title: The MYC-YBX1 Circuit in Maintaining Stem-like Vincristine-Resistant Cells in Rhabdomyosarcoma

status: Public on May 17 2023

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that causes significant devastation, with no effective therapy for relapsed disease. The mechanisms behind treatment failures are poorly understood. Our study showed that treatment of RMS cells with vincristine led to an increase in CD133-positive stem-like resistant cells. Single cell RNAseq analysis revealed that MYC and YBX1 were among the top-scoring transcription factors in CD133-high expressing cells. Targeting MYC and YBX1 using CRISPR/Cas9 reduced stem-like characteristics and viability of the vincristine-resistant cells. MYC and YBX1 showed mutual regulation, with MYC binding to the YBX1 promoter and YBX1 binding to MYC mRNA. The MYC inhibitor MYC361i synergized with vincristine to reduce tumor growth and stem-like cells in a zebrafish model of RMS. MYC and YBX expression showed a positive correlation in RMS patients, and high MYC expression correlated with poor survival. Targeting the MYC-YBX1 axis holds promise for improving survival in RMS patients.

overall_design: Cells derived from the rhabdomyosarcoma RD cell line were induced for form spheres in the stem cell medium.  Spheres were serially passaged.  Parental cell as well as spheres at passages 1 and  5 were subjected to single cell RNA sequencing.

first: Madeline

last: Fritzke

first: Kenian

last: Chen

first: Weiliang

last: Tang

first: Spencer

last: Stinson

first: Thao

last: Pham

first: Yadong

last: Wang

first: Lin

last: Xu

first: Eleanor


title: c-Myc supports polyploidy and prevents senescence in the murine placenta

status: Public on May 12 2023

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: c-Myc supports polyploidy and prevents senescence in the murine placenta [RNA-seq]

summary: To understand differential gene expression between wildtype and c-Myc null mouse trophoblast giant cells.

overall_design: TGCs from 9.5 dpc stage were dissected as mentioned previously (Hannibal and Baker, 2016) cold PBS and embryos were used for genotyping. Total RNA from TGCs was isolated using TRIzol (#15596026, Thermo Fisher Scientific). rRNA was depleted using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB # E6310L). cDNA synthesis was performed using NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760S) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (NEB # E7335S). Sequencing was performed using an Illumina NextSeq 500  with 75bp single read runs.

first: Vijay

middle: P

last: Singh

first: Jennifer

middle: L

last: Gerton


title: Genome-wide Nutlin-3 Sensitizing Gene (NSG) loss-of-function CRISPR screen data

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: SLN screen highlights the 26s proteasome as a putitive theraputic target.

overall_design: 94T778 cells transduced with the GeCKOv2 A and B libraries were treated with Nutlin3a for 72 hrs.

first: Michael

last: Ludwig

first: Kelly

last: Sullivan

first: Joaquín

middle: M

last: Espinosa


title: APR-246 enhances colorectal cancer sensitivity to radiotherapy

city: Linkoping

first: Chuanwen

last: Fan

address: US campus

country: Sweden

institute: Linkoping university

summary: p53 mutation is common and highly related to radiotherapy resistance in rectal cancer. APR-246, as a small molecule, can restore the tumor-suppressor function to mutant p53. There is no study on combining APR-246 with radiation in rectal cancer; therefore, we examined whether APR-246 sensitized colorectal cancer cells with different p53 status to radiation. The combination treatment had synergistic effects on HCT116p53-R248W/-(p53Mut) cells, followed by HCT116p53+/+(p53WT) cells, and exhibited an additive effect on HCT116p53-/-(p53Null) cells through inhibiting proliferation, enhancing reactive oxygen species, and apoptosis. The results were confirmed in zebrafish xenografts. Comparison of the transcriptome in colorectal cancer cells with different p53 status 72hrs post-treatment with APR-246, irradiation, or the combination of APR-246 with irradiation was carried out. p53Mut and p53WT cells shared more activated pathways and differentially expressed genes following the combination treatment, compared to p53Null cells, although the combination treatment regulated individual pathways in the different cell lines. APR-246 mediated radio-sensitization effects through p53-dependent and -independent ways.

overall_design: Samples of colorectal cancer cells were treated with APR-246, irradiation, and the combination of APR-246 with irradiation

first: Xuqin

last: Xie

first: Bin

last: Luo

first: Xiao-Feng

last: Sun


title: Proteasome Inhibition Sensitizes Liposarcoma to Nutlin-3-induced Apoptosis via the ATF4/CHOP Axis


title: PolyA RNA-seq from liposarcoma cells treated with Nutlin3R

summary: Analysis of steady-state mRNA levels in liposarcoma cells treated for 16 hr with 0.05% DMSO or 10 uM Nutlin3R

overall_design: Two independent biological replicates each of 94T778 and Lipo-246 cells, treated for 16 hr with 0.05% DMSO or 10 uM Nutlin

first: Joaquin


title: The Microbiome Modulates DNA Methylation in Mouse Colonic Mucosa

status: Public on May 09 2023

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an epigenetic mark that is altered in cancer and aging tissues. The effects of extrinsic factors on DNA methylation remain incompletely understood. Microbial dysbiosis is a hallmark of colorectal cancer, and infections have been linked to aberrant DNA methylation in cancers of the GI tract. To determine the microbiota’s impact on DNA methylation, we studied the DNA methylation of colorectal mucosa in germ-free (GF, no microbiome) and specific pathogen free (SPF, controlled microbiome) mice, as well as in interleukin 10 KO mice (Il10-/-) which are prone to inflammation and tumorigenesis in the presence of a microbiome. We compared DNA methylation changes to those seen in aging, and after exposure to the colon carcinogen azoxymethane (AOM). DNA methylation changes associated with aging were accelerated in the Il10-/- /SPF mice. By contrast, AOM induced profound hypomethylation that was distinct from the effects of aging or of the microbiome. CpG sites modified by the microbiome were over-represented among DNA methylation changes in colorectal cancer. Thus, the microbiome affects the DNA methylome of colorectal mucosa in patterns reminiscent of what is observed in colorectal cancer.

overall_design: DNA methylation profiling in mouse colonic mucosa.

first: Ang

first: Lauren

last: Cole

first: Shinji

last: Maegawa

first: Peace

last: Park

first: Kelsey

last: Keith

first: Jozef

last: Madzo

first: Christian

last: Jobin

first: Jean-Pierre

middle: J

last: Issa


title: Glutathione supplementation improves fat graft survival by inhibiting ferroptosis via the SLC7A11/GPX4 axis

status: Public on May 08 2023

city: Guangzhou

first: Zehua

last: Li

address: Huangpu Avenue

country: China

institute: Jinan University

summary:
Background: Autologous fat grafting is hampered by unpredictable graft survival, which is potentially regulated by ferroptosis. Glutathione (GSH), a powerful antioxidant used in tissue preservation, has ferroptosis-regulating activity; however, its effects on fat grafts are unclear. This study investigated the effects and mechanisms of GSH in fat graft survival.
Methods: Human lipoaspirates were transplanted subcutaneously into the backs of normal saline-treated (control) or GSH-treated nude mice. Graft survival was evaluated by magnetic resonance imaging and histology. RNA sequencing was performed to identify differentially expressed genes and enriched pathways. GSH activity was evaluated in vitro using an oxygen and glucose deprivation (OGD) model of adipose-derived stem cells.
Results: Compared with control group, GSH induced better outcomes, including superior graft retention, appearance, and histological structures. RNA sequencing suggested enhanced negative regulation of ferroptosis in the GSH-treated grafts, which showed reduced lipid peroxides, better mitochondrial ultrastructure, and SLC7A11/GPX4 axis activation. In vitro, OGD-induced ferroptosis was ameliorated by GSH, which restored cell proliferation, reduced oxidative stress, and upregulated ferroptosis defense factors.
Conclusions: Our study confirms that ferroptosis participates in regulating fat graft survival and that GSH exerts a protective effect by inhibiting ferroptosis. GSH-assisted lipotransfer is a promising therapeutic strategy for future clinical application.

overall_design: comparative gene expression profiling analysis of RNA-seq data for Glutathione treated fat grafts and normal saline treated fat grafts

first: Jinqiang

last: Lu

first: Zhiqin

last: Dong

first: Jiaji

last: Liang

first: Shenghong

first: Wenwen

last: Han

first: Taixing

last: Cui

first: Hongwei

last: Liu


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [RNA-seq]

status: Public on May 07 2023

city: Beijing

first: Dong

state: Beijing

address: No.5 Yiheyuan Road, Haidian District,

department: College of Life Science

institute: Peking University

summary: Mammalian erythroid cells development can be divided into three period: hematopoietic stem and progenitor cells (HSPC), erythroid progenitor (Ery-Pro) and erythroid precursor (Ery-Pre). To better understand human erythropoiesis and its regulation, we performed genome-wide studies of chromatin architecture, enhancer and select transcription factors binding, and transcriptomics profiling utilizing modified strategy to obtain defined progenitor and precursor populations from primary human erythroid cells. Integration and analysis of these data reveals that the TAD structure is stable but promoter - enhancer interactions are highly dynamic in a stage specific manner. Erythroid master regulator - GATA1 involves in the P-E interactions stepwisely. GATA1 binding is largely stable in erythroid progenitor and precursor, but dynamic GATA1 binding during this process regulate a productive erythroid gene expression and local chromatin rewiring. Additionally, we also have showed that dosage of GATA1 control the erythroid progenitor behavior and the erythroid progression. The valuable chromatin architecture and epigenome data will provide more comprehensive insight of human erythropoiesis and dynamic gene regulation of cellular differentiation even more broadly.

overall_design: RNA-seq assay for human cord blood CD34+ cells (HSPC) as well as derived erythroid progenitor (Ery-Pro) and (Ery-Pre) precursor: Also, RNA-seq of siGATA1 in erythroid  progenitor (Ery-Pro)

first: Hsiang-Ying

last: Lee


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [scRNA-seq]

overall_design: scRNA-seq of siGATA1/ siCon or untreated erythroid  progenitor (Ery-Pro)


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [MicroC]

overall_design: MicroC assay for human cord blood CD34+ cells (HSPC) as well as derived erythroid progenitor (Ery-Pro) and (Ery-Pre) precursor


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [Cap-C]

overall_design: Capture-C of WT, GATA1 binding site1 knock-out and GATA1 binding site2 knock-out in differentiated HUDEP-1 cell line; Also Capture-C of siControl and siGATA1 in differentiated HUDEP-1 cell line


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [HiChIP]

overall_design: GATA1 HiChIP of Erythroid progenitor (Day5) and Erythroid precursor (Day12)


title: miR-223 limits hemogenic endothelial cell specification and myelopoiesis [scRNA-seq]

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: miR-223 is a novel regulator of murine hemogenic endothelial cell specification and endothelial-to-hematopoietic transition. miR-223-deficient mouse embryos exhibit significant increase in hemogenic endothelial cells and HSPCs.

overall_design: Single cell transcriptomic profiles of miR-223 WT and KO endothelial cells from mouse AGM (10.5)

first: Yinyu

last: Wu

first: Umadevi

first: Gael

last: Genet

first: Karen

middle: K

last: Hirschi


title: Delayed denervation-induced muscle atrophy in Opg knockout mice

status: Public on May 01 2023

first: Mingming

last: Zhang

address: No.28 Fuxing Road

institute: Chinese PLA general hospital

summary: Recent evidence has shown a crucial role for the osteoprotegerin/receptor activator of nuclear factor κ-B ligand/RANK (OPG/RANKL/RANK) signaling axis not only in bone but also in muscle tissue; however, there is still a lack of understanding of its effects on muscle atrophy. Here, we found that denervated Opg knockout mice displayed better functional recovery and delayed muscle atrophy, especially in a specific type IIB fiber. Moreover, OPG deficiency promoted milder activation of the ubiquitin-proteasome pathway, which further verified the protective role of Opg knockout in denervated muscle damage. Furthermore, transcriptome sequencing indicated that Opg knockout upregulated the expression of Inpp5k, Rbm3, and Tet2 and downregulated that of Deptor in denervated muscle. In vitro experiments revealed that satellite cells derived from Opg knockout mice displayed a better differentiation ability than those acquired from wild-type littermates. Higher expression levels of Tet2 were also observed in satellite cells derived from Opg knockout mice, which provided a mechanistic basis for the protective effects of Opg knockout on muscle atrophy. Taken together, our findings uncover the novel role of Opg in muscle atrophy process and extend the current understanding in the OPG/RANKL/RANK signaling axis.

overall_design: C57BL/6 wild-type and Opg knockout mice were treated with sciatic nerve transection to model denervation-induced muscle atrophy. Transcriptome sequencing was performed to analyze the potential molecular mechanism.

first: Ming

last: Chen

first: Yi

first: Man

last: Rao


title: Epigenetic Control of Androgen Production by Histone H2A Lys130 acetylation

status: Public on May 02 2023

city: St Louis

first: Tiandao

address: 4444 Forest Park Ave

institute: Washington University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The biosynthesis of androgen from cholesterol in testis is well understood, however, how cancer cells gauge dwindling androgen to dexterously initiate its de novo synthesis remained elusive. We uncovered that sterol regulatory element-binding protein 1 (SREBP1) and its switch to hitherto unknown dual-phosphorylated form (pY673/951-SREBP1), acts as an androgen sensor. Androgen deficiency promoted SREBP1 dual-phosphorylation, causing its dissociation from androgen receptor (AR) in its androgen-unbound state, followed by nuclear translocation. SREBP1 recruited KAT2A/GCN5 and deposited novel epigenetic marks, histone H2A Lys130-acetylation (H2A-K130ac) in SREBF1, reigniting de novo lipogenesis & steroidogenesis. Tumor-derived androgen retained SREBP1 in cytosol, promoting T cell exhaustion, reflected in elevated PD-1 and Tim3. Reversal of H2A-K130ac or pY-SREBP1 sensitized castration-resistant prostate cancer (CRPC) resistant to androgen synthesis inhibitor, Abiraterone. Further, nuclear SREBP1 and H2A-K130ac levels were significantly increased and directly correlated with late stage prostate cancer patients. Global lipidomics analysis revealed a distinct lipid signature in androgen-deprived CRPCs, resembling the lipid profile of prostate cancers of African-American (AA) men. Overall, self-perpetuating pY-SREBP1/H2A-K130ac signaling explains sex bias in cancers and reveal a novel therapeutic vulnerability wherein synchronous inhibition of GCN5 and Tyr-kinases could overcome drug-resistant disease, benefiting AA men with aggressive prostate cancer.

overall_design: Romidepsin (0.5 µM, 18h) treated VCaP cells were cross-linked, chromatin was isolated, and ChIP was performed using H2A-K130ac antibody, followed by sequencing

first: Nupam

last: Mahajan


title: BHLHE40 is key hypoxia-induced transcriptional repressor in beta cells

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto university

summary: To assess the impact of hypoxia on global gene expression of beta cells, we performed bulk RNA-seq on mouse islets, human islets and MIN6 cells. Bhlhe40 was transcriptional repressor which was highly induced by hypoxia in beta cells. Thus, we established Bhlhe40 overexpressing MIN6 cells and performed RNA-seq to identify the targets of Bhlhe40.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq for human islets, mouse islets and MIN6 cells cultured in normoxic or hypoxic condition . Comparative gene expression profiling analysis of RNA-seq for MIN6 cells with or without Bhlhe40 overexpression.

first: Kazuya

last: Yamagata


title: Effect of androgen induction and AR depletion on gene expression of metastatic prostate cancer-specific long noncoding RNAs in prostate cancer cells.

status: Public on May 04 2023

city: Tampere

first: Tapio

last: Visakorpi

address: Kalevantie 4

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

type: Non-coding RNA profiling by high throughput sequencing

summary: We identified 27 long noncoding RNAs with differential expression (DE-lncRNAs) between prostate cancer metastases and corresponding primary tumors, suggesting that they are metastatic castration resistant prostate cancer (mCRPC)-specific lncRNAs. To assess androgen regulation of the DE-lncRNAs, we investigated their expression in LNCaP and VCaP cells induced with dihydrotestosterone (DHT) as well as in androgen receptor (AR)-silenced cells by using RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP and VCaP cells that were treated with 0 or 10 nM DHT for 24 hours or with AR siRNA or negative control (NC) siRNA for 48 hours. Three biological replicates were sequenced on each treatment type.

first: Mina

last: Sattari

first: Annika

last: Kohvakka

first: Bryn

last: Autio-Kimura

first: Hanna

last: Rauhala

first: Matti

last: Nykter

first: Leena

last: Latonen

first: Juha

last: Kesseli


title: Transcriptome analysis of aortas from aged WT and Sirt2KO mice

city: Chengdu

first: Xiaoqiang

last: Tang

address: Renminnan Road

institute: Sichuan University

summary: We analyzed the transcriptome of aortas from aged WT and Sirt2KO mice by bulk RNA-seq

overall_design: Three mice were included in each group.

first: Yang

first: Xiao-Man

last: Wang

first: Hou-Zao


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [CUT&RUN]

first: Dong

last: Li

overall_design: CUT&RUN assay for H3K27ac, GATA1, GATA2, ETV6, RUNX1, CEBPA and IgG in human cord blood CD34+ cells (HSPC) as well as derived erythroid progenitor (Ery-Pro) and (Ery-Pre) precursor; Also CUT&RUN for GATA1 of WT, GATA1 binding site1 KO, GATA1 binding site 1&2 KO, siControl and siGATA1  differentiaed HUDEP-1 cells

first: Hsiang-Ying

last: Lee


title: Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis

status: Public on May 06 2023

overall_design: Refer to individual Series


title: Hepatic stellate cell stearoyl co-A desaturase activates leukotrien B4 receptor 2-β-catanin cascade to promote liver tumorigenesis.

status: Public on Apr 30 2023

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

summary: Hepatocellular carcinoma (HCC) is the 3rd most deadly malignancy. Activated hepatic stellate cells (aHSC) give rise to cancer-associated fibroblasts in HCC and are considered a potential therapeutic target. Here we report that selective ablation of stearoyl CoA desaturase-2 (Scd2) in aHSC globally suppresses nuclear CTNNB1 and YAP1 in tumors and tumor microenvironment and prevents liver tumorigenesis in male mice. Tumor suppression is associated with reduced leukotriene B4 receptor 2 (LTB4R2) and its high affinity oxylipin ligand, 12-hydroxyheptadecatrienoic acid (12-HHTrE).  Genetic or pharmacological inhibition of LTB4R2, recapitulates CTNNB1 and YAP1 inactivation and tumor suppression in culture and in vivo. Single cell RNA sequencing identifies a subset of tumor-associated aHSC expressing Cyp1b1 but no other 12-HHTrE biosynthetic genes.  aHSC release 12-HHTrE in a manner dependent on SCD and CYP1B1 and their conditioned medium reproduces the LTB4R2-mediated tumor-promoting effects of 12-HHTrE in HCC cells.  CYP1B1-expressing aHSC are detected in proximity of LTB4R2-positive HCC cells and the growth of patient HCC organoids is blunted by LTB4R2 antagonism or knockdown.  Collectively, our findings suggest aHSC-initiated 12-HHTrE-LTB4R2-CTNNB1-YAP1 pathway as a potential HCC therapeutic target.

overall_design: To examine cell types expressing Cyp1b1 in tumor microenvironment (TME), screening of cell type clusters was done  by scRNA-seq and we found that Cyp1b1 was dominantly expression by Fbln2+ cells. To further characterize these Fbln2+ cells, we enriched Col1a1 expressing cells by isolating GFP+ cells by FACS from DEN+WAD-subjected Rosa26mTmG; Col1a1-Cre (mTmG;CC) mice.This allowed separation of VitA+GFP- quiescent HSC, VitA+GFP+ aHSC and VitA-GFP+ VitA-depleted aHSC and activated PF.

first: Sonal

last: Sinha

first: Satoka

last: Aizawa

first: Yasuhiro

last: Nakano

first: Alexander

last: Rialdi

first: Yibu

last: Chen

first: Meng

first: Hye Yeon

last: Choi

first: Rajan

last: Srestha

first: Stephanie

last: Pan

first: Audrey

last: Kapelanski-Lamoureux

first: Gregory

last: Yochum

first: Linda

last: Sher

first: Satdarshan

last: Monga

first: Anthoula

last: Lazaris

first: Keigo

last: Machida

first: Michael

last: Karin

first: Ernesto

last: Guccione


title: Global gene expression changes in E9.5 cardiopharyngeal mesoderm (CPM) of Chd7 mutants versus controls

status: Public on Apr 29 2023

city: London

first: Athanasia

last: Stathopoulou

address: 30 Guilford Street

country: United Kingdom

institute: University College London

summary: To investigate the role of Chd7 in the CPM we performed RNA-seq on two microdissections from Mesp1-Cre; Chd7 fl/fl (referred to as cKO) and control (Mesp1-Cre) embryos. The first involved the distal pharyngeal apparatus, i.e. arches two through six including the dorsal pericardial wall (DPW) which encompasses the SHF before these cells migrate to the poles of heart. For simplicity we refer to this dissection as “SHF” (we use inverted commas in this denotation to recognise the presence of other cell types). The second microdissection included the cells that have entered the heart (i.e. SHF-derived outflow tract (OFT), right ventricle (RV) and parts of the atrium, and FHF-derived left ventricle and atria). The OFT and heart tissue was collected from the same embryos (labelled “HEART”).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SHF and HEART tissue, from cKO (Mesp1-Cre; Chd7 fl/fl) and control (Mesp1-Cre) embryos. Tissue from each embryo was processed individually and sequenced as a single sample. Each “SHF” sample originated from a single embryo, and similarly each “HEART” sample originated from a single heart and OFT.

first: Ping

last: Wang

first: Deyou

last: Zheng

first: Peter

last: Scambler


title: Genome-wide analysis of CHD7 in cardiac progenitor cells

status: Public on Apr 28 2023


title: Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI


title: PRMT1 is required for antibody affinity maturation by preventing premature B cell differentiation

status: Public on Apr 27 2023

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Germinal center (GC) B cells undergo cycles of somatic hypermutation and selection, thus increasing their antibody affinity before differentiating into plasma or memory cells. The mechanisms dictating the dynamics of GC B cells are incompletely understood. We show that ablating the Protein arginine methyltransferase 1 (PRMT1) in GC B cells reduces antibody affinity maturation by impairing GC dynamics, as shown by compromised GC expansion, accumulation of CXCR4- B cells, and increased memory B cell differentiation, partly, at the expense of plasma cell production. Furthermore, PRMT1 distinguishes the subset of GC B cells that reenter the GC dark zone after positive selection, in which it is upregulated by Myc in conjunction with mTORC signaling. PRMT1 opposes mature B cell differentiation, as shown by higher plasma cell differentiation of PRMT1-deficient B cells activated ex vivo, a function co-opted by B cell lymphoma cells, in which PRMT1 expression also correlates with Myc expression and outcome.

overall_design: 6 RNA-seq mouse samples (2 conditions, 3 biological replicates per condition).

first: Ludivine

middle: C

last: Litzler

first: Astrid

last: Zahn

first: Adrien

last: Sprumont

first: Kiersten

last: Dionne

first: Silvana

middle: R

last: Ferreira

last: Slattery

first: Stephen

last: Methot

first: Anne

last: Patenaude

first: Steven

last: Hébert

first: Nisha

last: Kabir

first: P

middle: G

last: Subramani

first: Seolkyoung

last: Jung

first: Stéphane

last: Richard

first: Javier

last: Di Noia


title: Effect of mouse and human progranulin haploinsufficiency on mouse cortical transcriptome at 18 months of age.

city: Vancouver

first: Ben

last: Life

state: BC

address: 950 W 28th Ave

institute: University of British Columbia

summary: We performed RNAseq on mouse progranulin deficient and humanized mouse progranulin deficient cortical tissue at 18 months to investigate the functional differences between mouse and human progranulin and identify transcriptomic changes for therapeutic endpoints.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of n=5 wild type (Grn+/+), n=4 mouse progranulin deficient (Grn+/-), and n=4 humanized progranulin deficient (Grn-/-; GRNtg).

first: Benjamin

first: Blair

last: Leavitt


title: Extracellular Vesicles from Hypoxia Culture of Human Mesenchymal Stem Cells

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

summary: In current study, hMSCs were grown under Hypoxia condition. mRNA sequencing reveals global transcriptome alterations for hypoxia condition.

overall_design: MSC cell were cultured under either 2D or hypoxia conditions.

first: Li

last: Sun

first: Xuegang

last: Yuan


title: Lineage-specific iPSC-Derived SMC Modeling Predicts Integrin Alpha-V Antagonism Reduces Aortic Root Aneurysm Formation in Marfan Syndrome Mice

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

summary: Aortic single-cell RNA sequencing data from Fbn1C1041G/+ mice treated with GLPG0187 or vehicle control.

overall_design: Fbn1C1041G/+ (Marfan syndrome) mice were treated with GLPG0187 (Integrin av inhibitor) or vehicle control daily from 6-16 weeks. Aortic tissue from 16-week-old mice was subjected to tissue digestion and single-cell RNA sequencing. Male and female replicate pools from each treatment were used, yielding 2 samples total.

first: A

first: M

last: Fischbein


title: Genome-wide analysis of CHD7 binding sites in cardiac progenitor cells [CUT&RUN]

first: Athanasia

last: Stathopoulou

summary: To identify primary and direct targets of CHD7 during the early stages of cardiac commitment and differentiation, we decided to map the genome-wide binding sites of CHD7. We used an in vitro approach of directed differentiation of mouse embryonic stem cells (ESCs) towards cardiomyocytes (CM). We isolated cells at the cardiac progenitor (CP) stage (Day 5) and used CUT&RUN (“Cleavage Under Targets & Release Using Nuclease”) technique, followed by NGS. The assay was performed in 3 biological replicates using anti-CHD7, and IgG as negative control.

overall_design: CUT&RUN was performed using cardiac progenitor (CP) cells at day 5 during cardiomyocyte (CM) differentiation. Three biological replicates were processed for each condition, using antobodies anti-CHD7 and anti IgG (negative control).

first: Ping

last: Wang

first: Deyou

last: Zheng

first: Peter

last: Scambler


title: Metformin promotes female germline stem cell proliferation by upregulating Gata-binding protein 2 with histone β-hydroxybutyrylation [ChIP-seq]

status: Public on Apr 26 2023

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use ChIP-seq to report the most comprehensive survey to date of chromatin organization in female germline stem cells

overall_design: Examination of H2BK5bhb binding sites in FGSCs

first: Xiang


title: Spenito-dependent metabolic sexual dimorphism intrinsic to fat storage cells

status: Public on Apr 25 2023

city: Aurora

first: Jay

middle: R.

last: Hesselberth

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Metabolism in males and females is distinct. Differences are usually linked to sexual reproduction, with circulating signals (e.g. hormones) playing major roles. By contrast, sex differences prior to sexual maturity and intrinsic to individual metabolic tissues are less understood. We analyzed Drosophila melanogaster larvae and find that males store more fat than females, the opposite of the sexual dimorphism in adults. We show that metabolic differences are intrinsic to the major fat storage tissue, including many differences in the expression of metabolic genes. Our previous work identified fat storage roles for Spenito (Nito), a conserved RNA-binding protein and regulator of sex determination. Nito knockdown specifically in the fat storage tissue abolished fat differences between males and females. We further show that Nito is required for sex-specific expression of the master regulator of sex determination, Sex-lethal (Sxl). “Feminization” of fat storage cells via tissue-specific overexpression of a Sxl target gene made larvae lean, reduced the fat differences between males and females, and induced female-like metabolic gene expression. Altogether, this study supports a model in which Nito autonomously controls sexual dimorphisms and differential expression of metabolic genes in fat cells in part through its regulation of the sex determination pathway.

overall_design: Total RNA from 50 dissected sexed, third-instar-larval fat bodies was extracted from 50 third-instar FBs dissected from sexed larvae using 500uL of TRIzol (ambion Cat # 15596018cat number), volumes and purified using the Direct-zol Miniprep Plus kit digested with DNase I (Zymo Cat # R2072cat number). cDNA was generated with 500ng of RNA sequencing and library prep was performed at the University of Colorado Anschutz medical campus Genomics Core. Transcriptome analysis was performed using pseudo-alignment with salmon [PMID 28263959] using the D. melanogaster transcriptome (version dmel_r6.48_FB2022_05). DESeq2 [59] (version 1.40.1) was used for differential expression analysis. Pathway analysis was performed using gProfiler [44] (version 0.2.1).

first: Arely

middle: V

last: Diaz

first: Tyler

last: Matheny

first: Daniel

last: Stephenson

first: Travis

last: Nemkov

first: Angelo

last: D’Alessandro

first: Tânia

last: Reis


title: Human patient iPS cell-derived hepatostellate organoids establish a cellular and molecular basis for liver pathologies in telomeropathies

city: Phiadelphia

first: Corbett

middle: T

last: Berry

address: 3800 Spruce St

institute: University of Pennsylvania

summary: Patients with dyskeratosis congenita (DC) and related telomeropathies resulting from premature telomere dysfunction suffer from multi-organ failure.  In the liver, DC patients present with nodular hyperplasia and cirrhosis.  We model DC liver pathologies using isogenic human induced pluripotent stem (iPS) cells harboring a causal DC mutation in DKC1, or a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-corrected control allele. Differentiation of these iPS cells into hepatocytes or hepatic stellate cells reveals a dominant phenotype in the parenchyma.  Generation of genotype admixed hepatostellate organoids indicates that DC hepatocytes elicit a pathogenic hyperplastic response in stellate cells independent of stellate cell genotype.  Phenotypic rescue was achieved via suppression of AKT activity, a central regulator of mTORC1, MYC, and DC hepatocyte-driven hyperplasia.  Thus, isogenic, iPS-derived admixed hepatostellate organoids offer insight into the liver pathologies in telomeropathies and provide a framework for evaluating emerging therapies.

overall_design: HB vs. HEP, Amino acid 353 Ala vs. Val

first: Young-Jun

last: Choi

first: Melissa

last: Kim

first: Joshua

middle: H

last: Rhodes

first: Christopher

last: Lengner


title: Metformin promotes female germline stem cell proliferation by upregulating Gata-binding protein 2 with histone β-hydroxybutyrylation [RNA-seq]

summary: The expression profile data was obtained by RNA-Seq data.

overall_design: the expression profile of FGSCs and treated with metformin


title: Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation [scRNA-Seq]

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

summary: Progress in clinical translation of gene edited porcine kidney xenotransplantation is accelerating. However, kidney function entails more than removal of metabolic waste products and it is unknown if all endocrine functions will be faithfully reproduced by porcine kidneys in primate recipients. Seventeen cynomolgus macaques with survival >60days after life sustaining kidney xenotransplantation (LSKX) from gene edited Yucatan minipigs underwent measurement of xenograft growth and two kidney dependent endocrine pathways: renin-angiotensin-aldosterone-system (RAAS) and calcium-vitamin D-parathyroid-hormone. Clinical chemistries, plasma-renin-activity, Beta-C-terminal-telopeptide (CTx) assay, RNA-seq, single-cell RNA-seq, and serial ultrasonography were conducted and generalized linear models assessed statistical relationships. Xenografts transplanted from minipigs demonstrated only modest growth (estimated ~8.0% per year) and didn’t significantly contribute to recipient RAAS pathway. However, PTH-independent hypercalcemia and hypophosphatemia were observed and might be xenograft intrinsic suggesting close monitoring and timely intervention during the first month post-transplant. Further study of these phenotypes is warranted in designing prospective clinical trials.

overall_design: Comparative gene expression analysis of biopsy tissue from xenotransplanted as compared to contralateral, untransplanted kidneys.

first: Firl

last: Daniel James

first: Hall

last: Katherine


title: Longitudinal study of DNA methylation changes during mouse pregnancy

status: Public on Apr 21 2023

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. We characterized several models in which biological age, assessed primarily through analysis of DNA methylation, undergoes reversible changes. Pregnancy is one such example.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We studied a mouse model of pregnancy. Following a baseline blood sample, C57Bl/6 mice were mated, and two blood samples were taken during the early and late phases of their pregnancies. Following parturition and a period of recovery, a final blood sample was collected. We subjected DNA isolated from these blood samples to the HorvathMammalMethylChip40 for methylation profiling.

first: Bohan

last: Zhang

first: Gurpreet

middle: S

last: Baht

first: Alexander

last: Tyshkovskiy

first: Amy

last: Deik

first: Csaba

last: Kerepesi

first: Sun

last: Yim

first: Ake

last: Lu

first: Amin

last: Haghani

first: Tong

last: Gong

first: Anna

last: Hedman

first: Ellika

last: Andolf

first: Gören

last: Pershagen

first: Catarina

last: Almqvist

first: Clary

middle: B

last: Clish

first: Steve

last: Horvath

first: James

last: White

first: Vadim

middle: N

last: Gladyshev


title: Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation

first: Robert

last: Policastro

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


title: Rio1 downregulates centromeric RNA levels to promote the timely assembly of structurally fit kinetochores

status: Public on Apr 20 2023

city: Trento

first: Peter

last: De Wulf

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology

country: Italy

institute: University of Trento

summary: Kinetochores assemble on centromeres via histone H3 variant CENP-A and low levels of noncoding centromere transcripts (cenRNAs). The latter are ensured by downregulation of RNA polymerase II (RNAPII) and turnover by the nuclear exosome. Using S. cerevisiae, we now add kinase Rio1 to this scheme. Yeast cenRNAs are produced in very low amounts either as short (median lengths of 231nt) or long (4,458nt) transcripts, in a 1:1 ratio. Rio1 limits their production by reducing RNAPII access and transcription activity, and promotes their turnover by the 5’-3’exoribonuclease Rat1. Rio1 similarly curtails the concentrations of noncoding pericenRNAs, which also exist as short transcripts (225nt) at a magnitude higher level than the cenRNAs. In yeast depleted of Rio1, cen- and pericenRNAs accumulatre, and kinetochores misform causing chromosomal instability. The latter phenotypes were also observed with human cells lacking orthologue RioK1, suggesting that CEN regulation by Rio1/RioK1 is evolutionary conserved.

overall_design: RNA-Seq analysis of RIO1( RIO1-AID) and RIO1 depleted cells (RIO1-AID treated with 500 uM Auxin for 1 hour )

first: Ksenia

last: Smurova

first: Eric

last: Dassi


title: Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation [RNA-Seq]

first: Daniel

last: Firl

first: Katherine

last: Hall


title: The CDK7 inhibitor CT7001 (Samuraciclib) targets proliferation pathways to inhibit advanced prostate cancer

first: Theodora

middle: Alexandra

last: Constantin

address: Du Cane Rd, ICTEM Building, 1st Floor Office, Imperial College London

department: Surgery & Cancer

institute: Imperial College London

summary: Aberrant activation of the androgen receptor (AR) plays a key role in the progression of prostate cancer. Current strategies to ablate AR signalling are circumvented when castration resistant prostate cancer (CRPC) emerges. Cyclin dependent kinase 7 (CDK7) is necessary for transcription and regulates cell cycle progression, two processes that are commonly deregulated in CRPC. Emerging evidence also suggests a pivotal role for CDK7 in AR-driven transcription, providing a rationale for targeting it in prostate cancer. CT7001, an orally bioavailable compound, was used to achieve pharmacological inhibition of CDK7. CT7001 preferentially engaged with CDK7, resulting in suppression of proliferation, cell cycle arrest, and induction of apoptosis in prostate cancer cell lines. Additionally, CT7001 interfered with transcription mediated by full-length AR as well as constitutively active AR splice variants. Oral administration of CT7001 alone effectively repressed growth in CRPC xenografts, while co-administration with enzalutamide resulted in considerably greater growth inhibition. Transcriptome analysis of treated xenografts affirmed the additive relationship between CT7001 and enzalutamide, both of which targeted pathways involved in AR signalling and cell cycle control.

overall_design: C4-2B xenograft-bearing mice were randomly allocated to 4 treatment arms: vehicle (5% DMSO, 30% SBE-beta-CD, 65% H2O), CT7001 (50 mg/kg), enzalutamide (25 mg/kg) or combination. Treatments were administered once daily, and xenografts were recovered on day 21 of treatment. A total of 15 samples were analysed in this study: 4 vehicle-treated, 4 enzalutamide-treated, 3 CT7001-treated, and 4 combination-treated xenografts. RNA was extracted using the Monarch Total RNA Miniprep Kit, and samples submitted for RNA-sequencing to Novogene UK.

middle: A

first: Anabel

last: Varela Carver

first: Charlotte

last: Bevan


title: Metformin promotes female germline stem cell proliferation by upregulating Gata-binding protein 2 with histone β-hydroxybutyrylation.

first: Ji

last: Wu


title: H4K16ac activates retrotransposons and contributes to their cis regulatory function [ATAC-seq]

status: Public on Apr 13 2023

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

summary: Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition, however, they have evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Here we show that the male-specific lethal (MSL) complex-mediated acetylation of histone H4 lysine 16 (H4K16ac) regulates the transcription of TEs. Furthermore, H4K16ac marked TEs function as a rich source of cis regulatory elements in the human genome, wherein H4K16ac acts by maintaining the permissive chromatin structure and promoting the transcription of these TEs.

overall_design: ATAC-Seq was performed for H9 hPSCs stable cell lines expressing non-targeting shRNA (control/Scr.) and MSL3 knockdown (MSL3 KD, two independent shRNAs). Each sample was processed in three biological replicates.   For TDFs, wild type (icas9) iCAS9 line and MSL3 knockout (MSL3 KO) line were used. Each sample was processed in two biological replicates.

first: Debosree

last: Pal

first: Manthan

last: Patel

first: Madapura

last: Pradeepa


title: H4K16ac activates retrotransposons and contributes to their cis regulatory function [CUT&TAG]

overall_design: Cleavage Under Targets and Tagmentation DNA-sequencing (CUT&Tag-Seq) for histone modifications H4K16ac, H3K27ac, H3K122ac, H4K12ac, H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9me3 and IgG in H9 hPSCs, Transformed dermal fibroblasts (TDF), HEK293T, HeLa, K562, LnCaP, PC3, RWPE and ShSY5Y. For H9 and all cancer lines, wild type cells were used. For TDFs, wild type (iacs9) iCAS9 line, MSL1 knockout (MSL1 KO) line and MSL3 KO lines were used. For each cell line and histone modification, samples were processed in a minimum of two biological replicates (except for TDF MSL3 KO, TDF H3K27ac, IgGs for cancer lines, LnCaP H4K16ac and RWPE).

first: Jayakumar

last: Sundarraj


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections [1]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of targeted long-distance axonal projections to allow interactions between specific cell types. Here we have used Epi-Retro-Seq to link single cell epigenomes and associated cell types to their long-distance projections for 33,034 neurons dissected from 32 different source regions projecting to 24 different targets (225 source→target combinations) across the whole mouse brain. We highlight uses of this large data set for interrogating both overarching principles relating projection cell types to their transcriptomic and epigenomic properties and for addressing and developing specific hypotheses about cell types and connections as they relate to genetics. We provide an overall synthesis of the data set with 926 statistical comparisons of the discriminability of neurons projecting to each target for every dissected source region. We integrate this dataset into the larger, annotated BICCN cell type atlas composed of millions of neurons to link projection cell types to consensus clusters. Integration with spatial transcriptomic data further assigns projection-enriched clusters to much smaller source regions than afforded by the original dissections. We exemplify these capabilities by presenting in-depth analyses of neurons with identified projections from the hypothalamus, thalamus, hindbrain, amygdala, and midbrain to provide new insights into the properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription factor binding motifs, and neurotransmitter usage.

overall_design: In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from 4 mice (2 male and 2 female) for each projection target. Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2/3 to profile their genome-wide DNA methylation signatures. Low-quality nuclei were removed.

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

first: Hanqing

last: Liu

first: Yan

last: Pang

first: Anna

last: Bartlett

first: Angeline

last: Rivkin

first: Will

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

middle: I

last: Aldridge

first: Qiurui

last: Zeng

first: J

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

last: Castanon

first: Neelakshi

last: Patne

first: Minh

last: Vu

first: Mohammad

last: Rashid

first: Matthew

middle: W

last: Jacobs

first: Tony

last: Ito-Cole

first: Julia

last: Osteen

first: Sharon

last: Huang

first: António

last: Pinto-Duartec

first: Bertha

last: Dominguez

first: Jared

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Eran

last: Mukamel

first: Xin

last: Jin

first: M

last: Behrens


title: ChIP-seq and RNA-seq of wildtype and NNMT-KO SUM159PT breast cancer cells

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

overall_design: Refer to individual Series


title: RNA-seq data for H-23 and H-358 parental and sotorasib-resistant lines

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: We measured gene expression using RNA-sequencing for two cell lines (H-23 and H-358) parental and their sotorasib-resistant equivalent without treatment or treated with with G12C KRAS inhibitor sotorasib (AMG510)

overall_design: Expression profiling by high throughput sequencing

first: Ayush

last: Kishore

last: Ye


title: Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase

status: Public on Apr 12 2023

city: Vienna

first: Paul

last: Batty

address: Zimmermann Platz 10

country: Austria

institute: CCRI

summary: Genetic information is stored in linear DNA molecules, which fold extensively inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in a highly intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics pre-segregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin’s looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.

overall_design: Sister-chromatid-sensitive Hi-C (scs-Hi-C) samples for G2 and prometaphase HeLa Kyoto cells. Individual replicates are uploaded. G2 samples depleted of SMC4, NIPBL, WAPL, or WAPL+Sororin. Prometaphase samples are wild type, or depleted of SMC4 or NIPBL. Processed files are pairs files (https://github.com/open2c/pairlib).

first: Christoph

last: Langer

first: Zsuzsanna

last: Takacs

first: Wen

last: Tang

first: Claudia

last: Blaukopf

first: Jan-Michael

last: Peters

first: Daniel

last: Gerlich


title: mRNA sequencing SUM159PT WT, Kod and KOs cells cultured in adherent or suspension (i.e. secondary tumorspheres) conditions.

summary: The cellular heterogeneity within a tumor can be determined by core genetic and epigenetic programs that operate in certain cells (tumor initiating cells – TICs), providing them with the degree of plasticity needed for induction of metastasis and resistance to therapy. Here we show that the metabolic enzyme nicotinamide N-methyl transferase (NNMT) promotes TIC plasticity in Estrogen Receptor (ER) alpha negative breast cancer. NNMT downregulation delays tumor formation and its full depletion impairs metastasis formation in mice. At the transcriptomic level, NNMT loss results in dowregulation of stem cell and mesenchymal gene signatures, and in the upregulation of luminal features and oxidative metabolism related genes.

overall_design:
SUM159PT cells were cultured in adherent conditions until they reached 80% confluency. At this time point, the cells were collected for mRNA extraction with the Qiagen RNeasy Plus Mini Kit. For breast cancer cell line tumorsphere culture, cells were plated at 10’000-30'000 cells per mL density in ultra-low attachment plates for 6 days. Primary tumorspheres were dissociated with 0.05% trypsin and replated at the same density for additional 6 days for secondary tumorsphere formation. RNA was extracted with the Qiagen RNeasy micro kit.

NNMT was knocked out SUM159PT using two different strategies: one single guide (sg) RNA targeting the transcription start site (KOs) and two sgRNAs that generate a deletion of exon 1 (KOd). Several clones from each strategy were mixed to generate two oligoclonal pools of cells, KOd and KOs.

first: Joana

last: Silva

first: Robert

last: Ivanek

first: Mohamed

last: Bentires-Alj


title: CXCR4 DRIVES HEPATOCYTE REPROGRAMMING IN ALCOHOL-RELATED LIVER DISEASE

status: Public on Apr 06 2023

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Backgruound and aims:  Loss of hepatocyte identity is associated with impaired liver function in alcohol-related hepatitis (AH). However, the mechanisms and the impact of hepatocyte reprogramming in liver disease are poorly understood. Here we show that both hepatocytes expressing KRT7 (hepatobiliary (HB) cells) and ductular reaction cells were increased in decompensated cirrhotic patients and AH, but only HB cells correlated with poor liver function, reduced liver synthetic capacity and poor outcome. Transcriptomic analysis of microdissected HB cells revealed the expression of biliary-specific genes and a mild reduction of hepatocyte metabolism. Functional analysis identified pathways involved in hepatocyte reprogramming together with inflammatory, stemness and cancer gene programs. In this context, CXCR4 pathway was highly enriched in HB cells, and CXCR4 correlated with disease severity and reduced expression of hepatocyte transcription factors and albumin. Mechanistically, TGFβ induced the expression of CXCR4 in primary hepatocytes, and its ligand CXCL12 promoted hepatocyte reprogramming. Liver overexpression of CXCR4 in chronic liver injury decreased hepatocyte gene expression and promoted liver injury. Pharmacological inhibition of CXCR4 reverted hepatocyte loss of identity and reduced ductular reaction and fibrosis progression. Conclusions: This study shows the association of hepatocyte reprogramming with disease progression and poor outcome in AH. Moreover, we identify CXCR4 as a driver of hepatocyte reprogramming as well as a potential therapeutic target in chronic liver injury.

overall_design: KC were isolatrd from decompensated cirrhosis that underwent liver transplantation (n=4) and a control group of patients with liver tumours (except hepatocellular carcinoma) and without underlying liver disease (n=5). Morever, whole liver tissue from the same patients were aso sequenced.

first: B

last: Aguilar-Bravo

first: P

last: Sancho-Bru


title: Engineered tRNAs suppress nonsense mutations in cells and in vivo

status: Public on Apr 04 2023

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

type:
Expression profiling by array
Other

summary: Comparison of the overall tRNA expression level and detection of the suppressor tRNA

overall_design: Cells transfected with suppressor tRNA and time samples analyzed to determine the half-life time of the suppressor tRNA

first: Marcos

last: Davyt


summary: we introduce a strategy to repurpose sense-codon decoding tRNA into efficient suppressors of the three nonsense mutation-induced PTCs (UGA, UAG and UAA). The suppressor tRNAs restore function of a model and disease-related protein

overall_design: Suppressor tRNAs are administered both in mice (intraveneous in liver or intratracheal in lung) or in immortalized cell culture and tissues/cells are collected and subjected to ribosome profiling (Ribo-Seq)

first: Leonardo

last: Santos

first: Nikhil

last: Bharti

first: Daiki

last: Matsuda

first: Kiyoshi

last: Tachikawa

first: Pad

last: Chivukula

first: Miguel

last: Delgado-Toscano

first: Elizabeth

last: Allen

first: Suki

last: Albers

first: Amit

last: Sagi

first: Rajesh

last: Mukthavaram

first: Grishma

last: Acharya

first: Priya

last: Karmali

first: Kristen

last: Kuakini

first: Kyoung-Joo

middle: J

last: Park

first: Carlos

last: Perez-Garcia

first: Maher

last: Alayyoubi


title: Structural basis for pre-miRNA-31 biogenesis

status: Public on Apr 24 2023

first: Silvi

last: Rouskin

department: Microbiology

institute: Harvard Medical School

summary: MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate protein gene expression post-transcriptionally. By base pairing with target mRNAs, miRNAs triggers mRNA degradation or translational suppression[1-4]. Abnormal miRNAs levels are associated with cancers, diabetes, neurological and other diseases[5-8]. RNA polymerase II transcribes primary miRNA (pri-miR) in the nucleus and pri-miRs are subsequently processed by Microprocessor, which is composed of Drosha and DiGeorge syndrome critical region 8 (DGCR8) proteins, to generate precursor miRNAs (pre-miRs). Pre-miRs are exported from the nucleus to the cytoplasm in a GTP-dependent manner by Exportin-5. In the cytoplasm, a pre-miRs are further processed by Dicer to generate 21-22 nt mature miRNA[4, 9]. Argonaute (Ago) protein loads one of mature miRNAs into protein and forms miRNA-induced silencing complex, which is responsible for mRNA degradation or translational suppression[2, 4].

overall_design: We performed DMS-MaPseq in order to examine the effect of secondary and tertiary structural elements on post-transcriptional regulation of pre-miR-31

first: Sicong

last: Ma

first: Peggy

last: Kirstetter

first: Scott

last: Grote

first: Sarah

last: Keane


title: Longitudinal study of DNA methylation changes in patients with severe COVID-19

first: Jesse

last: Poganik

type: Methylation profiling by genome tiling array

summary: Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. We characterized several models in which biological age, assessed primarily through analysis of DNA methylation, undergoes reversible changes. Severe COVID-19 is one such example.

overall_design: To test how biological age markers change over the course of severe infectious disease, we obtained longitudinal blood samples from patients with severe COVID-19. Our cohort consisted of patients who tested positive for COVID-19 by RT-PCR, were admitted to an intensive care unit, survived the disease, and provided multiple blood samples spanning the course of their hospitalization. DNA isolated from these samples was subjected to the Illumina Infinium MethylationEPIC array for methylation profiling.

first: Bohan

last: Zhang

first: Gurpreet

last: Baht

first: Alexander

last: Tyshkovskiy

first: Amy

last: Deik

first: Csaba

last: Kerepesi

first: Sun

last: Yim

first: Ake

last: Lu

first: Amin

last: Haghani

first: Tong

last: Gong

first: Anna

middle: M

last: Hedman

first: Ellika

last: Andolf

first: Gören

last: Pershagen

first: Catarina

last: Almqvist

first: Clary

last: Clish

first: Steve

last: Horvath

first: James

middle: P

last: White

first: Vadim

last: Gladyshev


title: ETHYLENE RESPONSE DNA-BINDING FACTORs are transcriptional repressors responsible for hormone cross-regulation during the ethylene response

city: Bundoora

first: Mathew

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

institute: La Trobe University

summary: Ethylene is a gaseous plant hormone that regulates plant growth and development. Broad reprogramming of gene expression is required for ethylene responses. The primary ethylene transcription factor (TF) ETHYLENE INSENSITIVE3 (EIN3) drives expression of secondary TFs including the ETHYLENE RESPONSE DNA-BINDING FACTORS (EDFs), but the role of the EDFs within the ethylene genome regulatory network is not understood. Here, we describe an investigation into the function of the EDFs in ethylene signalling and hormonal cross-regulation. We determined the target genes and binding dynamics of EDFs 1, 2, 3 during an ethylene response and the effects of edf1234 quadruple mutation on gene expression. The EDFs and EIN3 shared a large proportion of their target genes but had different functions. The EDFs were associated with repression of target genes, but this was superseded by activation when EIN3 bound the same genes. Genes important in other hormone signalling pathways, in particular abscisic acid (ABA), were targets of the EDFs. This demonstrates how ethylene engages hormonal cross-regulation to repress genes in competing signalling pathways and prioritize itself.

overall_design: ChIP-seq and RNA-seq were applied to comprehensively profile the transcriptional regulation in response to ethylene in Col-0 and edf1234 mutants seedlings

first: Lingling

last: Yin

first: Elizabeth

last: Hann

first: J

last: Guzmán

last: Stepanova

first: Bart

last: Janssen

first: Joseph

last: Nery

first: Ziv

last: Bar-Joseph

last: Ecker


title: Exhaustion-associated cholesterol deficiency dampens the cytotoxic arm of antitumor immunity

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: The concept of targeting cholesterol metabolism to treat cancer has been widely tested in clinics but the benefits are modest, calling for a complete understanding of cholesterol metabolism of intratumoral cells. Low cholesterol levels inhibit T-cell proliferation and cause autophagy mediated apoptosis, particularly for cytotoxic T cells. In the tumor microenvironment, oxysterols mediate reciprocal alterations of the LXR and SREBP2 pathways to cause cholesterol deficiency of T cells, subsequently leading to aberrant metabolic and signaling pathways that drive T cell exhaustion/dysfunction. LXR depletion in CAR-T cells led to improved antitumor function against solid tumor.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCAP CKO mouse T cells, in vitro/intratumoral CAR-T cells, RO 48-8071/RGX-104/GW3965 treated CAR-T cells and 27-HC treated CAR-T cells,

first: Chengsong

last: Yan

first: Lin

last: Zheng

first: Shutan

last: Jiang

first: Jun

last: Guo

first: Lu-yi

first: Tongzhou

last: Li

first: Haosong

last: Zhang

first: Yibing

last: Bai

first: Yu

last: Lou

first: Qi

first: Tingbo

last: Liang

first: Wolfgang

last: Schamel

first: Haopeng

last: Wang

first: Zheng-jiang

last: Zhu

first: Bao-Liang

last: Song

first: Chenqi

last: Xu


title: RNA-seq analysis of epidermal cells from mice fed with a diet deprived or not in AHR ligands

status: Public on Apr 18 2023

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

summary: Mice were fed with a synthetic diet enriched or not in Indole-3-carbinol (I3C). Papain or vehicle (PBS) was injected in the footpad. After 6h, epidermal cells were extracted and subjected to RNA-seq analysis.

first: Adeline

last: Cros


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [batch1-3]

status: Public on Apr 03 2023

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

institute: Cochin Institute

summary: While transcription factor C/AAT-enhancer binding protein α (C/EBPα) is critical for normal and leukemic differentiation, its role on cell and metabolic homeostasis is largely unknown in cancer. Here, multi-omics analyses uncovered a coordinated activation of C/EBPα and Fms-like tyrosine kinase 3 (FLT3) that increased lipid anabolism in vivo and in patients with FLT3-mutant acute myeloid leukemia (AML). Mechanistically, C/EBPα regulated FASN-SCD axis to promote fatty acid (FA) biosynthesis and desaturation. We further demonstrated that FLT3 or C/EBPα inactivation decreased mono-unsaturated FAs incorporation to membrane phospholipids through SCD downregulation. Consequently, SCD inhibition enhanced susceptibility to lipid redox stress, which was exploited by combining FLT3 and glutathione peroxidase 4 inhibition to trigger lipid oxidative stress, enhancing ferroptotic death of FLT3-mutant AML cells. Altogether, our study reveals a C/EBPα function in lipid homeostasis and adaptation to redox stress, and a previously unreported vulnerability of FLT3-mutant AML to ferroptosis with promising therapeutic application.

overall_design: Total RNA was prepared with GenElute Mammalian Total RNA miniprep (Sigma-Aldrich). RNA quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit, Santa Clara, USA). RNA sequencing library preparation was performed using Illumina TruSeq stranded mRNA protocol. We mapped the reads to the human genome reference “hg38_chr_only_and_herpes.fa” using STAR aligner (STAR v2.6.1a). Base-calling accuracy scores (Phred quality score, Q30) were obtained from demultiplexer bcl2fastq v2.20.. Paired-end reads were aligned to the human reference transcriptome “Homo_sapiens.GRCh38.cdna.all.fa.gz” using Salmon 1.3.0. For mapping, we used salmon quant command with parameters like –gcBias, --useVBOpt, --seqBias, and –validateMappings, correcting specific biases in the sequenced reads and increasing the sensitivity and specificity of the mapping. After mapping, R (R version R version 4.0.2) packages tximport (version 1.14.0) and DESeq2 (version 1.26.0) were used to summarize transcript-level estimate to the gene-level estimates. Further, we used the raw gene-level abundance estimates from salmon to perform to identify differentially expressed genes.

first: Marie

last: Sabatier

first: Rudy

last: Birsen

first: Laura

last: Lauture

first: Sarah

last: Mouche

first: Jean-Emmanuel

last: Sarry


title: H3K9me3, H3K27me3, H3K27ac and H3K4me3 ChIP-sequencing in SUM159PT NNMT-WT, NNMT-KOd and NNMT KOs breast cancer cells.

first: DBM Bioinformatics

last: Core Facility

summary: The cellular heterogeneity within a tumor can be determined by core genetic and epigenetic programs that operate in certain cells (tumor initiating cells – TICs), providing them with the degree of plasticity needed for induction of metastasis and resistance to therapy. Here we show that the metabolic enzyme nicotinamide N-methyl transferase (NNMT) promotes TIC plasticity in   Estrogen Receptor (ER) alpha negative breast cancer. NNMT downregulation delays tumor formation and its full depletion impairs metastasis formation in mice. Mechanistically, NNMT loss increases deposition of H3K9-me2/3 and H3K27-me3 at the promoter of genes involved in stem cell regulation, shutting down their expression and upregulating luminal differentiation genes. This study reveals a major function of NNMT in maintaining core epigenetic programmes that promote TIC self-renewal and metastasis and that repress luminal differentiation.

overall_design:
These sequencing files include data from pulldowns of acetylated H3K27, trimethylated H3K27, H3K4 and H3K9 and the respective input samples. The cohort includes 3 biological samples derived from SUM159PT cells where NNMT expression has not been modified (WT) or it has been deleted by CRISPR-Cas9 using two different KO strategies (described in the correspondent reference and below), KOd and KOs. Each biological sample has been cultured and processed 3 independent times (1, 2 and 3): triplicates.

NNMT was knocked out SUM159PT using two different strategies: one single guide (sg) RNA targeting the transcription start site (KOs) and two sgRNAs that generate a deletion of exon 1 (KOd). Several clones from each strategy were mixed to generate two oligoclonal pools of cells, KOd and KOs.

first: Joana

last: Silva

first: Robert

last: Ivanek

first: Mohamed

last: Bentires-Alj


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia

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


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MOLM14_siCEBPA]

overall_design: 6 conditions from MOLM-14 human AML cell line transduced with control (CTL) or anti-CEBPA siRNA


first: Zoya

last: Ignatova

overall_design: Mice were transfected with suppressor tRNA and sacrificed after 6 or 72 h. RNA from mice liver were analyzed to determine the half-life time of the suppressor tRNA

first: Marcos

last: Davyt


title: A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial-temporal regulation of histone arginine methylation in  neurodevelopment

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

summary: We report a loss-of-function mutation in the TLDc domain of human Oxidation Resistance 1 (OXR1) gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generated patient derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identified that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1 dependent mechanisms regulating gene expression during neurodevelopment. We modeled the function of OXR1 in early human brain development using patient derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions. Our work provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency, highlighting the therapeutic potential of OXR1 in numerous neurodegenerative and neurodevelopmental disorders.

overall_design: We generated patient derived induced pluripotent stem cells (iPSCs) and performed neural differentiation assay. Three clones of control and the patient were used. The samples were collected at the stages of iPSCs, neural aggregates (NAs) and neurons(Neu), respectively.

first: Xiaolin

last: Lin

first: Marco

last: Pannone

first: Wei

last: Wang

first: Mingyi

last: Yang

first: Elise

last: Kristiansen

first: Simon

last: Edvardson

first: Jing

last: Ye


title: Single cell RNA sequencing of mouse submandibular glands transferred with GFP or Shh gene

status: Public on Apr 10 2023

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

summary: To determine how Hedgehog signaling regulates salivary function, we performed single cell RNA sequencing (scRNA-seq) of adult mouse submandibular glands (SMGs) harvested 7 days after intra-SMG delivery of adenoviral vectors (Ad) carrying rat Sonic Hedgehog (Shh)  or control GFP gene.

overall_design: Examination of single cell transcriptomes in organs after gene therapy

first: Linying

last: Zhang


title: Transcription factor activity in cross-regulation between seedling hormone responses

first: Mathew

last: Lewsey

summary: Cross-regulation between hormone signalling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity are poorly understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors coupled with thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. A group of MITOGEN-ACTIVATED PROTEIN KINASES were also identified as potential key points of cross-regulation between multiple hormones. Loss of functional MPK6 disrupted the global proteome and phosphoproteome, and transcriptome in the response to hormones. Finally, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.

overall_design: ChIP-seq and RNA-seq were applied to comprehensively profile the transcriptional regulation in response to multiple hormones in Col-0 and mpk6 mutants seedlings

first: Lingling

last: Yin

first: Mark

last: Zander

first: Shao-shan

middle: C

last: Huang

first: Mingtang

last: Xie

first: Liang

last: Song

first: J

last: Guzmán

first: Elizabeth

last: Hann

first: Raul

last: Serrano

first: Siddhartha

last: Jain

first: Aaron

last: Wise

first: Bart

last: Janssen

first: Ziv

last: Bar-Joseph

first: Joseph

last: Ecker


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [scRNA-seq]

first: Jerome

last: Tamburini

overall_design: 6 samples

first: Marie

last: Sabatier

first: Rudy

last: Birsen

first: Laura

last: Lauture

first: Sarah

last: Mouche

first: Jean-Emmanuel

last: Sarry


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MOLM14_QUIZ]

overall_design: 6 conditions from MOLM-14 human AML cell line incubated with vehicle or quizartinib (QUIZ)


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [ATAC-seq]

overall_design: shCTL and shC/EBPα MOLM14 cells (in biological duplicates) were FACS-sorted, and ATAC-seq was performed as previously described (94) with minor modifications. Briefly, 50 000 cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase at 37°C for 30 min. DNA was purified using the QIAGEN MinElute kit (QIAGEN). The libraries were prepared using Tagment DNA Enzyme and Buffer kits (Illumina), NEBNext High-Fidelity 2X PCR Master Mix (NEB, catalog # M0541S) with custom sequencing primers (95–98). The libraries were purified twice using AMPure XP beads (Beckman) following a double-sided protocol to remove primer dimers and large fragments. Libraries quality was assessed using the NGS High Sensitivity Kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Only high-quality libraries were subsequently equimolarly pooled and sequencing was performed at the Pôle Technologique du CRCT – Plateau de Génomique et Transcriptomique (Inserm-UMR1037, Toulouse, France). The pool of libraries was quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification. Sequencing was then performed on one flowcell of the Illumina NextSeq 550 instrument (Illumina, San Diego, USA), using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles), and a paired-end 2 x 75 pb strategy. A minimum of 2x80 million raw reads were produced per sample.


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MOLM14_shFLT3]

overall_design: 6 conditions from MOLM-14 human AML cell line transduced with control (CTL) or anti-FLT3 shRNAs


title: A platform for efficient establishment and drug response profiling of high-grade serous ovarian cancer organoids

city: Helsinki

first: Matías

last: M. Falco

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

institute: University of Helsinki

summary: The broad research use of organoids from high-grade serous ovarian carcinoma (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here we describe a method for generation and long-term expansion of HGSC organoids with efficacy markedly improved over previous reports (53% vs. 23-38%). We established organoids from cryopreserved material, demonstrating the feasibility of using viably biobanked tissue for HGSC organoid derivation. Genomic, histologic and single-cell transcriptomic analyses revealed that organoids recapitulated genetic and phenotypic features of original tumors. Organoid drug responses correlated with clinical treatment outcomes, although in culture conditions-dependent manner and only in organoids maintained in human plasma-like medium (HPLM). Organoids from consenting patients are available to the research community through a public biobank and organoid genomic data explorable through an interactive online tool. Taken together, this resource facilitates the application of HGSC organoids in basic and translational ovarian cancer research.

overall_design:
This study includes scRNAseq data from 7 HGSOC patient-derived organoids and their tumor tissue/ascites of origin.
-----------------------------
Authors state "The raw data has been uploaded to EGA(EGAS00001006246) in order to comply with data protection regulations".

first: W

last: Senkowski

first: K

last: Wennerberg

first: M

last: Falco

first: A

last: Vähärautio


title: Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication

city: Chapel Hill

first: Mark

last: Boerneke

state: NC

address: Campus Box 3290

department: Chemistry

institute: University of North Carolina

summary: The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and have been extensively described for well-characterized viruses. However, the extent to which viral RNA genomes contain functional structural elements – unable to be detected by sequence alone – that nonetheless are critical to viral fitness is largely unknown. Here, we devise a structure-first experimental strategy and use it to identify 22 structure-similar motifs across the coding sequences of the RNA genomes for the four dengue virus (DENV) serotypes. At least ten of these motifs modulate viral fitness, revealing a significant unnoticed extent of RNA structure-mediated regulation within viral coding sequences. These viral RNA structures promote a compact global genome architecture, interact with proteins, and regulate the viral replication cycle. These motifs are also thus constrained at the levels of both RNA structure and protein sequence and are potential resistance-refractory targets for antivirals and live-attenuated vaccines. Structure-first identification of conserved RNA structure enables efficient discovery of pervasive RNA-mediated regulation in viral genomes and, likely, other cellular RNAs.

sample_organism:
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4

overall_design: RNA gently extracted from purified virus particles (ex virion RNA) was treated with 1M7 or DMSO (control) for SHAPE-MaP RNA structure probing experiments. RNA within cells was treated with the bivalent chemical crosslinker SDA or DMSO (control) to assess engagement by proteins for RNP-MaP probing experiments. Chemically modified RNA samples from SHAPE-MaP and RNP-MaP experiments were subjected to MaP reverse transcription, which encodes the position of chemical adducts as non-templated nucleotides or deletions in the product cDNA. Sequencing libraries were generated using the Nextera XT workflow and sequenced on an Illumin MiSeq instrument. The ShapeMapper 2 software was used to align reads and call modification-induced mutations. Software analysis pipelines were employed to create SHAPE and RNP-MaP profiles and model RNA structures.

first: Kevin

last: Weeks


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [CEBPAOE_QUIZ]

overall_design: 12 conditions from MOLM-14 human AML cell line transduced with empty vector or CEBPA overexpression (OE) vector and treated with vehicle or quizartinib (QUIZ)


title: Human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic, chondrogenic, or osteogenic induction fates.

status: Public on Apr 01 2023

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

summary: We demonstrated the multipotent potential and change of cell identity of human adipose tissue-derived progenitors by subjecting cells to adipogenic, chondrogenic, and osteogenic induction. mRNA transcriptomic profiling results demonstrated the detection of lineage-specific markers.

overall_design: Human adipose tissue derived mesenchymal progenitor cells were split into 4 experimental groups and underwent non-induced, adipogenic, chondrogenic, or osteogenic induction for 10 days.

first: Zinger

last: Yang Loureiro


title: Ctnnb1/β-catenin inactivation in UCP1-positive adipocytes augments the browning of white adipose tissue

status: Public on Mar 31 2023

city: Shanghai

first: Mingyang

last: Yuan

address: No. 573, Xujiahui Road, Huangpu District

institute: Shanghai Institute of Endocrine and Metabolic Diseases

summary: Canonical WNT pathway in mature adipocytes exacerbates obesity. In this study, we constructed UCP1-positive adipocytes-specific Ctnnb1 knockout mice (UBKO) and observed increased “browning” of white adipose tissue (WAT) following cold exposure or CL-316,243 administration compared to controls. UBKO mice also displayed increased energy expenditure. Furthermore, β-catenin (encoded by Ctnnb1) inhibited thermogenic genes expression in differentiated beige adipocytes and repressed Ucp1 expression at transcription level. Transcriptome analysis revealed UBKO mice treated with CL-316,243 had enhanced mitochondrial function and downregulated immunerelated genes in WAT. Improved glucose tolerance and insulin sensitivity were observed in 50-week-old UBKO mice. Public datasets indicated CTNNB1 expression inversely correlated with several thermogenic genes expression in human adipose/adipocytes, and positively correlated with body mass index (BMI) or waist-hip ratio (WHR). We proposed that intervention of β-catenin in adipocytes could be an effective strategy to enhance energy expenditure and improve age-related metabolic performance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for epididymal white adipose tissue (eWAT) of control and UBKO mice treated with CL316,243.

last: Chen

first: Ningning

last: Zhang

first: Maopei

first: Ruixin

last: Liu

first: Jiqiu

last: Wang

first: Peng

last: Lu


title: Environmental influences on Streptococcus sanguinis membrane vesicle biogenesis

city: Portland

first: Emily

last: Helliwell

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB433

institute: Oregon Health and Science University

summary:
To look for transcriptomic changes that resulted in membrane vesicle biogenesis, we performed RNA sequencing on S.sanguinis in different culture and community conditions
We then examined three separate differential expression analyses, as well as correlated the phenotypic vesicle quantification with normalized count data across all samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S.sanguinis at late log phase growth under glucose and sucrose media, or with the presence of oral microbes C.durum, F.alocis, and P.gingivalis

first: Jens

last: Kreth


title: Time course profiling of human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic fate

summary: To further understand mechanisms governing adipogenic fate commitment, we perform a time course transcriptomic study of progenitors at 0, 3, 7 and 14 days post adipogenic induction. The progenitor cells undergo large scale gene expression changes within 3 days of exposure to adipogenic induction and adiponectin expression is strongly induced at day 3. The early detection of ADIPOQ expression suggests fate commitment occurs within 3 days of induction.

overall_design: Human adipose tissue derived mesenchymal progenitor cells from two separate donors were induced toward adipogenic fate.  mRNA at day 0,3,7,14 days post induction were profiled.


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [PDX_QUIZ_ex vivo]

first: Jerome

last: Tamburini

overall_design: 6 conditions from human patient-derived xenograft (PDX) AML cells (n=3 different patients, PDXTUH06, PDXTUH84 and PDXTUH93) incubated ex vivo with vehicle or quizartinib (QUIZ)

first: Marie

last: Sabatier

first: Rudy

last: Birsen

first: Laura

last: Lauture

first: Sarah

last: Mouche

first: Jean-Emmanuel

last: Sarry


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MOLM14_shCEBPAconstit]

overall_design: 6 conditions from MOLM-14 human AML cell line transduced with control (CTL) or anti-CEBPA constitutive (shCTLconsti and shCEBPA#1) shRNAs


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [PDX_GILT_in vivo]

overall_design: 6 conditions from human patient-derived xenograft (PDX) AML cells (n=3 different patients, PDXTUH73, PDXTUH86 and PDXTUH110), with immunodeficient NSG mice treated in vivo with vehicle or gilteritinib (GILT)


title: METTL3 mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling

city: Zhanjiang

first: Shuhua

last: Luo

state: guangdong

address: 2 Wenming East Roadan

institute: Guangdong Medical University

overall_design: Refer to individual Series


title: METTL3 mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling (Ribosome-Seq)

summary:
To investigate the effect of METTL3 function in the regulation of neutrophil activation,  we established neutrophil METTL3 knock out mice by crossing METTL3flox/flox mice with Lyzm-cre mice.
We then performed gene expression profiling analysis using data obtained from Ribosome-seq of isolated neutrophil from METTL3f/f and METTL3f/f Lyzm-Cre mice .

overall_design: Comparative gene expression profiling analysis of Ribosome-seq data and RNA-seq data for METTL3flox/flox neutrophil and METTL3flox/flox-Lyzmcre neutrophil.

first: Jing

last: Tang


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MV411_QUIZ]

overall_design: 6 conditions from MV4-11 human AML cell line incubated with vehicle or quizartinib (QUIZ)


title: METTL3 mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling (RNA-Seq)

summary:
To investigate the effect of METTL3 function in the regulation of neutrophil activation,  we established neutrophil METTL3 knock out mice by crossing METTL3flox/flox mice with Lyzm-cre mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of isolated neutrophil from METTL3f/f and METTL3f/f Lyzm-Cre mice with or without  intraperitoneal injection of lipopolysaccharide (LPS) treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for METTL3flox/flox neutrophil and METTL3flox/flox-Lyzmcre neutrophil.


title: METTL3 mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling (meRIP-Seq)

summary:
To investigate the effect of METTL3 function in the regulation of neutrophil activation,  we established neutrophil METTL3 knock out mice by crossing METTL3flox/flox mice with Lyzm-cre mice.
We then performed gene expression profiling analysis using data obtained from MeRIP-seq of isolated neutrophil from METTL3f/f and METTL3f/f Lyzm-Cre mice .

overall_design: Comparative gene expression profiling analysis of MeRIP-seq data for METTL3flox/flox neutrophil and METTL3flox/flox-Lyzmcre neutrophil.


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MOLM14_shCEBPA+DOX]

overall_design: 6 conditions from MOLM-14 human AML cell line transduced with control (CTL) or anti-CEBPA doxycycline-inducible (+DOX) shRNAs


title: Human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic fates for 7 days and 2 subpopulations were separated and collected by percoll density gradient

first: Silvia

last: Corvera

summary: The study aims to identify gene signature of 7-day adipogenic induced cells for the high density (non-differentiated) and low-density (adipocyte) cells.

overall_design: Human adipose tissue derived mesenchymal progenitor cells were grown under adipogenic inducing condition for 7-cays and placed into a percoll density gradient.  After centrifugation, cells were separated into two populations (high and low densities) and collected for bulk RNA sequencing

first: Zinger

last: Yang Loureiro


title: Single-cell profiling of human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic fate.

summary: To understand the specific transcriptomic changes in cells undergoing adipogenic differentiation, we performed single cell RNA-seq on two separate cultures: one corresponding to multipotent progenitors grown to confluency but not subjected to differentiation stimuli, and the second corresponding to progenitors exposed to adipogenic media for 3 days. Homogenous multipotent progenitors underwent two distinct fate trajectories rapidly upon induction of adipose differentiation, one toward the adipocyte fate, and the other towards a distinct, undifferentiated state.

overall_design: Human adipose tissue-derived mesenchymal progenitor cells underwent non-induced or adipogenic induction for 3 days.


title: Characterization of the BFD2-bound transcriptome in chronic-stage T. gondii

city: Cambridge

first: Sebastian

last: Lourido

address: 455 Main Street, Rm 555

institute: Whitehead Institute

summary:
The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome and can be induced by alkaline stress.
Prior work identified the master regulator of this process: a MYB-like transcription factor named BFD1 that is specifically induced under stress and is both necessary and sufficient to drive differentiation.
Recently, we found that parasites lacking a CCCH-type zinc finger RNA-binding protein (BFD2) are also unable to produce chronic forms due to an inability to robustly express BFD1.
To test whether the influence of BFD2 on BFD1 expression involves interaction with this or other transcripts, we performed BFD2 immunoprecipitation and sequencing (RIP-seq) under alkaline stress.

overall_design: HA-BFD2 was immunoprecipitated from alkaline-stressed parasites and enriched transcripts (as well as an unenriched 'input' sample) were analyzed by next generation sequencing.

first: M

last: Licon


title: Effect of depleting BFD1-regulated gene-expression factors (TGME49_253790, TGME49_208020, TGME49_224630, TGME49_306620, TGME49_311100) on the Toxoplasma transcriptome during alkaline stress

summary:
The transcription factor BFD1 is the master regulator of the Toxoplasma chronic-stage differentiation program, which is induced under alkaline stress.
Prior work indicated that BFD1 transcriptionally activates five other putative RNA- and DNA-binding proteins during differentiation, suggesting potential secondary roles in shaping the Toxoplasma chronic-stage transcriptome.
To describe the distinct genetic cohorts controlled by these factors, we generated individual knockdown strains for each candidate using the auxin inducible degron system (TIR1/AID) and examined the transcriptomic effects of their depletion under alkaline stress.

overall_design:
Comparative gene expression RNA-seq analysis of conditional knockdown strains of ME49 Toxoplasma, cultured for 96h under alkaline stress in either the presence or absence of TGME49_200385 (BFD1), TGME49_306620, TGME49_311100, TGME49_224630, TGME49_253790, or TGME49_208020.
Experiments were performed in biological duplicate (separate infections).


title: Effects of BFD1 (TGME49_200385) and BFD2 (TGME49_311100) deletion on gene expression in Toxoplasma gondii during infection in neurons

summary:
Differentiation of proliferative acute stages into semi-quiescent chronic stages is key for Toxoplasma gondii persistence within an infected host.
During natural infection, chronic stages are almost exclusively found in neurons, and it is well appreciated that neurons support high rates of spontaneous differentiation in cell culture.
Recently, we found that parasites lacking the RNA-binding protein BFD2 are unable to produce chronic forms, consistent with a block in this develomental program.
To compare the effects of BFD1 and BFD2 on chronic-stage transcriptional reprogramming in T. gondii, we profiled the transcriptomes of both 'wildtype' and BFD1- and BFD2-knockout parasites during infection of murine primary neurons.

overall_design:
Comparative RNA-seq analysis of ∆bfd1, ∆bfd2 and the parental strain of Toxoplasma (PRU), after  48h of culture in primary neurons from Cre reporter mice (Jacksons Laboratories #007906).
Experiments were performed in biological triplicate (separate infections).


title: Human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic, chondrogenic, or osteogenic induction fates for 3 days.

summary: The study aims to identify early osteogenic and chondrogenic lineage markers with time course bulk RNA-seq profiling of 3-day differentiation induced cells.

overall_design: Human adipose tissue derived mesenchymal progenitor cells from two different donors were each split into 4 experimental groups and underwent non-induced, adipogenic, chondrogenic, or osteogenic induction for 3 days.


title: C/EBPα confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia [MV411_shFLT3]

summary: While transcription factor C/AAT-enhancer binding protein α (C/EBPα) is critical for normal and leukemic differentiation, its role on cell and metabolic homeostasis is largely unknown in cancer. Here, multi-omics analyses uncovered a coordinated activation of C/EBPα and Fms-like tyrosine kinase 3 (FLT3) that increased lipid anabolism in vivo and in patients with FLT3-mutant acute myeloid leukemia (AML). Mechanistically, C/EBPα regulated FASN-SCD axis to promote fatty acid (FA) biosynthesis and desaturation. We further demonstrated that FLT3 or C/EBPα inactivation decreased mono-unsaturated FAs incorporation to membrane phospholipids through SCD downregulation. Consequently, SCD inhibition enhanced susceptibility to lipid redox stress, which was exploited by combining FLT3 and glutathione peroxidase 4 inhibition to trigger lipid oxidative stress, enhancing ferroptotic death of FLT3-mutant AML cells. Altogether, our study reveals a C/EBPα function in lipid homeostasis and adaptation to redox stress, and a previously unreported vulnerability of FLT3-mutant AML to ferroptosis with promising therapeutic application.

overall_design: 6 conditions from MV4-11 human AML cell line transduced with control (CTL) or anti-FLT3 shRNAs


title: Single-cell TCR-sequencing of T cells in crescentic glomerulonephritis

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Single-cell TCR sequencing of T cells from ANCA-associated glomerulonephritis patients and experimental crescentic glomerulonephritis mouse model.

overall_design: Single-cell TCR sequencing of C57BL6 mice with crescentic glomerulonephritis induction, and single-cell TCR sequencing of blood and kidney T cells from ANCA-associated glomerulonephritis patients.

first: Christian

middle: F

last: Krebs