatohepatitis (NASH). Patients with NASH are at increased risk for the development of hepatocellular carcinoma (HCC). However, the molecular and cellular nature of liver microenvironment remodeling that links NASH to liver carcinogenesis remains obscure. Here we show that diet-induced NASH is characterized by induction of tumor-associated macrophage (TAM)-like macrophages and exhaustion of cytotoxic T cells in mouse liver. The adipose-derived endocrine factor Neuregulin 4 (NRG4) serves as a hormonal checkpoint that restrains this pathological reprogramming during NASH. NRG4 deficiency exacerbates the induction of tumor-prone liver immune microenvironment and NASH-associated HCC, whereas transgenic NRG4 overexpression elicits protective effects in mice. In a therapeutic setting, recombinant NRG4 protein exhibits remarkable efficacy in inhibiting HCC in mice with NASH, thereby paving the way for future therapeutic development.

overall_design: RNA-seq on nonalcoholic steatohepatitis (NASH) mouse liver in different genotypes; Single cell RNA-seq on non-parenchymal cells of NASH mouse liver.

first: Zhimin

last: Chen

first: Peng

last: Zhang

first: Tongyu

last: Liu

first: Jiaqiang

last: Zhu

first: Xiaoxue

last: Qiu


title: Influence of catalytic and non-catalytic functions of class I HDACs on the cellular transcriptome

status: Public on Aug 14 2022

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: We generated a cellular class I HDAC toolbox allowing to discriminate between catalytic and non-catalytic roles of class I HDACs. Our study reveals a comprehensive, functional analysis of class I HDACs.

overall_design: HAP1 cell lines lacking individual HDACs or expressing catalytically inactive, transgenic isoforms were used for gene expression analysis. We demonstrate that HDAC1 and HDAC2 have crucial, partially overlapping functions in the regulation of gene expression. Disrupting HDAC3 caused major changes in the transcriptome, indicating that this enzyme has unique regulatory roles. Furthermore, cells expressing inactive HDAC1, HDAC2 and HDAC8 better mimicked HDAC inhibitor treated cells compared to their respective knockouts.  3 biological replica were analyzed of each cell line or treatment condition, including:  1) control cell line (untreated), 2) cells with knockout of individual class I HDACs, 3) cells expressing inactive transgenic HDAC from the AAVS1 locus in the control background, 4) cells expressing either active or inactive transgenic HDAC from the AAVS1 locus in the corresponding knockout background, 4) cells treated with MS-275, 5) cells treated with JQ12

first: Lena

last: Hess

first: Verena

last: Moos

first: Arnel

last: Lauber

first: Wolfgang

last: Reiter

last: Schuster

first: Natascha

last: Hartl

first: Daniel

last: Lackner

first: Thorina

last: Boenke

first: Anna

last: Koren

first: Paloma

last: Guzzardo

first: Brigitte

last: Gundacker

last: Riegler

first: Petra

last: Vician

first: Claudia

last: Miccolo

first: Susanna

last: Leiter

first: Mahesh

last: Chandrasekharan

first: Terezia

last: Vcelkova

first: Andrea

last: Tanzer

first: Jun

middle: Q

last: Jun

last: Bradner

first: Gerald

last: Brosch

first: Markus

first: Christoph

last: Bock

first: Tilmann

last: Bürckstümmer

first: Stefan

last: Kubicek

last: Chiocca

first: Srividya

last: Bhaskara


title: Impact of ALK inhibition or phospho-deficient mutation of CDK9 on gene expression in ovarian cancer cells

city: Houston

first: YU YI

last: CHU

state: Texas

address: 6565 MD Anderson Blvd

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

summary: The goal of this study is to determine the impact of ALK inhibition or phospho-deficient mutation of CDK9 on gene expresion profiles in ovarian cancer cells

overall_design: We performed bulk RNA sequencing on three cellular phenotypes: (1) cells expressing WT CDK9, (2) cells expressing WT CDK9 treated with an ALK inhibitor, and (3) cells expressing Y19F-mutant (phospho-deficient) CDK9

first: Mien-Chie

last: Hung

first: Yu-Yi

last: Chu


title: Characterization of alpha-globin locus chromatin accessibility in erythroid cells following insertion of PP7 stem-loops at the Hba-a1 gene

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: PP7 stem-loop DNA was inserted into the Hba-a1 gene in order to monitor nascent transcription dynamics of alpha-globin during erythroid differentiation. To confirm that this genetic modification does not influence the chromatin accessibility of the locus in erythroid cells we performed ATAC-seq in wild-type and Hba-a1-PP7 (PP7) cells, as well as Hba-a1-PP7 clones with a stably integrated PP7 coat protein (PCP) expression construct. No differences were observed between these cell lines in terms of chromatin accessibility at the alpha-globin locus, indicating the PP7 modification likely did not disrupt normal gene activation in these cells.

overall_design: Hba-a1-PP7 cells were created by insertion of 24 PP7 repeats in the first exon of the Hba-a1 gene by recombinase-mediated cassette exchange (RMCE). PP7 repeats were synthesized (GenScript) and inserted into the first exon of Hba-a1 in a plasmid containing DNA sequence surrounding Hba-a1 recovered from a mouse BAC clone (RP22-289A22, BACPAC Resources Centre). This construct was exchanged into cells containing an acceptor site (loxP, lox511 sites) at the Hba-a1 gene. A clone in which successful exchange had occurred (PP7) was transfected with a PGK:PCP-EGFP construct (a gift from Jonathan Chubb). Three clones with stable integration of the construct (PCP B7, B11, C12) were taken forward for analysis. ATAC-seq was performed in duplicate on WT and PP7 cells and on the three PCP clones.

first: Danuta

last: Jeziorska

first: Edward

last: Tunnacliffe


title: Sg SCS suppresses inflammation and oral microbiome

city: Iowa City

first: Erliang

last: Zeng

state: IOWA

address: 801 Newton Rd, DSB N101-9, College of Dentistry

institute: University of Iowa

summary: To investigate the properties of Sg spent culture supernatant (SCS) on the proliferation of periodontal pathogens and the expression of proinflammatory cytokines by human macrophages, epithelial cells, and gingival fibroblasts.

overall_design: Sg SCS was collected from Sg cultures grown in DMEM medium and added to the growth media of representative health and disease related oral species: Sg, Streptococcus sanguinis (Ss), Streptococcus mitis (Sm), Streptococcus oralis (So), Pg, Tanneralla forsythia (Tf), and Treponema denticola (Td). The Sg SCS was also tested for its ability to regulate expression of proinflammatory cytokines by human macrophages, epithelial cells, and gingival fibroblasts upon stimulation with Pg-derived lipopolysaccharide (Pg-LPS).

first: Yi

last: Shu

first: Chawin

last: Upara

first: Qiong

last: Ding

first: Jeffrey

last: Banas

first: Liu

last: Hong