title: Single-cell sequecing of LCMV-specific WT and HIF-1a-deficient CD8 T cells isolated from LCMV-Clone13 infected host mice

first: hao

last: wu

summary: To determine the role of hypoxia-inducible factor 1 alpha (HIF-1a) in exhausted T cells, we crossed Hif1a-fl/fl Cd4-Cre mice to tdTomato+ P14 animals and adoptively co-transferred equal numbers of WT and HIF-1a-deficient P14 CD8+ T cells into chronically infected WT host mice. 21 days post infection, we retrieved GFP+ (WT) and tdTomato+ (HIF-1a-deficient) donor P14 T cells by FACS sorting and subjected CITE-seq antibody-barcoded WT and HIF-1a-deficient CD8+ P14 T cells to multiplexed scRNA sequencing analysis.

overall_design: CD8+ tdTomato+ (HIF-1a-deficient) and CD8+ tdTomato+ GFP+ (WT) P14 T cells were FACS-sorted from the spleen and LNs of chronically infected mice using a FACSAria III cell sorter (BD Biosciences). To multiplex different samples for scRNA sequencing, single-cell suspensions after FACS sorting were labelled with different TotalSeqA antibodies (Biolegend). Each sample was labelled with one specific hashtag (1:400 dilution) and CITE-seq antibodies (1:800 dilution, all Biolegend). After labelling for 30 min at 4 °C, samples were washed three times and multiplexed in equal cell numbers at a density of 106 cells/ml.

first: Martin

last: Vaeth

first: Hao

last: Wu


title: DUX4-r exerts a neomorphic activity that depends on GTF2I in acute lymphoblastic leukemia

status: Public on Sep 15 2023

city: Milan

first: Davide

last: Gabellini

address: Via Olgettina 60

department: Division of Genetics and Cell Biology

country: Italy

institute: SAN RAFFAELE SCIENTIFIC INSTITUTE

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single-cell epigenetic, transcriptional, and protein states of HIV-1-infected cells [Feature_Barcoding]

status: Public on Sep 20 2023

city: New Haven

first: Yulong

last: Wei

state: CT

address: 295 Congress Avenue

department: Microbial Pathogenesis

country: USA

institute: Yale University

summary: The heterogeneity and rarity of HIV-1-infected cells hampers effective cure strategies. We used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, 156 surface proteins, HIV-1 DNA, and HIV-1 RNA from six HIV-1+ individuals during viremia and after suppressive antiretroviral therapy. We identified 252 transcriptionally inactive (HIV-1 DNA+ RNA–) and 270 transcriptionally active (HIV-1 RNA+) HIV-1-infected cells from 82,549 memory CD4+ T cells. We identified increased transcription factor accessibility in HIV-1 DNA+ RNA– cells (RORC) and HIV-1 RNA+ cells (IRF and AP-1), in addition to CNC and MAF in both. Both HIV-1 DNA+ RNA– and HIV-1 RNA+ cells upregulate IKZF3 (Aiolos) that correlates with proliferation of HIV-1-infected cells. We revealed that the heterogeneous HIV-1-infected T cells comprise four distinct immune programs driven by epigenetic regulators – IRF-activation, Eomes-cytotoxic effector, AP-1-migration, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of transcriptionally inactive and active HIV-1-infected cells.

overall_design: Paired PBMC samples from 6 HIV-1-infected individuals from the Sabes cohort during viremia and after viral suppression and PBMC samples from 4 uninfected controls were processed for DOGMA-seq. Memory CD4+ T cells were isolated from dead-cell removed PBMC by negative selection. Purified memory CD4+ T cells from participants were each stained with uniquely barcoded TotalSeq-A hashing antibodies and pooled. Cells were stained with a panel of 154 cell surface proteins and 9 isotype controls included in TotalSeq-A Human Universal Cocktail. After staining, cells were permeabilized with 0.01% digitonin. Cells were then loaded into the 10x Genomics Chromium Controller for DOGMA-seq (3’ Single Cell 10x Multiome (ATAC + GEX) with feature barcoding). This resulted in libraries for the single cell epigenome, transcriptome, and surface proteome. Six DOGMA-seq runs from virally suppressed HIV-1 infection samples (YW1 – YW6); three DOGMA-seq runs from viremic HIV-1 infection (YW8 – YW10); one DOGMA-seq runs from uninfected controls (HD1). Supplementary file “Participant Hashtags” contains the hashtag IDs for each participant in each pooled samples.

first: Timothy

middle: C

last: Davenport

first: Jack

middle: A

last: Collora

first: Haocong

middle: K

last: Ma

first: Delia

last: Pinto-Santini

first: Javier

last: Lama

first: Ricardo

last: Alfaro

first: Ann

last: Duerr

first: Ya-Chi

last: Ho


title: Nucleus-Independent Transgenerational Small RNA Inheritance in Caenorhabditis elegans

status: Public on Sep 22 2023

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

type: Non-coding RNA profiling by high throughput sequencing

summary: In C. elegans worms, epigenetic information transmits transgenerationally. Still, it is unknown whether the effects transfer to the next generation inside or outside of the nucleus. Here we use the tractability of gene-specific double-stranded RNA-induced silencing to demonstrate that RNAi can be inherited independently of any nuclear factors via mothers that are genetically engineered to transmit only their ooplasm but not the oocytes’ nuclei to the next generation. We characterize the mechanisms and, utilizing RNA sequencing, chimeric worms and sequence polymorphism between different isolates, identify endogenous small RNAs which, similarly to exogenous siRNAs, are inherited in a nucleus-independent manner. From an historical perspective, these results might be regarded as partial vindication of discredited cytoplasmic inheritance theories from the 19th century, such as Darwin’s “pangenesis” theory.

overall_design: RNA was extracted from "day one" adult nematodes of different isolates (N2 and MY16). The samples include 3 biological replicates of worms in four  conditions (MY16, MY16_star, N2, N2_star). 11 samples are from small RNA sequencing (one sample from MY16_star failed to yield sufficient RNA) and 12 samples are from total RNA sequencing, yielding a total of 23 samples.

first: Itai

last: Rieger

first: Guy

last: Weintraub

first: Itamar

last: Lev

first: Kesem

last: Goldstein

first: Dana

last: Bar-Zvi

first: Sarit

last: Anava

first: Shai

last: Shaham

first: Oded

last: Rechavi


title: Elucidation of E3 Ubiquitin Ligase Specificity Through Proteome-wide Internal Degron Mapping

status: Public on Sep 21 2023

city: Boston

first: Stephen

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The ubiquitin-proteasome system plays critical roles in biology by regulating protein degradation. Despite their importance, precise recognition specificity is known for few of the 600 E3s. Here we establish a two-pronged strategy for identifying and mapping critical residues of internal degrons on a genome scale in HEK-293T cells.  We employ Global Protein Stability profiling combined with machine learning to identify 15,800 peptides likely to contain sequence-dependent degrons. We combine this with scanning mutagenesis to define critical residues for over 5,000 predicted degrons.  Focusing on Cullin-RING ligase degrons, we generated mutational fingerprints for 219 degrons and developed DegronID, a computational algorithm enabling the clustering of degron peptides with similar motifs.  CRISPR analysis enabled the discovery of E3-degron pairs of which we uncover 16 pairs that revealed extensive degron variability and structural determinants. We provide the visualization of this data on the public DegronID Data Browser as a resource for future exploration.

overall_design: We performed the global protein stability (GPS) in HEK-293T cells using a human peptidome and performed CRISPR screens with an sgRNA library targetting genes related to the ubiquitin proteasome system.

first: Zhang

last: Zhiqian

first: Sie

last: Brandon

first: Chang

last: Aiquan

first: Leng

last: Yumei

first: Nardone

last: Christopher

first: Timms

last: Richard T.

first: Elledge

last: Stephen J.


title: MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer’s disease II

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: Neuronal cell loss is a defining feature of Alzheimer’s disease (AD), but the underlying mechanisms remain unclear. We xenografted human or mouse neurons into the brain of a mouse model of AD. Only human neurons displayed tangles, Gallyas silver staining, granulovacuolar neurodegeneration (GVD), phosphorylated tau blood biomarkers, and considerable neuronal cell loss. The long noncoding RNA MEG3 was strongly up-regulated in human neurons. This neuron-specific long noncoding RNA is also up-regulated in AD patients. MEG3 expression alone was sufficient to induce necroptosis in human neurons in vitro. Down-regulation of MEG3 and inhibition of necroptosis using pharmacological or genetic manipulation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, or mixed lineage kinase domain-like protein (MLKL) rescued neuronal cell loss in xenografted human neurons. This model suggests potential therapeutic approaches for AD and reveals a human-specific vulnerability to AD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H9-stem cell-derived GFP positive neuronal progenitors were grafted (100,000 cells/mice) in control and amyloid mice at P1. GFP-positive grafted regions were extracted using a dissection microscope at 2, 6, and 18 months post-transplantation.

first: Sriram

last: Balusu

first: Katrien

last: Horre

first: Nicola

last: Thrupp

first: An

last: Snellinx

first: Lutgarde

last: Serneels

first: Iordana

last: Chrysidou

first: Amaia

middle: M

last: Arranz

first: Annerieke

last: Sierksma

first: Joel

last: Simren

first: Thomas

last: Karikari

first: Henrik

last: Zetterberg

first: Wei-Ting

last: Chen

first: Dietmar

middle: R

last: Thal

first: Evgenia

last: Salta

first: Mark

last: Fiers

last: De Strooper


title: Oncogenic KRAS drives lipo-fibrogenesis to promote angiogenesis and colon cancer progression

city: Houston

first: Wen-Hao

last: Hsu

address: 1901 East Rd

institute: MD Anderson

summary: Oncogenic KRAS (KRAS*) contributes to many cancer hallmarks. In colorectal cancer (CRC), KRAS* has been shown to suppress anti-tumor immunity which promotes tumor metastasis. Here, we show that the protumor actions of KRAS* extend to the adipogenic transformation of fibroblasts into lipid-laden cancer-associated fibroblasts (CAFs), which spur angiogenesis. Mechanistically, KRAS*-mediated activation of the transcription factor CP2 (TFCP2) resulted in TFCP2-mediated transcriptional upregulation of pro-adipogenic factors BMP4 and WNT5B to drive lipid-rich CAF transformation. Functionally, these lipid-rich CAFs promoted tumor growth via their production of vascular endothelial growth factor A (VEGFA). Correspondingly, genetic and pharmacological neutralization of TFCP2 decreased the abundance of lipid-rich CAFs, reduced tumor angiogenesis, and increased survival in an autochthonous KRAS*–driven CRC mouse model. These murine findings mirror translational profiles in human CRC. Thus, KRAS* transforms the stromal cell state to promote tumor angiogenesis and disease progression, providing an actionable therapeutic intervention for KRAS*–driven CRC.

overall_design: Three independent samples each from iKAP, iAP, and iKAP-DOXoff (KRAS*-off) CRC tumors were collected for tumor dissociation and single cell sequencing analyses. All tumors were collected in size of 1 cm3 at 2 months after TAM/DOX tumor induction following the procedure described above. For the iKAP-DOXoff (KRAS*-off) CRC tumors, Doxycycline was retrieved for 7 days after 7 weeks of TAM/DOX tumor induction. scRNA Sequencing was performed by MD Anderson’s CPRITSingle Core.

first: Kyle

last: LaBella

first: Yiyun

last: Lin

first: Ping

last: Xu

first: Rumi

last: Lee

first: Cheng-En

last: Hsieh

first: Lei

last: Yang

first: Ashley

last: Zhou

first: Jonathan

last: Blecher

first: Chang-Jiun

last: Wu

first: Kangyu

first: Xiaoying

last: Shang

first: Shan

last: Jiang

first: Denise

middle: J

last: Spring

first: Yan

last: Xia

first: Peiwen

first: John

last: Shen

first: Scott

last: Kopetz

first: Ronald

last: DePinho


title: MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer’s disease

first: Bart

last: de Strooper

summary:
Neuronal cell loss is a defining feature of Alzheimer’s disease (AD), but the underlying mechanisms remain unclear. We xenografted human or mouse neurons into the brain of a mouse model of AD. Only human neurons displayed tangles, Gallyas silver staining, granulovacuolar neurodegeneration (GVD), phosphorylated tau blood biomarkers, and considerable neuronal cell loss. The long noncoding RNA MEG3 was strongly up-regulated in human neurons. This neuron-specific long noncoding RNA is also up-regulated in AD patients. MEG3 expression alone was sufficient to induce necroptosis in human neurons in vitro. Down-regulation of MEG3 and inhibition of necroptosis using pharmacological or genetic manipulation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, or mixed lineage kinase domain-like protein (MLKL) rescued neuronal cell loss in xenografted human neurons. This model suggests
potential therapeutic approaches for AD and reveals a human-specific vulnerability to AD.

overall_design: mRNA profile of H9-derived neurons (DIV75), 7-day post tranduction with either control virus or MEG3 lentiviral vector.

first: Sriram

last: Balusu

first: Katrien

last: Horre

first: Nicola

last: Thrupp

first: Katleen

last: Craessaerts

first: An

last: Snellinx

first: Lutgarde

last: Serneels

first: Dries

last: T’Syen

first: Iordana

last: Chrysidou

first: Amaia

last: Arranz

first: Annerieke

last: Sierksma

first: Joel

last: Simren

first: Thomas

last: Karikari

first: Henrik

last: Zetterberg

first: Wei-Ting

last: Chen

first: Dietmar

last: Thal

first: Evgenia

last: Salta

first: Mark

last: Fiers

last: De Strooper


title: Effect of existence or depletion of LIN28B on gene expression during tumor growth of PDAC cells

status: Public on Sep 14 2023

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

country: China

institute: Peking Univ.

summary: To investigate the effect of existence or depletion of LIN28B in PDAC growth , we established cell lines with or without LIN28B expression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.Additionally, we performed the whole exome sequencing of 14837T and 15376T to compare their differences

overall_design: 9 samples. RNA of 15376T, LIN28B KO 15376T and 14837T were harvested using Trizol reagent. 3 ug of total RNA is used for the construction of sequencing libraries by Hiseq 4000 PE150. Additionally, 3 samples. Genomic DNA of 15376T, 14837T and WT tail tissue were harvested. 1 ug of genomic DNA is used for the construction of sequencing libraries

first: Zhaoqi

last: Shu

first: Ying

last: Zhao


title: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [Nanopore]

city: WuHan

first: zou

last: yanyan

address: SHIZISHAN

institute: HZAU

summary: We developed MGA-seq for detecting both chromatin spatial contacts and WGS information at the same time in clinical samples,  then we combine the two kind of information to detecte small variation, large structural variation, homogenously staining regions, and extrachromosomal DNA.

overall_design: Nanopore

first: Da

last: Lin

first: Yanyan

last: Zou


title: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [WGS]

overall_design: WGS


title: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [MGA-Seq]

overall_design: MGA-seq just needs 9 hours and 56 dollars to complete all the experimental steps in one tub, which is very suitable for clinical translation.


title: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [RNA-Seq]

summary:
We developed MGA-seq for detecting both chromatin spatial contacts and WGS information at the same time in clinical samples,  then we combine the two kind of information to detecte small variation, large structural variation, homogenously staining regions, and extrachromosomal DNA.
RNA-seq was employed to measured the RNA transcription level of genes within the amplified region

overall_design: RNA was extracted using the RNAiso Plus (Takara, 9109) according to manufacturer’s protocol. Sequencing libraries were prepared using the VAHTS Stranded mRNA-Seq Library Prep Kit (Vazyme, NR602-02) according to manufacturer's protocol.


title: Exploring the Mechanism of Resistance to vincristine in Breast Cancer Cells through Transcriptome Sequencing Technology

status: Public on Sep 12 2023

city: Dalian

first: chang

middle: miao

last: wang

address: Lianhe Road

department: Τhe First Affiliated Hospital of Dalian Medical University

institute: Department of General Surgery

summary: Breast cancer has replaced lung cancer as the leading cancer globally, but various chemotherapy drugs for breast cancer are prone to generate resistance, especially in patients with distant metastases who are susceptible to multiple chemotherapy drug resistance, these always leading to treatment failure. vincristine (VCR) is an alkaloid extracted from Catharanthus roseus and is often used in combination with other chemotherapy drugs to treat various types of cancer, including breast cancer. Recently, we conducted research on the development of resistance to VCR using transcriptome sequencing technology. Firstly, we used the gradient increase of VCR concentration to produce a VCR-resistant breast cancer cell line. Mechanistically, we further extracted RNA from the VCR-resistant breast cancer cell line and sequenced the transcriptome. Further analysis showed changes in various gene expression levels in the VCR-resistant breast cancer cell line. Meanwhile, the analysis of splicing events also indicated that variable splicing events change in the VCR-resistant breast cancer cell line. Further validation showed that multiple gene expression levels, including 1L1B, were altered in the VCR-resistant breast cancer cell line, and these gene expression changes were related to VCR resistance. Our results provide a theoretical basis for exploring the mechanism of VCR resistance clinically.

overall_design: In order to investigate the specific mechanism underlying the development of Vincristine resistance in breast cancer treatment, we constructed a Vincristine-resistant breast cancer cell line MCF7/VCR. Firstly, we treated MCF7 cells with different concentrations of VCR in a 96-well plate, using 1nM for 5 days, followed by 5nM, 10nM, 50nM, 100nM, 500nM, 1000nM, 5000nM, and 10000nM for 5 days each. Eventually, the surviving MCF7 cells were expanded and screened to obtain the Vincristine-resistant MCF7 cell line. The IC50 of wild-type and MCF7/VCR cells to Vincristine were measured using the CCK8 method, and were found to be 7.371 nM and 10574 nM, respectively

first: Yao

first: C

last: Wang


title: Loss of Grem1-lineage chondrogenic progenitor 1 cells causes osteoarthritis

status: Public on Sep 19 2023

city: NEW YORK

first: Abdullah

last: Ali

state: NY

address: 1130 SAINT NICHOLAS AVE, ICRC 601

institute: Columbia University Irving Medical Center

summary: Osteoarthritis (OA) is characterised by an irreversible degeneration of articular cartilage. Here we show that the BMP-antagonist Gremlin 1 (Grem1) marks a bipotent chondrogenic and osteogenic progenitor cell population within the articular surface. Notably, these progenitors are depleted by injury-induced OA and increasing age. OA is also caused by ablation of Grem1 cells in mice. Transcriptomic and functional analysis in mice found that articular surface Grem1-lineage cells are dependent on Foxo1 and ablation of Foxo1 in Grem1-lineage cells caused OA. FGFR3 signalling was confirmed as a promising therapeutic pathway by administration of pathway activator, FGF18, resulting in Grem1-lineage chondrocyte progenitor cell proliferation, increased cartilage thickness and reduced OA. These findings suggest that OA, in part, is caused by mechanical, developmental or age-related attrition of Grem1 expressing articular cartilage progenitor cells. These cells, and the FGFR3 signalling pathway that sustains them, may be effective future targets for biological management of OA.

overall_design: Grem1-CreErt TdT mice were treated with Tamoxifen for 10 days starting at age 6 week and to collect articular cartilage (AC) tissue from  knee joint at age 9 week for scRNAseq analysis.

first: Toghrul

middle: H

last: Jafarov

first: Siddhartha

last: Mukherjee


title: PP2Ac knockdown attenuates lipotoxicity-induced pancreatic β-cell dysfunction and apoptosis

status: Public on Sep 13 2023

city: Wuhan

first: Zhengwei

last: Zhang

address: 169 Donghu Road

institute: Zhongnan Hospital of Wuhan University

summary: Protein phosphatase 2A (PP2A) is one of the most common serine/threonine phosphatases in mammalian cells and primarily functions to regulate cell signaling, glycolipid metabolism, and apoptosis. Its PP2A catalytic subunit (PP2Ac) plays an important role in its function. Nonetheless, at present, there are only a few reports on the regulatory role of PP2Ac in pancreatic β-cells under lipotoxicity. Mouse pancreatic insulinoma (MIN6) cells were transfected by lentiviruses to generate PP2Ac knockdown cells and incubated with palmitate (PA) to establish the lipotoxicity model. Serine/Threonine Phosphatase Assay System kit, Cell Counting Kit-8 (CCK-8), flow cytometry, enzyme-linked immunosorbent assay (ELISA), Western Blotting (WB) and other techniques were used to measure PP2A activity, cell viability, apoptosis, oxidative stress, and insulin secretion. An animal model of lipotoxicity with knockdown of PP2Ac was established by a high-fat diet (HFD) after using adeno-associated viruses (AAV) to interfere with PP2Ac expression in mouse pancreatic tissues. Serine/Threonine Phosphatase Assay System kit, ELISA, pancreatic tissue immunofluorescence and other techniques were used to measure PP2A activity in pancreatic tissue, serum insulin level and the proliferation of mouse pancreatic β-cells. We found that PP2Ac knockdown inhibited lipotoxicity-induced PP2A hyperactivation, increased the resistance of pancreatic β-cells to lipotoxicity, decreased PA-induced apoptosis in MIN6 cells, protected the function of both the endoplasmic reticulum (ER) and mitochondria, and improved insulin secretion. By mRNA sequencing and Western blotting analysis, we hypothesized that the protective effects of PP2Ac knockdown in MIN6 cells may be mediated by the MAPK pathway. Moreover, the results obtained from animal experiments suggest that the specific knockdown of pancreatic PP2Ac could effectively attenuate HFD-induced insulin resistance and reduce the compensatory proliferation of pancreatic β-cells in mice. The present study revealed the effects and mechanisms of interfering with PP2Ac gene expression on pancreatic β-cells in vivo and in vitro, which might provide insights for the treatment of type 2 diabetes in the clinic.

overall_design: We detected genetic differences between PP2Ac knockdown and control groups by sequencing

first: Beier

last: Tong

first: Jie

last: Liu

first: Jieyuan

last: Feng


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Singlecell_mouse_invitro

status: Public on Sep 11 2023

city: Milano

first: Renato

last: Ostuni

address: Via Olgettina 58

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to therapy. Inflammatory and immunomodulatory signals co-exist in the tumor microenvironment (TME), leading to dysregulated reparative and cytotoxic responses. Tumor-associated macrophages (TAMs) control immune dynamics in the TME, but their heterogeneity and plasticity have hampered understanding of the underlying mechanisms. Here, we combined single-cell and spatial genomics with functional experiments to elucidate macrophage functions in PDAC. We uncovered an inflammatory loop between tumor cells and interleukin (IL)-1b+ TAMs, a subset of macrophages elicited by a local synergy between prostaglandin E2 (PGE2) and tumor necrosis factor (TNF)-a. Interfering with the PGE2-IL-1b axis elicited TAM reprogramming and antagonized tumor-intrinsic inflammation, leading to PDAC control in vivo. IL-1b+ TAMs are conserved across human cancers and correlate with inflammation and patient prognosis in a context-dependent manner. Our study highlights how TAMs govern between inflammation and immune suppression in cancer, with significant therapeutic implications.

overall_design: scRNA-seq of epithelial organoids from murine PDAC

first: Nicoletta

last: Caronni

first: Federica

last: La Terza

first: Francesco

last: Vittoria

first: Giulia

last: Barbiera

first: Marco

last: Genua


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Molecular Cartography of human PDAC samples

overall_design: Spatial transcriptomics data obtained by Molecular Cartography (Resolve Biosciences) of tumor samples from human PDAC


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

type: Methylation profiling by genome tiling array

overall_design: Refer to individual Series


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Bulk_mouse_invitro

overall_design: Bulk RNA-seq of KC and KPC cell line in 2D and 3D cultures upon IL1-b stimulation.


title: MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer’s disease I

first: Bart

last: de Strooper


title: Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [DNAmeth_EPICarray]

summary: Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosisand the precise anatomic origin of brain tumors in the Rosa26; Cre-ERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for  MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.

overall_design: DNA methylation array (EPIC) data from 54 primary ATRT samples already deposited in GEO dataset (GSE175892) were re-analysed in this study.

first: Maria

last: Lobon-Iglesias

last: Andrianteranagna

first: Zhi-Yan

last: Han

first: Julien

last: Masliah-Planchon

first: Céline

last: Chauvin

first: Nicolas

last: Servant

first: Franck

last: Bourdeaut


title: Cancer-associated fibroblasts actively compress cancer cells and modulate mechanotransduction

city: SANTIAGO DE COMPOSTELA

first: Jorge

last: Barbazan

state: A Coruña

address: Trav Choupana s/n

country: Spain

institute: Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS)

summary: During tumor progression, cancer-associated fibroblasts (CAFs) accumulate in tumors and produce an excessive extracellular matrix (ECM), forming a capsule that enwraps cancer cells. This capsule acts as a barrier that restricts tumor growth leading to the buildup of intratumoral pressure. Combining genetic and physical manipulations in vivo with microfabrication and force measurements in vitro, we found that the CAFs capsule is not a passive barrier but instead actively compresses cancer cells using actomyosin contractility. Abrogation of CAFs contractility in vivo leads to the dissipation of compressive forces and impairment of capsule formation. By mapping CAF force patterns in 3D, we show that compression is a CAF-intrinsic property independent of cancer cell growth. Supracellular coordination of CAFs is achieved through fibronectin cables that serve as scaffolds allowing force transmission. Cancer cells mechanosense CAF compression, resulting in an altered localization of the transcriptional regulator YAP and a decrease in proliferation. Our study unveils that the contractile capsule actively compresses cancer cells, modulates their mechanical signaling, and reorganizes tumor morphology.

overall_design: We used RNAseq to investigate the gene expression profiles of different types of murine cancer-associated fibroblasts included in the study. This includes WT CAFs, CAFs SiRNA Control, CAFs SiRNA Fn1, and CAFs MyosinIIA KO

first: Carlos

last: Perez-Gonzalez

first: Manuel

last: Gomez-Gonzalez

first: Mathieu

last: Dedenon

first: Sophie

last: Richon

first: Ernest

last: Latorre

last: Serra

first: Pascale

last: Mariani

first: Stephanie

last: Descroix

first: Pierre

last: Sens

first: Xavier

last: Trepat

first: Danijela

last: Matic-Vignjevic


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Spatial transcriptomics of mouse PDAC samples

first: Renato

last: Ostuni

overall_design: Spatial transcriptomics of tumor samples from murine PDAC models

first: Nicoletta

last: Caronni

first: Federica

last: La Terza

first: Francesco

last: Vittoria

first: Giulia

last: Barbiera

first: Marco

last: Genua


title: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell

first: zou

last: yanyan


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Bulk RNA-seq

overall_design: Bulk RNA-seq of BMDMs stimulated with TNFa and PGE2, alone or in combination for 1, 2 or 4 hours respectively, or left untreated.


title: Formate supplementation enhances anti-tumor CD8+ T cell fitness and efficacy of PD-1 blockade

first: Osmaan

last: Shahid

department: Department of Immunology

summary: Metabolic support of the response to immune checkpoint blockage is unknown. We used scRNA-seq to determine the response of CD8+ cells to metabolic supplementation with the one carbon donor formate in combination with anti-PD-1

overall_design: Tumor infiltrating CD8+ cells were purified by FACS on day 12 post implantation from B16-OVA tumors after treatment with formate (starting day  9) and antibody (starting day 10). Four treatment groups, control drinking water with isotype control antibody (C.I.), formate drinking water with isotype control antibody (F.I.), control drinking water with anti-PD-1 antibody (C.P.), and formate drinking water with anti-PD-1 antibody (F.P.).

first: Sharpe

last: Arlene

first: Haigis

last: Marcia

first: Rowe

last: Jared

first: Elia

last: Ilaria


title: Transcriptomic profiling of an in vivo mouse model of immune checkpoint induced colitis

status: Public on Sep 08 2023

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

summary: Immune checkpoint inhibitors (CPIs) have revolutionised cancer treatment, with previously untreatable disease now amenable to potential cure. Combination regimens of anti-CTLA-4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. CPI-induced colitis is a common and serious complication. To probe the impact of immune checkpoints on intestinal homeostasis, mice were challenged with anti-CTLA-4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. Colonic immune responses were profiled using bulk RNA-sequencing.

overall_design: Comparative analysis of transcriptomic profiles from distal colon segments of untreated Balb/c wild type mice compared to Balb/c wild type mice treated with either faecal microbiota transplant, combination ofboth  anti-CTLA-4 and anti-PD-1 therapy, or mice treated with both of these. All treatments lasting 3 weeks.

first: Jonathan

middle: W

last: Lo

first: Domenico

last: Cozzetto


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - scRNAseq of human PDAC samples

overall_design: scRNA-seq of resected primary PDAC and peripheral blood (PB) human samples


title: Transcriptomic profile comparison of an in vivo model of dual combination immune checkpoint colitis or monotherapy immune checkpoint colitis

summary: Immune checkpoint inhibitors (CPIs) have revolutionised cancer treatment, with previously untreatable disease now amenable to potential cure. Combination regimens of anti-CTLA-4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. CPI-induced colitis is a common and serious complication. A higher proportion of patients undergoing monotherapy anti-CTLA-4 treatment tend to develop colitis compared to monotherapy treated anti-PD-1 treated patients. This effect is enhanced when patients are treated with both drugs. To probe the impact of either anti-CTLA4 or anti-PD1 on intestinal homeostasis, mice were challenged with anti-CTLA-4 and anti-PD-1 immunotherapy in either monotherapy or together in combination. Manipulation of the intestinal microbiota has also been shown to be important in both this model, from previous data, and in patients. Colonic immune responses were then profiled using bulk RNA-sequencing.

overall_design: Comparative analysis of transcriptomic profiles from distal colon segments of untreated Balb/c wild type mice compared to Balb/c wild type mice treated with either anti-CTLA-4 monotherapy, anti-PD-1 monotherapy, or mice treated with both of these. All mice treated with immune checkpoint druh were given an oral gavage of a proinflammatory microbiota at the beginning. All treatments lasted 3 weeks.


title: iPSC-derived microglia export cholesterol to neuronal cells in human brain organoids and promote their maturation

status: Public on Sep 16 2023

city: Singapore

first: Jinmiao

last: Chen

address: 8a Biomedical Grove

department: SigN

country: Singapore

institute: A*STAR

summary: Microglia are specialised brain-resident macrophages that arise from primitive macrophages colonising the embryonic brain. Microglia contribute to multiple aspects of brain development, but their precise roles in early human brain remain poorly understood due to limited access to relevant tissues. The generation of brain organoids from induced human pluripotent stem cells (iPSC) recapitulates some key features of human embryonic brain development, but current approaches do not incorporate microglia and thus are lacking. Here, we generated microgliasufficient brain organoids by co-culturing brain organoids with primitive-like macrophages generated from the same human iPSC (iMac). In organoid co-cultures, iMac differentiated into cells with microglia-like phenotypes and functions (iMicro), and modulated neuronal progenitor cell (NPC) differentiation, limiting NPC proliferation and promoting axonogenesis. Mechanistically, iMicro contained high levels of PLIN2+ lipid droplets that exported cholesterol and its esters which weretaken up by NPC in the organoids. We also detected PLIN2+ lipid droplet-loaded microglia in mouse and human embryonic brain. Overall, our approach significantly advances current human brain organoid approaches by incorporating microglial

overall_design: 8 samples;  3 cerebral organoids and 3 co-cultured cerebral organoids on day 18 of co-culture, iPSC-dreived macrophages (iMac) on day 18 of mono-culture

first: DongShin

last: Park

first: Sethi

last: Raman

first: Chen

last: Jinmiao

first: Florent

last: Ginhoux


title: Effect of depletion of Zeb1 in CD11c+ dendritic cells

status: Public on Sep 07 2023

city: Xiamen

first: Nengming

last: Xiao

state: 福建

address: Xiang an Campus Xiang an south Road Xiamen University, fengting 2 -2044

institute: Xiamen University

summary:
To investigate potential target genes of Zeb1 that were involved in regulation of antigen cross-presentation.
We then performed gene expression profiling analysis using data obtained from RNA-seq from WT and Zeb1-deficient BMDC .

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from WT and Zeb1-deficient BMDC.
Nengming Xiao

first: Yan

last: Wang

first: Quan

last: Zhang


title: Gene expression profile at single cell level of splenic cDC

summary: We used single cell RNA sequencing (scRNA-seq) to analyze different genes between WT splenic cDC and KO splenic cDC.

overall_design: splenic cDC were isolated by FACS and construct libraries by using BD Rhapsody Single-Cell Analysis System Instrument User Guide.

first: NengMing


title: A rationally designed dual PI3-kinase (PI3K) and BET-inhibitory chimeric small molecule demonstrates potent anti-neoplastic activity versus MYC-driven haematological cancers in vivo [scRNA-seq]

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: We hypothesised that PI3K and BET inhibition would synergise in the context of MYC-dysregulation and overcome resistance to single-target inhibition. We then synthesised a series of chimeric molecules linking BET- and PI3K-selective pharmacophores, including our lead molecule, 18D(S). RNA-Seq profiling following acute 18D(S) treatment demonstrated robust transcriptional modulation with concomitant BET and PI3K inhibitory signatures. Our data provides proof-of-concept for the design of potent PI3K- and BET-inhibitors, providing ‘synergy in a single molecule’.

overall_design: The OPM2 multiple myeloma cell line was treated in vitro with 500 nM each of JQ1, BKM120, JQ1+BKM120, 18DS, or vehicle for 2 hours prior to single-cell RNA-sequencing (scRNA-seq).

first: D

last: Oh

first: S

first: J

last: Shortt


title: Effect of depletion of Zeb1 in CD11c+ dendritic cells [RNA-seq]

summary:
To investigate potential target genes of Zeb1 that were involved in regulation of antigen cross-presentation.
We then performed gene expression profiling analysis using data obtained from RNA-seq from WT and Zeb1-deficient BMDC after HKLM-OVA stimulating for 4 hours.


title: Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transposable elements hold regulatory functions to impact cell fate determination by controlling gene expression, which when altered can promote oncogenesis. Despite accounting for half of the human genome, little is known about the transcriptional mechanisms that confer regulatory properties to transposable elements in pluripotent, mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequence of H3K27ac ChIP-seq from 32 different normal cell and tissue states, we report pluripotent stem and mature cell states-specific “regulatory transposable elements”. Those specific to pluripotent stem cells are binding sites for the pluripotency factors NANOG, SOX2 and OCT4. In mature cell and tissue states, regulatory transposable elements are docking sites for lineage-specific transcription factors, such as AR and FOXA1 in benign prostate epithelium. Expanding the positional analysis to localized prostate tumors, we show how cancer cell states remaining dependent on AR share regulatory transposable elements with pluripotent stem cells. These include regulatory transposable elements, such as Tigger3a, that serve as binding sites for AR and whose regulatory functions are required for prostate cancer cell growth. Together, our results suggest that oncogenesis differs from normal cell fate determination by hijacking pluripotent stem cells regulatory transposable elements that serve as docking sites for lineage-specific transcription factors.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac and H3K9me3 in prostate cancer cell lines as well as RNA-seq and Cut&Run pull-downs for dCas9-KRAB H3K27ac or AR in clonal CRISPRi prostate cancer cells
*** Submitter declares that raw data were not provided for some ChIP-seq samples dues to patient privacy concerns. ***

first: Giacomo

last: Grillo

first: Ken

last: Kron

first: Ankita

last: Nand


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer

first: Renato

last: Ostuni

summary: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumor microenvironment (TME), leading to dysregulated repair and cytotoxic responses. Tumor-associated macrophages (TAMs) are key players in PDAC, but their diversity prevented therapeutic exploitation. Here, we combined single-cell and spatial genomics with functional experiments to elucidate macrophage functions in pancreatic cancer. We uncovered an inflammatory loop between tumor cells and interleukin (IL)-1B+ TAMs, a subset of macrophages elicited by a local synergy between prostaglandin E2 (PGE2) and tumor necrosis factor (TNF)-A. Physical proximity with IL-1B+ TAMs was associated with inflammatory reprogramming and acquisition of pathogenic properties by a subset of PDAC cells. This occurrence was an early event in pancreatic tumorigenesis and led to persistent transcriptional changes associated with disease progression and poor patient outcome. Blocking PGE2 or IL-1B elicited TAM reprogramming and antagonized tumor cell-intrinsic and -extrinsic inflammation, leading to PDAC control in vivo. Targeting the PGE2-IL-1B axis may enable preventive or therapeutic strategy to reprogramming of immune dynamics in pancreatic cancer.


title: A Genetic Selection for Mycobacterium smegmatis Mutants Tolerant to Killing by Sodium Citrate Defines a Combined Role for Magnesium Homeostasis and Osmotic Stress in Cell Death

status: Public on Sep 06 2023

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Regulation of Mycobacterium smegmatis gene expression by treatment with sodium citrate.

overall_design: M. smegmatis was treated for 3 hours in the presence or absence of 100 mM sodium citrate.

middle: T

last: Williams

first: R

middle: B


title: Neuron-specific RNA responses to EAE and cuprizone

status: Public on Sep 05 2023

city: Rochester

first: Charles

middle: L

last: Howe

state: MN

address: 200 First St SW

department: Neurology

institute: Mayo Clinic

summary: Ribotag mice were crossed to synapsin-CRE mice to induce expression of HA-tagged Rpl22 subunits in neurons. Mice were fed cuprizone to induce demyelination or were induced with MOG(35-55) peptide to establish experimental autoimmune encephalomyelitis. Brain was collected from EAE mice at 18 days after induction (peak disease) and from cuprizone-fed mice at 6 weeks on chow. Brain was also collected from unmanipulated control mice fed normal chow. Brain lysates were immunoprecipated with anti-HA antibody to isolated neuron-specific polyribosomes. RNA was extracted from the IP and analyzed by Affymetrix GeneChip® Mouse Gene 2.0 ST Arrays.

overall_design: 4 control mice vs 6 EAE mice vs 6 cuprizone mice


title: A2B5 and CD140 sorted cells from human adult or fetal brain samples for comparative species analysis

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Cells were isolated from adult or fetal samples, using either A2B5 or CD140 as selection marker.

overall_design: Human mRNA was isolated from glial progenitor cells sorted on either A2B5 (adult WM from epileptic resection) or CD140a (fetal cortex, 19-20.1 week), with four biological replicates per group. cDNA was generated with the SMARTer Ultra Low RNA kit (Clontech), and libraries were created for sequencing with the NexteraXT DNA kit (Illumina). Sequencing was performed on an Illumina HiSeq 2500v4, with all samples in one batch. An average of about 30 million 100bp reads per sample were obtained after trimming and filtering reads with Trimmomatic. Reads were aligned to the human genome with STAR, read counts for genes were generated by RSEM, and differential expression analysis was performed with DESeq2.

first: John

middle: N

last: Mariani


title: IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - scRNA-seq of murine PDAC samples

overall_design: scRNA-seq of tumor samples from murine PDAC models

first: Nicoletta

last: Caronni

first: Federica

last: La Terza

first: Francesco

last: Vittoria

first: Giulia

last: Barbiera

first: Marco

last: Genua


title: Transcriptomic analysis of early HSV-1 transcription in the absence of the immediate early protein, ICP4 [Nanopore]

city: Ithaca

first: Joel

last: Baines

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: Herpes simplex virus 1 (HSV-1) transcription is tightly regulated in a temporal cascade, utilizing cellular RNA polymerase (Pol). We previously observed that infection with HSV-1 mutants lacking immediate early (IE) genes a0, a4 and a22 exhibited unusually high levels of aberrant transcription across the viral genome at just 1.5 hpi. The strongest effect occurred in the absence of a4, which is both an essential transcriptional activator and repressor. The goal of the current study was to define the mechanism of ICP4-mediated early transcriptional repression on the viral genome. Using the transcriptomic tools PRO-Cap, PRO-Seq, GRO-Seq and Nanopore direct RNA sequencing we found that initiation was elevated at viral promoters of all temporal classes in the absence of ICP4. Despite higher levels of initiation, transcription of non-IE genes was stalled within gene bodies and did not lead to production of mature mRNA. We therefore posit that HSV-1 retains additional ICP4-independent mechanisms to limit expression of viral genes that initiate prematurely. The data also indicated rapid release from promoter proximal pausing and progression along HSV IE genes and revealed termination as an important rate -limiting regulatory step. These findings highlight multiple mechanisms that HSV-1 employs to regulate early transcription and identify ICP4’s repressive role is to restrict initiation on non IE genes, thereby ensuring correct progression of the temporal cascade.

overall_design: To investigate the role of ICP4 in early HSV-1 transcription, HEp-2 cells infected with ICP4 HSV-1 mutant, n12, or its cognate repair were subjected to either PRO-Seq, PRO-Cap, GRO-Seq or Nanopore direct RNA sequencing.

first: Laura

middle: E

last: Dunn

middle: D


title: Single cell transcriptomics reveals colonic lymphocyte remodelling and emergence of polyfunctional, cytolytic lymphocyte responses in CPI-induced colitis

first: Nick

last: Powell

summary: Immune checkpoint inhibitors (CPIs) have revolutionised cancer treatment, with previously untreatable disease now amenable to potential cure. Combination regimens of anti-CTLA-4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homeostasis, mice were challenged with anti-CTLA-4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. Single-cell RNA-sequencing revealed remodelling of mucosal lymphocytes with induction of polyfunctional lymphocyte responses characterized by increased expression of Ifng, other pro-inflammatory cytokines/chemokines (Il22, Il17a Ccl3, Ccl4 and Ccl9), cytotoxicity molecules (Gzmb, Gzma, Prf1, Nkg7) and the chemokine receptor Cxcr6. In comparison with mucosal lymphocytes in the steady state, polyfunctional lymphocytes from both CD4+ and CD8+ lineages upregulated costimulatory molecules and checkpoint molecules in CPI-colitis, indicating that these cells are tightly regulated.

overall_design: Single cell RNA-sequencing study of CD45+ lymphocytes from the colons of mice with CPI-colitis and healthy controls.

first: Jonathan

last: Lo

first: Domenico

last: Cozzetto


title: Transcriptomic analysis of early HSV-1 transcription in the absence of the immediate early protein, ICP4 [GRO-seq]


title: Transcriptomic analysis of early HSV-1 transcription in the absence of the immediate early protein, ICP4 [PROCap]


title: Transcriptomic analysis of early HSV-1 transcription in the absence of the immediate early protein, ICP4 [PROSeq]


title: Gene expression profile of canine Chimeric Antigen Receptor (CAR) Engineered invariant Natural Killer T (iNKT) cells

city: Philadelphia

first: Antonia

last: Rotolo

state: PA

address: 3900 Chestnut Street, Apt 521

institute: University of Pennsylvania

summary: We used Nanostring gene expression profiling to characterize CAR-engineered  canine iNKT cells

overall_design: The anti-IL13Rα2-28-ζ CAR construct was expressed along with a truncated canine CD19 marker. End-of-expansion, resting CAR-iNKTs were stimulated for 4-8 hours with anti-CD3/CD28-coated beads at 1:1 ratio. RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Gene expression profiling was performed using NanoString Canine Immuno-Oncology panel and nCounter instrument (Wistar Institute) according to the manufacturer’s instructions.

first: Eoin

middle: C

last: Whelan

first: Matthew

last: Atherton

first: Irina

last: Kulikovskaya

first: Danuta

last: Jarocha

first: Joseph

last: Fraietta

first: Michele

last: Kim

first: Eric

middle: S

last: Diffenderfer

first: Keith

last: Cengel

first: Martina

last: Piviani

first: Enrico

last: Radaelli

first: Raimon

last: Duran-Struuck

first: Nicola

last: Mason


title: Identification of the alternative sigma factor regulons of Chlamydia trachomatis using multiplexed CRISPR interference

city: Omaha

first: Scot

middle: P.

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: RNAseq analysis was performed for C. trachomatis serovar L2 after knocking down or overexpressing different sigma factors.

overall_design: RNA was collected from C. trachomatis L2 infected cells following 14 hours of sigma factor knockdown or 4 hours of sigma factor overexpression. Each strain was tested in triplicate, resulting in 48 total samples. Induced knockdown samples were compared to their respective uninduced samples as well as an induced non-targeting knockdown sample. Overexpression samples were compared to their respective uninduced samples.

first: Nathan

last: Hatch

middle: P


title: Global profiling of prostate cancer cell expression upon treatment with media conditioned from human stromal cells ectopically expressing PDK4

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Technical advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiles of human prostate cancer cell lines exposed to conditioned media from human primary stromal cells engineered to express pyruvate dehydrogenase kinase 4 (PDK4), a key enzyme that is correlated with glucose metabolism, negatively regulates the conversion of pyruvate to acetyl-CoA and plays important roles in cancer progression and multiple other pathological events.

overall_design: Transcript profiles of prostate cancer cell lines mainly PC3, DU145 and M12 were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

first: Xuefeng

last: Dou


title: A single amino acid substitution in the capsid protein of Zika virus contributes to the African lineage-specific virulence phenotypes

status: Public on Sep 01 2023

city: Hang zhou

first: guangyuan

last: Song

address: No. 17 Shilongshan Street

institute: westlake university

summary: The re-emerged Zika virus (ZIKV) can cause severe neurological complications termed congenital Zika syndrome (CZS) in infants born to ZIKV-infected mothers. However, increasing evidence shows the ancestral African lineage ZIKV displays more virulent phenotype than the contemporary Asian ZIKV in multiple cell and animal models. However, the viral determinants and underlying mechanism of this lineage specific virulence phenotype remain largely unknown. In the present study, phylogenetic analysis and sequence alignment identified a panel of lineage specific amino acid substitutions between African and Asian ZIKVs. Then, these amino acid substitutions were introduced into an infectious clone of Asian ZIKV by standard reverse genetic technology. Further characterization in vitro demonstrated that the recovered mutant virus with a lysine to arginine substitution at position 101 of capsid (C) protein (termed K101R) produced larger plaques in BHK-21 cells, and replicated more efficiently and induced more severe cytopathic effects (CPE) in multiple cells including human neuronal precursor cells (NPCs). More importantly, the K101R mutant virus replicated more efficiently in mouse brain tissues, and induced stronger inflammatory responses, leading to higher mortality than the wild type (WT) virus in neonatal mice. Despite no effect on RNA binding affinity of recombinant C protein to viral RNA, structural modeling and biochemical assays showed that the K101R substitution increased the viral protease cleavage efficiency of full C protein. Taken together, our study identified a single amino acid substitution K101R in the capsid protein responsible for the well-characterized virulence enhancement phenotypes, highlighting the importance of viral determinants for the co-circulating of two lineages of ZIKV.

overall_design: Retinal mRNA profiles of infected WT or K101R mutant virus mice (11 d.p.i.)were generated by deep sequencing ,in triplicate.

first: Cheng-Feng

last: Qin

first: Xiao-Feng

last: Li

first: Guang-Yuan


title: Mouse duodenal and ileal Paneth cell single cell RNA sequencing

city: Newark

last: Gao

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

summary: An indepth analysis of Paneth cell transcriptome at single cell level has not been available. Existing intestinal epithelial cell scRNA dataset contain many cell types, where Paneth cells represent a small portion. We used a flow cytometry based approach to enrich and isolate relatively pure Panethc cells from a newly developed Paneth cell reporter mouse line (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). Single cell RNA sequencing was performed on purified duodenal and ileal Paneth cells of mice housed under specific pathogen free condition.

overall_design: Paneth cell reporter mice were intraperitoneally injected with a single dose of tamoxifen dissovled in corn oil. 48 hrs later, mice were sacrificed, duodenal and ileal crypts were isolated, digested into single cell suspension, and subjected to flow cytometry sorting of viable tdT+ cells. Viablity and purity of duodenal or ileal Paneth cells were confirmed by flow analysis. A total of 6626 duodenal and 6893 ileal Paneth cells were processed for library construction and single cell RNA sequencing by 10xGenomics.

first: Iyshwarya

last: Balasubramanian

first: Sheila

last: Bandyopadhyay

first: Juan

last: Flores


title: The Malate Shuttle Detoxifies Ammonia in Exhausted T Cells by Producing 2-Ketoglutarate

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: The malate shuttle is traditionally known to maintain the NAD+/NADH balance between the cytosol and mitochondria. Whether the malate shuttle has additional functions was unknown. Here we show that chronic viral infections induced the expression of GOT1, the key enzyme in the malate shuttle, in CD8+ T cells. Got1 deficiency indeed decreased the NAD+/NADH ratio and dampened antiviral CD8+ T cell responses to chronic infection; however, increasing the NAD+/NADH ratio did not restore antiviral T cell responses. Got1 deficiency reduced the production of the ammonia scavenger 2-ketoglutarate and led to toxic ammonia accumulation in CD8+ T cells. Supplementation with 2-ketoglutarate assimilated and detoxified ammonia in Got1-deficient T cells and restored antiviral responses. This study suggests that the major function of the malate shuttle in CD8+ T cells is not to maintain the NAD+/NADH ratio, but rather to detoxify ammonia and enable sustainable ammonia-neutral glutamine catabolism in CD8+ T cells during chronic infections.

overall_design: To compare the influences of Got1 deficiency versus ammonia treatment on the global transcriptional profiles and epigenetic landscapes of CD8+ T cells, we performed RNA sequencing and ATAC sequencing to compare groups of CD8+ T cells.

first: Nina

last: Weisshaar

first: Guoliang

last: Cui


title: Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae.

status: Public on Aug 31 2023

city: Tainan City

first: Hao-Jen

last: Huang

address: No. 1., University Road

country: Taiwan

institute: National Cheng Kung University

summary: Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species (ROS). Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1030 differentially expressed genes (DEGs) in the yeast. According to GO and KEGG analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall defenses, antioxidant defenses and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of fungal model.

overall_design: We first sought to determine whether mVCs released by P. ureafaciens have the potential to inhibit growth of phytopathogenic fungi. Then, to assess how fungi respond to mVCs and how toxicity occurs, we performed bioassays on the S. cervisiae fungal model.


title: Single cell RNA sequencing analysis of germ free (GF) mouse Paneth cells and microbiome-transferred exGF mouse Paneth cells.

summary: The single cell level Paneth cell transcriptome under gnotobiotic condition has not been resolved. How gut microbiome modulates Paneth cell transcriptome at single cell level in germ-free mice was not known. We used a flow cytometry method to isolate highly pure ileal Paneth cells from germ free (GF) Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER) and from exGF Paneth cell reporter mice that were transplanted with wild type C57B/l6 mouse gut microbiota (exGF+B6M). These isolated Paneth cells were subjected to single cell RNA sequencing by 10xGenomics.

overall_design: Germ-free (GF) Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER) were orally gavaged with sterile PBS to keep as germ-free controls, or orally gavaged with a freshly prepared fecal slurry collected from the cecum contents of C57B/L6 mice under anaerobic condition. 3 weeks later, mice were intraperitoneally injected with sterile tamoxifen to activate the reporter. Mice were sacrificed 2 days later when ileal Paneth cells were flow sorted for single cell RNA sequencing.


title: Perilipin 2-positive mononuclear phagocytes accumulate in diabetic retina and promote PPARγ-dependent vasodegeneration

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

summary: Type 2 diabetes mellitus (T2DM), characterized by hyperglycemia and dyslipidemia leads to non-proliferative diabetic retinopathy (NPDR). NPDR is associated with blood-retinal barrier disruption, plasma exudates, microvascular degeneration, elevated inflammatory cytokine levels and monocyte (Mo) infiltration. Whether and how the diabetes-associated changes in plasma lipid and carbohydrate levels modify Mo differentiation. Here, we show that mononuclear phagocytes (MPs) in areas of vascular leakage in DR donor retinas express PLIN2, a marker of intracellular lipid load. Strong upregulation of PLIN2 was also observed when healthy donor Mos were treated with plasma from T2DM patients or with palmitate concentrations typical of T2DM plasma, but not under high glucose conditions. PLIN2 expression correlated with the expression of other key genes involved in lipid metabolism (ACADVL, PDK4) and the DR biomarkers ANGPTL4 and CXCL8. Mechanistically, we show that lipid-exposed MPs induce capillary degeneration in ex vivo explants, which was inhibited by pharmaceutical inhibition of PPARγ signaling. Our study provides a novel mechanism linking dyslipidemia-induced MP polarization to the increased inflammatory cytokine levels and microvascular degeneration that characterize NPDR. This study provides comprehensive insights into the glycemia-independent activation of Mos in T2DM and identifies MP PPARγ as a target to inhibit lipid-activated MPs in DR

overall_design: To study monocyte differentiation in a lipid-rich environment, replicates of monocytes isolated from a healthy donor were cultured for 18h and treated with 500 µM Palmitate /0.88% BSA, BSA alone (0.88%) and compared to DMEM culture condition (3 replicate per condition). After 18h of culture, cells were collected and RNA extracted to build expression libraries

first: Guillaume

last: Blot

first: Frédéric

first: Florian

last: Sennlaub

first: Xavier

last: Guillonneau


title: Effect of Batf2 deficiency on gene epxression in murine alveolar macrophages treated ex vivo with IFNg and K. pneumoniae supernatant

city: Pittsburgh

first: Rick

last: van der Geest

address: 3459 Fifth Avenue

institute: University of Pittsburgh

summary: Basic leucine zipper transcription factor ATF-like 2 (BATF2) is a transcription factor that is emerging as an important regulator of the innate immune system. We previously identified BATF2 among the top upregulated genes in human alveolar macrophages treated with LPS, but the signaling pathways that induce BATF2 expression in response to Gram-negative stimuli are incompletely understood. In addition, the role of BATF2 in the host response to pulmonary infection with a Gram-negative pathogen like Klebsiella pneumoniae (Kp) is not known. We show that induction of Batf2 gene expression in macrophages in response to Kp in vitro requires TRIF and type I interferon (IFN) signaling, but not MyD88 signaling. Analysis of the impact of BATF2-deficiency on macrophage effector functions in vitro showed that BATF2 does not directly impact macrophage phagocytic uptake and intracellular killing of Kp. However, BATF2 markedly enhanced macrophage pro-inflammatory gene expression and Kp-induced cytokine responses. In vivo, we observed that Batf2 gene expression was elevated in the lung tissue of wild type (WT) mice 24 h after pulmonary Kp infection, and Kp-infected BATF2-deficient (Batf2-/-) mice displayed a modest but significant increase in bacterial burden in the lung, spleen and liver compared to WT mice. WT and Batf2-/- mice showed similar recruitment of leukocytes following infection, but in line with our in vitro observations, pro-inflammatory cytokine levels in the alveolar space were reduced in Batf2-/- mice. Altogether, these results suggest that BATF2 enhances pro-inflammatory cytokine responses in macrophages in response to Kp, and that as such, BATF2 contributes to the host defense against pulmonary Kp infection.

overall_design:
To investigate the impact of BATF2 on macrophage polarization, we obtained murine WT (C57BL/6J) and Batf2-/-  alvaolar macrophages and treated these ex vivo with IFNg (10 ng/mL) for 4 hours, followed by stimulation with 20% K. pneumoniae supernatant for 6 hours to induce M1-like macrophage polarization
We then performed gene expression profiling using data obtained from bulk mRNA-sequencing of 4 WT and 4 Batf2-/- alveolar macrophage samples
Each sample represents a biological replicate created by pooling alveolar macrophages from 4 individual mice (N=16 WT and N=16 Batf2-/- mice used in total for the experiment).

first: Hernán

middle: F

last: Peñaloza

first: Zeyu

last: Xiong

first: Shekina

last: Gonzalez-Ferrer

first: Xiaojing

last: An

first: Huihua

first: Hongye

last: Fan

first: Mohammadreza

last: Tabary

first: S

middle: M

last: Nouraie

first: Yanwu

last: Zhao

first: Yingze

last: Zhang

first: Kong

last: Chen

first: Jonathan

middle: K

last: Alder

first: William

middle: G

last: Bain

first: Janet

last: Lee


title: Quartet Methylomics

status: Public on Sep 04 2023

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary: The Quartet Project aims to provide resources for QC of multiple types of omic technologies and the effective integration of diverse datasets from various scenarios. Large quantities of multi-omics materials, datasets, and best practices for their QC utilities were developed for whole process QC of large-scale, multi-center, and longitudinal multi-omics profiling.

overall_design: Bisulphite converted DNA were hybridised to the Illumina Infinium MethylationEPIC BeadChip


title: To find target genes of Zeb1 [CUT&Tag-Seq]

first: Nengming

last: Xiao

address: Xiang an Campus Xiang an south Road Xiamen University, fengting 2 -2044

institute: Xiamen University

summary:
To investigate potential target genes of Zeb1 that were involved in regulation of antigen cross-presentation.
We then performed CUT&tag about Zeb1 gene from WT BMDC after HKLM-OVA stimulating for 4 hours

overall_design: NengMing Xiao

first: Yan

last: Wang

first: Quan


title: Inflammation-inducible promoters to overexpress immune inhibitory factors by MSCs

city: Hanover

first: Anton

last: Selich

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: Umbilical cord mesenchymal stromal cells (UC-MSCs) were treated with different concentration with hIL10 and the influences on the secretome analyzed

overall_design: UC-MSCs from 3 donors were treated with 0, 1 10 or 100 ng/mL IL10 for 24 h, the cells harvested and a microarray performed

first: Michael

last: Rothe


title: Fibromodulin FMOD promotes oral squamous cell carcinoma via activating EGFR signaling axis

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: As a Class II small leucine-rich proteoglycan, fibromodulin (FMOD) plays critical roles in collagen fibrillogenesis and angiogenesis. However, the biological function of FMOD in oral squamous cell carcinoma remains unknown to date. In this study, immunohistochemistry and immunofluorescence assays identified that FMOD protein was located in cytoplasm and nucleus and was overexpressed in OSCC tissues and cell lines. Clinical analysis confirmed that FMOD overexpression showed a significant association with malignant progression (P=0.011) and lymph node metastasis (P=0.032) in OSCC patients. Moreover, loss-of-function studies verified that knockdown of FMOD significantly inhibited OSCC growth and metastasis in vitro and in vivo. Mechanismly, RNA sequencing studies further confirmed that. Knockdown of FMOD expression inhibited OSCC cell proliferation, migration, invasion, and tumor growth probably through altering transcriptome leading to active cell cycle, down-regulating Cell adhesion molecules and ECM-receptor interaction and through inhibiting EGFR-ERK and EGFR-AKT pathways.

overall_design: To reveal the differentially expressed genes caused by FMOD depletion, we knocked down FMOD expression using 3 different shRNAs in OSCC cells. The transcriptome sequencing studies were performed by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Lingyun

last: Xia


title: ADSC secretome constrains NK cell activity by attenuating IL-2–mediated JAK-STAT and AKT signaling pathway via upregulation of CIS and DUSP4

city: Seoul

first: Eunhee

last: Ko

state: Seoul

address: Avison Biomedical Research Center (ABMRC), Yonsei University Health System, 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

summary: The aim of this study was to elucidate the role of the adipose tissue-derived stem cell (ADSC) secretome on NK cell activity. To elucidate the molecular mechanisms involved, we used mRNA sequencing to profile the transcriptional expression of human blood NK cells from 6 donors.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for human primary NK cells which are exposed to ADSC secretome or not.
>>>Submitter states that missing raw files are due to file loss.<<<

first: Taejun

last: Yoon

first: Yoojin

first: Jongsun

last: Kim

first: Yong-Beom

last: Park


title: Transcriptomic landscape of human primary stromal cells upon chemotherapeutic and/or PDK4-specific intervention

first: Yu

last: Sun

summary: Cellular senescence is a response elicited by acute or chronic damage signals. In humans, senescent cells accumulate in multiple tissues at different rates, from 2- to 20-fold when comparing young (<35 years) to old (>65 years) healthy donors. The pathogenic role of cellular senescence in diverse age-related diseases can be largely explained by the senescence-associated secretory phenotype (SASP). Senescent cells display changes in mitochondrial activity with increased ATP production and high lactate production, which are partially correlated with upregulation of pyruvate dehydrogenase kinase 4 (PDK4), an inhibitor of mitochondrial pyruvate dehydrogenase. We used a genotoxic agent, bleomycin, and/or a PDK4-targeting chemical, PDK4-IN, to treat human primary stromal cells and determined the influence of PDK4 inhibition on the transcriptomic expression profile of senescent cells. The data allow to disclose the importance of PDK4 activity in development of senescence-associated phenotypes, particularly the SASP.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of human primary stromal cells that underwent treatment by the chemotherapeutic agent bleomycin and/or a PDK4-specific inhibitor PDK4-IN.

first: Xuefeng

last: Dou


title: APOE4-dependent transcriptome changes in human iPSC-derived astrocytes

city: Tokyo

first: Hirotaka

last: Watanabe

state: Other

address: 35 Shinanomachi, Shinjuku-ku

department: Physiology

country: Japan

institute: Keio University School of Medicine

summary: APOE4 genotype is the strongest risk factor for the pathogenesis of sporadic Alzheimer’s disease (AD),  but the detailed molecular mechanism of APOE4-mediated synaptic impairment remains to be determined in  human cellular context. In this study, we generated human astrocyte model carrying APOE3 or APOE4 genotype  using human induced pluripotent stem cells (iPSCs), in which isogenic APOE4 iPSCs were genome-edited from  healthy control APOE3 iPSCs. By transcriptome analysis of human astrocytes between APOE genotypes, we showed the  upregulation of an extracellular matrix glycoprotein in human APOE4 astrocytes, which may cause  synaptic degeneration in concert with the equivocal reactive character and lipid change. Together, these results  demonstrate novel negative impact of human APOE4 astrocyte on synaptic integrity and lead to a promising  therapeutic intervention into APOE4-carriers.

overall_design: Total 7 total RNAs were analyzed, where 3 APOE3- and 4 APOE4-astrocytes were derived.

first: Kent

last: Imaizumi

first: Satoru

last: Morimoto

first: Hideyuki

last: Okano


title: BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

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

overall_design: Refer to individual Series


title: Dynamic O-GlcNAcylation of YTHDF proteins controls translation of m6A-modified mRNA

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most abundant internal mRNA nucleotide modification in mammals, regulating critical aspects of cell physiology and differentiation. The YTHDF proteins are the primary readers of m6A modifications and exert physiological functions of m6A in the cytosol. Elucidating the regulatory mechanisms of YTHDF proteins is critical to understanding m6A biology. Here, we report a mechanism that protein post-translational modifications control the biological functions of the YTHDF proteins. We find that YTHDF1 and YTHDF3, but not YTHDF2, carry high levels of nutrient-sensing O-GlcNAc modifications. O-GlcNAc modification attenuates the translation promoting function of YTHDF1 and YTHDF3 by blocking their interactions with proteins associated with mRNA translation. We further demonstrate that O-GlcNAc modifications on YTHDF1 and YTHDF2 regulate the assembly, stability, and disassembly of stress granule, facilitating rapid exchange of m6A-modified mRNAs in stress granules for recovery from stress. Therefore, our results discover an important regulatory pathway of YTHDF functions, adding an additional layer of complexity to the post-transcriptional regulation function of mRNA m6A.

overall_design: [Dataset 1] 8 samples. Duplicates for CLIP-seq samples in HEK293T cells with YTHDF1/3 knockdown and rescue with Flag-tagged YTHDF1 and YTHDF3 (WT or GlcNAcylation-null mutant (Mut)). [Dataset 2] 24 samples. Duplicates for RNA-seq and ribosome-protected fragments samples in HEK293T or HeLa cells with YTHDF1/3 knockdown and rescue with Flag-tagged YTHDF1 and YTHDF3 (na: no rescue, mut: rescue with GlcNAcylation-null mutant, wt: rescue with wild-type YTHDFs)

first: Zhongyu

last: Zou


title: BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes (Hi-C)

summary: Lymphocyte development consists of sequential and mutually exclusive cell states of proliferative selection and antigen receptor gene recombination. Transitions between each state require large, coordinated changes in epigenetic landscapes and transcriptional programs. How this occurs remains unclear. Herein, we demonstrate that in small pre-B cells, the lineage and stage-specific epigenetic reader BRWD1 reorders three-dimensional chromatin topology to affect transition between proliferative and gene recombination molecular programs. BRWD1 regulated the switch between poised and active enhancers interacting with promoters and coordinated this with Igk locus contraction. BRWD1 did so by converting chromatin-bound static cohesin to dynamic complexes competent to mediate long-range looping. Remarkably, ATP depletion recapitulated cohesin distributions observed in Brwd1-/- cells. Therefore, in small pre-B cells, cohesin conversion appears to be the main energetic mechanism dictating where dynamic looping occurs in the genome. Our findings provide a new mechanism of cohesin regulation and reveal how cohesin function can be regulated by lineage contextual mechanisms to facilitate specific cell fate transitions.

overall_design: Hi-C of small pre-B cells with WT, BRWD1KO genotypes; or Immature B cells in WT genotype from mice. Two biological replicates collected.

first: Malay

last: Mandal

first: Yeguang

last: Hu

first: Azam

last: Mohsin

first: Margaret

last: Veselits

first: Nathaniel

last: Wright

first: Michael

last: Okoreeh

first: Young

first: Jacob

first: Katia

last: Georgopoulos

first: Marcus

middle: R

last: Clark


title: Lysosomal cystine governs ferroptosis sensitivity in cancer via nuclear cysteine response

status: Public on Aug 30 2023

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

summary: The amino acid cysteine and its oxidized dimeric form cystine are commonly believed to be synonymous in metabolic functions. Cyst(e)ine depletion not only induces amino acid response, but also triggers ferroptosis, a non-apoptotic cell death. Here we report that, unlike general amino acid starvation, cyst(e)ine deprivation triggers ATF4 induction at the transcriptional level. Unexpectedly, it is the shortage of lysosomal cystine, but not the cytosolic cysteine, that elicits the adaptative ATF4 response. The lysosome-nucleus signaling pathway involves the aryl hydrocarbon receptor (AhR) that senses lysosomal cystine via the kynurenine pathway. A blockade of lysosomal cystine efflux attenuates ATF4 induction and sensitizes ferroptosis. To potentiate ferroptosis in cancer, we develop a synthetic mRNA reagent CysRx that converts cytosolic cysteine to lysosomal cystine. CysRx maximizes cancer cell ferroptosis and effectively suppresses tumor growth in vivo. Thus, intracellular nutrient reprogramming has the potential to induce selective ferroptosis in cancer without systematic perturbation.

overall_design: RNA-seq of MEF cells with no treatment, cyteine starvation, full amino acid starvation, cyteamine treatment, transfected with sh-CTNS, transfected with sh-CTNS and CTNS plasmid.

first: Robert

middle: V

last: Swanda

first: Quanquan

last: Ji

first: Xincheng

last: Wu

first: Jingyue

last: Yan

first: Leiming

last: Dong

first: Yuanhui

last: Mao

first: Yizhou

first: Shu-Bing

last: Qian


title: Transcriptomic analysis of early HSV-1 transcription in the absence of the immediate early protein, ICP4

first: Joel

last: Baines

address: Hungerford Hill Rd


title: Study the role and function of HP1 in embryonic stem cells

city: 南京

first: lixia

last: dong

address: 学府路12号

department: 模式动物研究所

institute: 南京大学

summary: In this article, we first obtained HP1 triple-knockout embryonic stem cells using Crispr-Cas9 and Cre-loxP systems. At the same time, we also obtained single-knock and double-knock cell lines respectively. On this basis, we studied The function of HP1 in embryonic stem cells was found to have a very important role in the regulation of differentiation and reproduction-related genes.In our follow-up study, we found that the deletion of HP1 leads to the differentiation tendency of embryonic stem cells into endoderm. Considering that HP1 has an important function of H3K9me3 recognition and binding, we examined the effect of HP1 deletion on histone modifications, we found that H3K9me2 and H3K9me3 modifications were significantly reduced, and then through rescue experiments, we thought that HP1 may be through OCT4 and NANOG and then further functional.

overall_design: Comparative gene expression profiling of RNA-seq data from HP1 single-knock-down and triple-knock cells versus WT embryonic stem cells. Comparative gene expression profiling of RNA-seq data from SETDB1 knockout cells and WT embryonic stem cells.

first: Lixia

first: Linchun

last: Zhao

first: Jinzhong

last: Qin


title: BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes (ChIP-Seq)

first: Mark

last: Maienschein-Cline

overall_design: ChIP-seq of CTCF, H3K27Ac, H3M4me1, NIPBL, RAD21, SMC3, and WAPL in small pre-B cells isolated from mice, with WT, BRWD1KO genotypes , and WT small pre-B cells treated with oligomycin (ATPneg). Two biological replicates were collected for each ChIP sample. Input samples were collected in duplicate, or were used as previously released (GSM2753125).

first: Malay

last: Mandal

first: Yeguang

last: Hu

first: Azam

last: Mohsin

first: Margaret

last: Veselits

first: Nathaniel

first: Michael

first: Young

last: Yoon

first: Jacob


title: miR-126 identifies a quiescent and chemo-resistant human B-ALL cell subset that correlates with minimal residual disease

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

institute: SR-TIGET


title: Transcriptome-wide marker gene expression analysis of stress-responsive Oleidesulfovibrio alaskensis

city: RAPID CITY

first: Venkataramana

last: Gadhamshetty

state: SD

address: 501 E St Joseph St, South Dakota Mines

department: Civil and Environmental Engineering

institute: South Dakota Mines

summary: Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses transcriptome-wide marker gene panel mapping to decipher the stress mechanisms in SRB. This project contains 3 control samples and 6 test samples of RNA-seq data of Oleidesulfovibrio alaskensis strain G20, exposed to pristine copper and graphene-coated copper.

overall_design: To investigate the gene expression profiling of Oleidesulfovibrio alaskensis exposed to pristine copper and graphene-coated copper

first: Jawahar

last: Kalimuthu


title: Genome-wide identification of circRNAs translated by eIF4A3

city: Daejeon

first: Jeeyoon

last: Chang

address: 291 Daehak-ro, Yuseong-gu, Daejeon

department: Life Science

institute: Korea Advanced Institute of Science & Technology

summary: Exon junction complexes (EJCs) deposited on spliced mRNAs play multifunctional roles in the regulation of gene expression. Whereas the formation and components of EJCs are well characterized, the underlying molecular mechanisms for gene regulation remain poorly understood. Here we find that a eukaryotic translation initiation factor (eIF) 4A3, a core component of EJC directly interacts with eIF3g, a subunit of eIF3 complex. This interaction serves as a linker between the EJC and eIF3 complex, consequently driving an internal ribosomal recruitment. Accordingly, artificially tethered EJC component or cellular EJC deposited on mRNA after splicing promotes internal initiation of translation in a way that is resistant to cellular stress induced by serum starvation. We also demonstrate that translatable endogenous or reporter circular RNAs depend on EJC for their association with polysomes. Our results uncover an internal initiation driven by EJC, expanding the protein-coding potential of human transcriptome including circular RNAs.

overall_design: HeLa cells were either undepleted or depleted of eIF4A3 by synthetic siRNAs. The cells were subjected to polysome fractionation experiments. Polysome or subpolysome (40S/60S/80S) were pooled according to the absorbance at 254 nm, and the RNAs in each pooled sample were extracted using TRIzol reagent. The RNAs were treated with RNase R to remove linear RNAs, followed by cRNA synthesis using Arraystar Super RNA Labeling Kit. After hybridization and scanning, the acquired signal intensities from polysome or subpolysome in each samples were utilized to calculate the relative polysome-subpolysome distribution of circRNAs upon eIF4A3 downregulation.

first: Min-Kyung

last: Shin

first: Joori

last: Park

first: Incheol

last: Ryu

first: Kwon

last: Jeong

first: Yoon Ki

last: Kim


title: Human monocyte stimulation with IL6

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

summary: To investegate how IL6 regulates human monocyte transcriptional profiles, we stimulated primary human monocytes in vitro with IL6 and IL6R.

overall_design: Primary human monocytes from five different donors were stimulated with either media alone (PRMI1640 plus 10% HI FBS) or a combination of media, 10ng/ml IL6, and 18.7ng/ml IL6R for 24 hours.

first: Xia

last: Gao

first: Thirumalai

last: Ramalingam

middle: A


title: Activated leukocyte cell adhesion molecule on human oligodendrocytes mediates Th17 cell adhesion

city: Montreal

first: Haritha

last: Desu

state: Québec

address: 900 R. Saint-Denis

department: Neurosciences

institute: Centre de recherche du Centre Hospitalier de l'Université de Montréal

summary: Multiple sclerosis is a chronic neuroinflammatory disorder characterized by demyelination, oligodendrocyte damage/loss and neuroaxonal injury in the context of immune cell infiltration in the central nervous system. No neuroprotective therapy is available to promote the survival of oligodendrocytes and protect their myelin processes in immune-mediated demyelinating diseases. Pro-inflammatory CD4 T helper (Th)17 cells can directly interact with oligodendrocytes in multiple sclerosis and its animal model, causing injury to myelinating processes and cell death through direct contact. However, the molecular mechanisms underlying the close contact and subsequent detrimental interaction of Th17 cells with oligodendrocytes remain unclear. In this study we conducted single cell RNA sequencing of human primary oligodendrocytes cultured alone, in contact or separated by an insert with primary Th17 polarized T cells and identified several cell adhesion molecules that may modulate T cell contact mediated damage of oligodendrocytes. Furthermore, we used flow cytometry and immunofluorescence studies on central nervous system tissue from multiple sclerosis subjects, its animal model and controls to characterize the expression of cell adhesion molecules by mature oligodendrocytes. We found that a significant proportion of human and murine mature oligodendrocytes express melanoma cell adhesion molecule and activated leukocyte cell adhesion molecule in multiple sclerosis, EAE and controls although their regulation differ between human and mouse. We observed that exposure to pro-inflammatory cytokines or to human activated T cells are associated with a marked downregulation of the expression of melanoma cell adhesion molecule but not activated leukocyte cell adhesion molecule at the surface of human primary oligodendrocytes. Furthermore, we used in vitro live-imaging, immunofluorescence, and flow cytometry to determine the contribution of these molecules to Th17-polarized cell adhesion and cytotoxicity towards human oligodendrocytes. Silencing and blocking activated leukocyte cell adhesion molecule but not melanoma cell adhesion molecule limited prolonged interactions between oligodendrocytes and Th17-polarized cells, resulting in decreased adhesion of Th17-polarized cells to oligodendrocytes and conferred significant protection of oligodendrocytic processes.

overall_design: Human oligodendrocytes in primary culture derived from the a brain sample from resection path of surgery for epilepsy were exposed to IL-23-polarized CD4 T cells (Th17 cells) at 1:2 ratio. They were either directly in contact (TCO condition) or separated by a an insert with a porous membrane of 0.4 µm size (insert, TCM condition).

first: Catherine

last: Larochelle

first: Jack

last: Antel

first: Jo

last: Stratton

first: Qiao-Ling

last: Cui

first: Helene

last: Jamann


title: Inhibition of EB3 activates the Meis2-Pax6 regenerative program in wet AMD [scATAC-seq]

first: Mark

last: Maienschein-Cline

summary: Wet age-related macular degeneration (AMD), characterized by leaky neovessels emanating from the choroid, is a main cause of blindness. As current treatments for wet AMD require regular intravitreal injections of anti-VEGF biologics, there is a need for the novel development of less invasive treatments. Here, we developed a novel inhibitor of microtubule-associated End Binding 3 protein (EB3), herein termed EBIN, which blocked pathological Ca2+ signaling in activated endothelial cells and suppressed leakage of choroidal neovessels. Delivery of EBIN via eye drops in mouse and non-human primate (NHP) models of AMD prevented neovascular leakage and neovascularization as effectively as intravitreal injection of anti-VEGF therapy. EBIN activated Meis2-Pax6 regenerative pathways in metabolic-active endothelial cells comprising neovessels and promoted tissue regeneration. Furthermore, single nuclei assay for transposase-accessible chromatin sequencing (sn-ATAC-seq) analysis demonstrated that in metabolic-active endothelial cells, the RPE, and photoreceptors, EBIN induced global increases in chromatin accessibility, the biological process progressively inhibited in AMD patients. These results suggest the unique therapeutic mode of action of this novel drug candidate, which can potentially promote regeneration of eye tissue by reversing the degenerative processes underlying both the neovascular and atrophic forms of AMD.

overall_design: Choroidal neovascularization was induced on day 0 in African green monkeys’ eye by laser photocoagulation targeting the Bruch’s membrane. Monkeys then received either 30 µL topical instillation of Myr-EBIN or vehicle in each eye twice daily for 7 days and once a day for another 14 days. After 21 days, the eyes were dissected and separated by different sections of the eyes. Samples that undergo sequencing were flash frozen and been sent to UC San Diego Center for Epigenomics for sample preparation and sequencing.

first: Quinn

last: Lee

first: Wan

last: Chan

first: Xinyan

last: Qu

first: Ying

last: Sun

first: Hazem

last: Abdelkarim

first: Jonathan

last: Le

first: Uzma

last: Saqib

first: Mitchell

middle: Y

first: Kevin

last: Kruse

first: Avik

last: Banerjee

first: Ben

last: Hitchinson

first: Melissa

last: Geyer

first: Fei

last: Huang

first: Victor

last: Guaiquil

first: Amelia

last: Mutso

first: Martin

last: Sanders

middle: I

last: Rosenblatt

first: Vadim

last: Gaponenko

first: Asrar

middle: B

last: Malik

first: Yulia

last: Komarova


title: c-Myc uses Cul4b to preserve genome stability and promote CD8+ T cell-mediated antiviral immune responses

city: Philadelphia

first: Paula

last: Oliver

address: 816F ARC, 3615 Civic Center Blvd.

department: Department of Pathology, Perelman School of Medicine

institute: University of Pennsylvania

summary: During infection, virus-specific CD8+ T cells undergo rapid bursts of proliferation and differentiate into effector cells that kill virus infected cells and reduce viral load. This rapid clonal expansion can put T cells at significant risk for replication-induced DNA damage. We found that c-Myc utilizes the E3 ubiquitin ligase, Cul4b, to inextricably link CD8+ T cell expansion to DNA damage response pathways. Following activation, c-Myc increased levels of Cul4b and other members of the CRL4 complex. Despite having abundant c-Myc expression, Cul4b-deficient CD8+ T cells were unable to expand and clear virus. Cul4b-deficient CD8+ T cells accrued DNA damage and succumbed to proliferative catastrophe early after antigen encounter. Mechanistically, Cul4b ablation induced a protracted accumulation of p21 and Cyclin E2 resulting in replication stress. Our data show that, to support cell proliferation, c-Myc must employ Cul4b to maintain genome stability, thereby directly coupling these two interdependent pathways. These data clarify how CD8+ T cells use c-Myc and Cul4b to sustain their potential for extraordinary population expansion, longevity and antiviral responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for purified CD8+ T cells from WT and Cul4b fl/fl CD4Cre mice.

first: Asif

last: Dar

first: Dale

last: Kim

first: Scott

last: Gordon

first: Kathleen

last: Klinzing

first: Siera

last: Rosen

first: Ipsita

last: Guha

first: Nadia

last: Porter

first: Yohaniz

last: Ortega

first: Katherine

last: Forsyth

first: Jennifer

last: Roof

first: Hossein

last: Fazelinia

first: Lynn

last: Spruce

first: Laurence

last: Eisenlohr

first: Edward

last: Behrens


title: Inhibition of EB3 activates the Meis2-Pax6 regenerative program in wet AMD

first: Mark

last: Maienschein-Cline

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus


title: Transcriptomic landscape of mouse pulmonary alveolar cells upon chronological aging and/or anti-senescence intervention

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

institute: Chinese Academy of Sciences

summary: As a critical hallmark of senescent cells, the senescence-associated secretory phenotype (SASP) develops over the course of chronological aging and in diverse age-related conditions, and is a key driver of chronic inflammation and age-associated phenotypes. For years, the identification, characterization and pharmacological targeting of senescent cells have gained substantial attention in the field of aging and age-related pathologies. Pyruvate dehydrogenase kinase 4 (PDK4) is an important mitochondrial matrix enzyme in cellular energy regulation, and drives the metabolic reprogramming of mammalian cells towards a Warburg-like effect. Upregulation of PDK4 is responsible for enhanced production of lactate in the tissue microenvironment of aged organisms, potentially causing chronic inflammation and contributing to accelerated aging. Targeting PDK4 holds the potential to prevent lactate accumulation, minimize tissue damage and postpone senescence-associated systemic aging. Here we profiled the genome-wide expression of cells (mainly fibroblasts) in mouse pulmonary alveolus, with the assistance of laser capture microdissection (LCM) of primary lung tissues. Animals were allowed to naturally age, or subject to treatment by PDK4-IN (an anthraquinone derivative, PDK4 inhibitor). These data may provide a baseline to further determine the effects of lactate reduction by PDK4-specific targeting on cellular senescence, tissue homeostasis, and explore the wide implications of PDK4 expression in organismal aging and age-related morbidity.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of pulmonary alveolar cells from aged mice in relative to those from young mice, as well as aged mice subject to intervention by a PDK4-targeting regimen.

first: Xuefeng

last: Dou