title: Continuous pioneer activity is required for maintaining pluripotency specific gene expression [TTchem-seq]

summary: Accessible chromatin enables the physical interaction of transcription factors  with DNA. Mapping accessible chromatin regions with ATACseq can be  used to identify the thousands of cis-regulatory elements in the  mammalian genome. However, which of them contributes to gene  expression remains an open question. In mouse embryonic stem cells  (mESC), canonical transcription factor SOX2 is, among others,  responsible for the establishment of chromatin accessibility. SOX2  acts as a pioneer factor that binds to inaccessible DNA and promotes  the opening of the chromatin. However, not all regions bound by the  pioneer factor undergo opening. To determine which accessible  chromatin regions are directly controlled by SOX2, we depleted SOX2  from mESC using acute degradation by dTAG at high temporal  resolution. The depletion leads to a rapid loss of chromatin  accessibility (within 30 minutes) at SOX2 associated sites and a  gradual gain of newly accessible sites. To understand the changes in  transcription after SOX2 depletion we performed nascent transcript  mapping using TTchemseq.  This revealed that expression of hundreds of transcription units are  also rapidly affected following SOX2 depletion.     The intersection of sites that lose accessibility and downregulated genes  shows an enrichment within 40 kb around the TSS. Importantly, this is  not the case for SOX2 binding sites as identified by ChIPseq.  Therefore, accessible sites created by SOX2, rather than SOX2  occupancy, are relevant for gene expression. Furthermore, 60-70% of  genes that lose expression can be explained by loss of accessibility.  To validate this finding, we used CRISPR-Cas9 to delete an element  that shows loss of accessibility in the vicinity of a downregulated  gene. The deletion alone results in decreased expression of the gene,  showing its importance in maintaining the transcription program.      Our approach of acute depletion of a pioneer transcription factor  combined with nascent transcript mapping allows us to predict  functional regulatory elements. We show that constant maintenance of  open chromatin regions relies directly on SOX2, and its disruption  has drastic consequences on transcription.

overall_design: Analysis of nascent RNA at a timeseries of depletion of the SOX2 transcription factor using the dTAG depletion system in mESC.

first: Michela

last: Maresca

first: Teun

last: van den Brand

first: Hans

last: Teunissen


title: Continuous pioneer activity is required for maintaining pluripotency specific gene expression [ATAC-Seq]

status: Public on Jul 24 2023

city: Amsterdam

first: Elzo

last: de Wit

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Analysis of accessible chromatin at a timeseries of depletion of the SOX2, OCT4 and NANOG transcription factors using the dTAG depletion system in mESC. Depletion happens on addition of dTAG-13, hence untreated samples serve as controls.  In addition, an analysis of accessible chromatin with ectopic expression vectors with (parts of) SOX2 after depletion of SOX2, wherein DMSO treated samples are controls.  Lastly, a profile of accessible chromatin after knockout of a differentially accessible region nearby the Klf2 gene.


title: TRPS1 impairs myogenic differentiation in embryonal rhabdomyosarcoma [RNA-seq]

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

type: Expression profiling by high throughput sequencing

summary:
We report here the analysis of embryonal rhabdomyosarcoma RD cells by transcriptional profiling (bulk RNA-Seq). We use here inducible shRNAs to deplete TRPS1 in RD cells.
RD cells were cultured in differentiation medium for 10 days and total RNA was extracted from control or shTRPS1 expressing cells and subjected to RNA-seq.

overall_design: Examination of transcriptional changes upon TRPS1 depletion in RD cells.

first: Julia

last: von Maltzahn

first: Soeren

middle: S

last: Huettner

first: Philipp

last: Koch

first: Marco

last: Groth


title: The transcriptome of HTLV-1-infected primary cells following reactivation reveals changes to host gene expression central to the proviral life cycle

city: London

first: Aris

last: Aristodemou

state: London

address: St Mary's Campus, Norfolk Place, Rear Lodge Immunology

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

summary: Infections by Human T cell Leukaemia Virus type 1 (HTLV-1) persist for the lifetime of the host by integrating into the genome of CD4+ T cells. Proviral gene expression is core to proviral survival and the maintenance of the proviral load, through the pro-proliferative changes it induces in infected cells. Despite their role in HTLV-1 infection and a persistent cytotoxic T lymphocyte response raised against them, proviral transcripts from the sense-strand are rarely detected in fresh cells extracted from the peripheral blood, and have recently been found to be expressed intermittently by a small subset of cells at a given time. Ex vivo culture of infected cells prompts synchronised proviral expression in infected cells from peripheral blood, allowing the study of factors involved in reactivation in primary cells. Here, we used bulk RNA-seq to examine the host transcriptome over six days in vitro, following proviral reactivation in primary peripheral CD4+ T cells isolated from subjects with non-malignant HTLV-1 infection. Infected cells displayed a conserved response to reactivation, characterised by discrete stages of gene expression, cell division and subsequently horizontal transmission of the virus. We observed widespread changes in Polycomb gene expression following reactivation, including an increase in PRC2 transcript levels and diverse changes in the expression of PRC1 components. We hypothesize that these transcriptional changes constitute a negative feedback loop that maintains proviral latency by re-deposition of H2AK119ub1 following the end of proviral expression. Using RNAi, we found that certain deubiquitinases, BAP1, USP14 and OTUD5 each promote proviral transcription. These data demonstrate the detailed trajectory of HTLV-1 proviral reactivation in primary HTLV-1-carrier lymphocytes and the impact on the host cell.

overall_design: RNA-seq of CD4+ T lymphocytes collected from six HTLV-1-positive and three HTLV-1-negative volunteers and cultured ex vivo. Sampling at 0, 24, 48, 96, 120 and 144 hours.

middle: E

first: Charles

middle: R

last: Bangham

first: David

last: Rueda

first: Graham

middle: G

last: Taylor


title: TRPS1 impairs myogenic differentiation in embryonal rhabdomyosarcoma

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

overall_design: Refer to individual Series


title: Regulation of Dermal Fibroblasts by Human Neutrophil Peptides

status: Public on Jul 23 2023

city: Pathum Wan

first: Thanawat

last: Chaisirirat

state: Bangkok

address: Rama IV Rd

department: Faculty of Medicine,

country: Thailand

institute: Chulalongkorn University

summary: Differential gene expression in HNP1-treated cells and genes involved in regulating intracellular pathways were explored.

overall_design: To compare gene expression profiling from RNA-seq data of human dermal fibroblast between treatment with HNP1 protein and control.

first: Direkrit

last: Chiewchengchol


title: A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia  (Single-cell expression analysis of  small intestine enteric nervous system developmental data)

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

summary: Glial cells have been proposed as an endogenous source of progenitors for the treatment of neural deficits. However, the cellular and molecular mechanisms underpinning the neurogenic potential of certain populations of adult glial cells, are not known. Using single cell transcriptomic profiling, we show here that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition during development along a linear default differentiation trajectory that allows them to retain neurogenic potential while acquiring a gene expression profile associated with their role in neuronal support and immunomodulation. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a novel cell culture system of enteric neurogenesis and a gut injury model, demonstrated that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the dynamic regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.

overall_design: We performed single cell RNA sequencing (scRNA-seq) of tdTomato+ (tdT+) cells from the small intestine of Sox10CreER|tdT reporter mice at different developmental stages

first: Anna

last: Laddach

first: Song

middle: H

last: Chng

first: Reena

last: Lasrado

first: Fränze

last: Progatzky

first: Michael

last: Shapiro

first: Alek

last: Erickson

first: Marisol

last: Sampedro-Castaneda

first: Artem

last: Artemov

first: Ana

middle: C

last: Bon-Frauches

first: Eleni-Maria

last: Amaniti

first: Jens

last: Kleinjung

first: Stefan

last: Boeing

first: Sila

last: Ultanir

first: Igor

last: Adameyko


title: Pioneer activity distinguishes activating from non-activating SOX2 binding sites [ChIP-Seq]

first: Elzo

last: de Wit

summary: Genome-wide transcriptional activity involves the binding of many transcription factors to thousands of sites in the genome. Determining which sites are directly driving transcription remains a challenge. Here we use acute protein depletion of the pioneer transcription factor SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of pioneer factors. To understand the relationship with transcription we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted largely at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.

overall_design: Analysis of SOX2 and OCT4 binding at a timeseries of depletion of the SOX2 and OCT4 transcription factors using the dTAG depletion system in mESC. Depletion happens on addition of dTAG-13, hence untreated samples serve as controls.

first: Michela

last: Maresca

first: Teun

last: van den Brand

first: Hans

last: Teunissen


title: Canonical and nuclear mTOR specify distinct transcriptional programs in androgen-dependent prostate cancer cells

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University


title: Combined phenotypic and transcriptomic analysis of soybean plants subjected to multifactorial stress combination

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

country: USA

institute: The Division of Plant Sciences and Technology

summary: Soybean plants were subjected to a multifactorial stress combination of up to five different stresses (water deficit, salinity, low phosphate, acidity, and cadmium), in an increasing level of complexity. All stresses were applied at the beginning of the experiment except for water deficit stress that was imposed after 21 days. Leaves and flowers were collected from 5-7 different plants under the mentioned stress conditions and after 10 days of starting water deficit conditions. Differential gene expression compared to control was studied using RNAseq method for all the possible stress combinations.

overall_design: Tissues from soybean plants (31 days old) subjected to water deficit, salinity, low phosphate, acidity, and cadmium alone or in combination of 2, 3, 4 and 5 stresses were collected in liquid nitrogen. Total RNA was isolated and mRNA profile was generated by deep sequencing using NovaSeq 6000 PE150.

first: María

middle: A

last: Peláez-Vico

first: Sai

middle: P

last: Induri

first: Ranjita

last: Sinha

first: Benjamin

last: Shostak

first: Zhen

last: Lyu

middle: D

last: Venigalla

first: Dinesh

last: Vasireddy

first: Pallav

last: Singh

first: Manish

last: Immadi

first: Lidia

last: Pascual

first: David

middle: M

last: Cozatl

first: Trupti

last: Joshi

first: Felix

middle: B

last: Fritschi

first: Sara

middle: I

last: Zandalinas


title: NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion [ATAC]

city: Epalinges

first: Grégory

last: Verdeil

state: Vaud

address: Chemin des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

summary: Persistent exposure to antigen during chronic infection or cancer renders T cells dysfunctional. The molecular mechanisms regulating this state of exhaustion are thought to be common in infection and cancer, despite obvious differences in their microenvironments. We discovered that NFAT5, an NFAT family member lacking an AP-1 docking site, is highly expressed in exhausted T cells responding to chronic infection and tumors but is a central player selectively in tumor-induced exhaustion. While NFAT5 overexpression in CD8+ T cells reduced tumor control, NFAT5 deletion improved tumor control by promoting the accumulation of tumor-specific CD8 T cells that expressed less TOX and PD-1 and produced more cytokines specifically among precursor exhausted cells. Conversely, NFAT5 did not promote T cell exhaustion during chronic infection. While NFAT5 expression was induced by TCR triggering, its transcriptional activity was specific to the tumor microenvironment and required hyperosmolarity. NFAT5 thus promotes CD8 T cell exhaustion in a tumor-selective fashion.

overall_design: 48 hours activated NFAT5flox/flox CD4-Cre-/- (WT) or NFAT5flox/flox CD4-Cre+/- (NFAT5 KO) P14 CD8 T cells were transferred into mice bearing subcutaneous gp33-expressing B16 melanoma (B16-gp33). Seven days post transfer CD8 TILs were sorted from the tumors and processed for scATAC sequencing.

first: Daniela

last: Cropp

first: Santiago

last: Carmona

first: Massimo

last: Andreatta

first: Joao

last: Lourenco


title: Assessing chromatin accessibility in human classical monocytes following vaccination with mRNA and adenoviral vectored COVID-19 vaccines

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: An increasing body of literature suggests that innate immune cells such as monocytes undergo epigenetic reprogramming following challenges such as infection or vaccination. We performed omni-ATACseq to assess chromatin accessibility in classical monocytes (CD14+CD16-) isolated from healthy participants before vaccination or 28 days following the second dose of an mRNA or adenoviral vectored COVID-19 vaccine.

overall_design: SARS-CoV-2 naïve participants from the COVIR study in South Australia were immunised with two doses of either BNT162b2 ‘Comirnaty’ vaccine 3 weeks apart, or 2 doses of ChAdOx1-s ‘Vaxzevria’ 3 months apart. There are 82 samples from 41 individuals prior to vaccination (V0) or 28 days following the second dose of vaccine (V2B). Cryopreserved PBMC were thawed and stained and classical monocytes (CD3-CD19-CD56-CD14+CD16-; 50,000 per sample) were sorted via flow cytometry and used for transposition with Tn5 transposase (illumina). Libraries were prepared from transposed DNA with custom primers and subjected to double-sided cleanup with SPRI beads to enrich for fragments in the 200-700bp range. Samples were sequenced on an illumina NovaSeq using paired end (2x150pb) sequencing.

first: Natalie

last: Stevens

last: Lynn


title: Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.

city: Saint Louis

first: Samantha

last: Morris

address: 660 S Euclid Ave

institute: Washington University School of Medicine


title: Comparative landscape of genetic dependencies in human and chimpanzee stem cells

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

summary:
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored.
We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes.
By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation.
These genes comprised coherent processes, including cell cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells.
Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: This GEO submission contains comparative gene expression profiling of the six human and six chimpanzee CRISPRi engineered cell lines used in this study.

first: She

last: Richard

first: Fair

last: Tyler

first: Schaefer

middle: K

last: Nathan

first: Saunders

last: Reuben

first: Pavlovic

last: Bryan

first: Weissman

last: Jonathan

first: Pollen

last: Alex


title: TRPS1 impairs myogenic differentiation in embryonal rhabdomyosarcoma [ChIP-seq]

first: Bjoern

last: von Eyss

summary:
We report here the analysis of TRPS1 chromatin binding by ChIP-Seq in embryonal rhabdomyosarcoma RD cells. We use here parental and TRPS1-KO RD cells.
RD cells and RD-TRPS1-KO cells were cultured in growth medium and chromatin was prepared. TRPS1 DNA binding in RD cells and RD-TRPS1-KO cells using a selfmade antibody (referenced in Elster et al.) was determined by ChIP-seq.

overall_design: Identification of TRPS1 DNA binding sites in RD cells.

first: Julia

last: von Maltzahn

first: Soeren

last: Huettner

first: Marco

last: Groth


title: Vitamin D Receptor Cross-talk with p63 Signaling Promotes Epidermal Cell Fate

status: Public on Jul 22 2023

city: Madison

first: Mark

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: The vitamin D receptor with its ligand 1,25 dihydroxy vitamin D3 (1,25D3) regulates epidermal stem cell fate, such that VDR removal from Krt14 expressing keratinocytes delays re-epithelialization of epidermis after wound injury in mice.  In this study we deleted Vdr from Lrig1 expressing stem cells in the isthmus of the hair follicle then used lineage tracing to evaluate the impact on re-epithelialization following injury. We showed that Vdr deletion from these cells prevents their migration to and regeneration of the interfollicular epidermis without impairing their ability to repopulate the sebaceous gland.  To pursue the molecular basis for these effects of VDR, we performed genome wide transcriptional analysis of keratinocytes from Vdr cKO and control littermate mice. Ingenuity Pathway analysis (IPA) pointed us to the TP53 family including p63 as a partner with VDR, a transcriptional factor that is essential for proliferation and differentiation of epidermal keratinocytes. Epigenetic studies on epidermal keratinocytes derived from interfollicular epidermis showed that VDR is colocalized with p63 within the specific regulatory region of MED1 containing super-enhancers of epidermal fate driven transcription factor genes such as Fos and Jun. Gene ontology analysis further implicated that Vdr and p63 associated genomic regions regulate genes involving stem cell fate and epidermal differentiation. To demonstrate the functional interaction between VDR and p63, we evaluated the response to 1,25(OH)2D3 of keratinocytes lacking p63 and noted a reduction in epidermal cell fate determining transcription factors such as Fos, Jun. We conclude that VDR is required for the epidermal stem cell fate orientation towards interfollicular epidermis following wounding. We propose that this role of VDR involves cross-talk with the epidermal master regulator p63 through super-enhancer mediated epigenetic dynamics.

overall_design: Duplicate or triplicate Chip-seq for cultured epidermal keratinocytes derived from human foreskin.  Pre-confluent keratinocytes are treated with vehicle (EtOH) or 1,25D3 (1x 10 -7M) for 4hr. Chip-seq is conducted by using antibodies against VDR, p63, CTCF, Med1 and H3K27ac.

first: Yuko

last: Oda

first: Daniel

last: Bikle


title: Single-cell RNA sequencing from PiKP-785 cancer cells under 4 treatment conditions: Kras* On, Kras* 3d off, Kras* 5d off, and  Kras* On off on

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Single-cell RNA sequencing analysis was performed on primary pancreatic ductal adenocarcinoma derrived cell line from PiKP (P48-Cre; R26-rtTa-IRES-EGFP; tetO-LSL-KrasG12D/+; Trp53L/L) murine tumors. In this study we establish that oncogenic Kras is the predominant driver of T cell paucity and myeloid infiltration in the pancreatic tumor microenvironment. Then, we use scRNA seq analysis of cultured PiKP cells with and without Kras* extinction to identify immune related genes involved in driving Kras* mediated immune supression in PDAC.

overall_design: PiKP-785 cancer cells were cultured under 4 treatment conditions (Kras* On, Kras* 3d off, Kras* 5d off, and  Kras* On off on). Cells were cultured in medium with 1 μg/mL Dox to ensure oncogenic Kras expression (Kras* on). To extinguish oncogenic Kras, Dox was withdrawn from the media (Kras* off).

first: Valerie

last: LeBleu

first: Bingrui

last: Li


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity

city: Melbourne

first: Kevin

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

institute: Peter MacCallum Cancer Centre

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Stress responsive gene FKBP5 mediates alcohol-induced liver injury through hippo pathway and CXCL1 signaling

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

summary: To better our understanding and obtain a mechanistic insight on the role of FKBP5 on alcohol-induced liver injury, we performed RNA-seq analysis and compared the alterations in gene expression from WT and Fkbp5-/- mice on ethanol and pair-fed diet.

overall_design: WT and Fkbp5-/- mice were subjected to NIAAA-Etoh-binge model. In brief, they were acclimatized for approximately 1 week before experiments, then were placed on either control (F1259SP) or ethanol containing diet (F1258SP) obtained from Bio-Serv (Flemington, NJ). Ethanol in the diet was incremented by 1% daily (vol/vol) until it reached 5% on day 5 when its concentration was kept constant for the subsequent 10 days. On the 11th day, the ethanol-fed mice received a single dose of ethanol (5 g/kg body weight, approximately 20% ethanol) via oral gavage in the early morning, while mice fed with control diet were gavaged with maltose. All mice were then anesthetized by isoflurane after 9 h of gavage, blood and liver tissue were immediately collected and snap-frozen for further experiments.

first: Praveen

last: Kusumanchi

first: Suthat

last: Liangpunsakul


title: The link between diabetes main metabolic alterations and breast cancer progression

city: Sheffield

first: Samrein

middle: BM

last: Ahmed

state: --- Select One ---

address: Owen building-731

institute: Sheffield Hallam University

summary: Several reports have linked diabetes to cancer development, however, the exact molecular mechanism of how diabetes-related traits contribute to cancer progression is not fully understood. The current study aimed to explore the molecular mechanism underlying the potential effect of hyperglycemia combined with hyperinsulinemia in the progression of breast cancer cells. To this end, gene dysregulation induced by the exposure of MCF-7 breast cancer cells to hyperglycemia, or a combination of hyperglycemia and hyperinsulinemia was analyzed using Microarray gene expression assay. Hyperglycemia combined with hyperinsulinemia induced differential expression of 45 genes (greater than or equal to two-fold), which were not shared by other treatments in this study.

overall_design: Agilent Human Whole Genome 8x60k Microarray Gene Expression : AMADID: 72363

first: Nada

last: Radwan

first: Sara

last: Amer

first: Narjes

last: Saheb Sharif-Askari

first: Kamel

last: Samara

first: Rabih

last: Halwani

first: Herbert

middle: F

last: Jelinek


title: A novel immune modulator IM33 mediates a glia-microbiota-neuronal axis that controls lifespan

status: Public on Jul 21 2023

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Using Drosophila we identified a glia-secreted antimicrobial peptide IM33, which alters gut microbiota to modulate sleep. To understand how the gut commensal Lactiplantibacillus plantarum functions in the brain to regulate sleep, we performed single-cell RNA sequencing.

overall_design: Single-cell RNA sequencing of fly brains from 3 age-matched groups: conventionally reared flies (CTRL), antibiotic-treated (8 days) flies (ABX) and Lactiplantibacillus plantarum-transferred (5-day ABX treatment + 3-day LP transfer) flies (LP). Briefly, 18 fly brains per group were dissected in cold Schneider’s medium, followed by papain (100 unit/mL) and collagenase I (1.11 mg/mL) digestion. SYTOX-green negative cells are FACS sorted and utilized for sequencing.

first: Wangchao

last: Xu

first: Taitea

last: Dykstra


title: Understanding the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung using single cell RNA sequencing.

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

summary: To understand the transcriptional consequences of Lamin A deficiency within the immune compartment of the lung we conducted single cell RNA sequencing on sorted immune cells from WT vs. Lmna-flox/flox Vav1-cre-/- mice (in duplicate, 2 mice per group).

overall_design: WT and Lmna KO lung immune cells were subjected to single cell RNA sequencing.

first: Nilushi

last: De Silva

first: Francesca

last: Nadalin

first: José

last: González Granado


title: Transcriptomics study on mouse treated with different doses of soman for 1, 3, 7 and 14 day.

status: Public on Jul 20 2023

city: Beijing

first: Zhenpeng

last: Zhang

address: 38 Life Science Park Road

country: China

institute: Beijing Proteome Research Center

summary: Soman is a highly toxic lipophilic chemical warfare nerve agent that can cause serious brain damage, leading to death due to intense seizures and neuronal injury. The potential risks of low-dose soman exposure have been a cause for concern for a long time. However, the understanding of the complex biological changes that lead to persistent neurocognitive dysfunction induced by soman is still limited. In this work, we studied the response of mice to soman by measuring transcriptomics experiments. Mice were administered soman subcutaneously at 1/10, 1/5 or 1/2 of the 50% lethal dose and were sampled at 1, 3, 7 and 14 days. Each group has 3 biological replicates.

first: Ping

first: Yuxu

last: Zhong

first: Tao

last: Zuo

first: Yong'an

last: Wang


title: Acetyl-methyllysine marks chromatin at active transcription start sites

city: Orange

first: Matthew

last: Simon

state: CT

address: 100 West Campus Drive, Ste MIC 231

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: Lysine residues in histones and other proteins can be modified by post-translational modifications (PTMs) that encode regulatory information. Acetylation and methylation of histone lysine residues are especially important for regulating chromatin and gene expression. Pathways involving these PTMs are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here, we report the discovery of cellular lysine residues that are both methylated and acetylated on the same sidechain to form acetyl-methyllysine (Kacme). We show that Kacme is found on histone H4 across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin and is regulated in response to biological signals. Analysis of nascent transcription and promoter-proximal pausing in human cells demonstrates that higher levels of Kacme are associated with higher levels of initiation and transcription. H4Kacme can be installed by enzymatic acetylation of monomethylated lysine peptides and is resistant to deacetylation by some HDACs in vitro. Further, Kacme can be bound by chromatin proteins that recognize modified lysine residues as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a new cellular PTM with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a PTM with fundamental importance to chromatin biology.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP-seq with Kacme and H4Kac antibodies in S2 cells +/- heatshock, ChIP-seq with Kacme and H4Kac antibodies in K562 and HEK 293T cells, ChIP-seq with H4Kacme antibodies in HEK 293T cells, and CUT&RUN with Kacme and H4Kac antibodies in K562 cells. TT-TL-seq and STL-seq performed in HEK 293T cells. TT-TL-seq performed in HEK 293T cells treated with TSA (400 nM) or DMSO for 15 hours. All experiments performed in duplicate. Inputs included.

first: William

last: Lu-Culligan

first: Leah

last: Connor

first: Yixuan

last: Xie

first: Babatunde

last: Ekundayo

first: Brendan

middle: T

last: Rose

first: Andreas

last: Pintado-Urbanc

first: Martin

last: Machyna

first: Joshua

last: Zimmer

first: Isaac

middle: W

last: Vock

first: Natarajan

middle: V

last: Bhanu

first: Megan

last: King

first: Benjamin

last: Garcia

first: Franziska

last: Bleichert


title: Nucleocytoplasmic mRNA redistribution in ALS motor neurons and is reversed by VCP ATPase inhibition

first: Oliver

last: Ziff

address: 1 Midland Road

institute: Francis Crick Institute

summary: Although the pathological hallmark of amyotrophic lateral sclerosis (ALS) is the nucleocytoplasmic mislocalisation of RNA binding proteins (RBPs), such as TDP-43 and FUS, the nucleocytoplasmic distribution of mRNA remains uncharacterised. Here, we used subcellular fractionation with RNA sequencing to assess nucleocytoplasmic mRNA localisation in human induced pluripotent stem cell-derived motor neurons (iPSNs) from ALS patients with TARDBP mutations, VCP mutations, and controls with VCP mutations isogenically knocked in with CRISPR/Cas9. In each mutant group, we found substantial nucleocytoplasmic mRNA redistribution, particularly in transcripts involved in protein binding. Redistributed transcripts in ALS iPSNs were enriched in protein-coding biotypes, exhibited longer lengths, and had enhanced interactions with RBPs, including TDP-43 and FUS. Treatment with the VCP D2 ATPase domain inhibitor ML240 partially restored nucleocytoplasmic mRNA redistribution not only in VCP mutants but also in TARDBP mutant iPSNs.

overall_design: Induced pluripotent stem cell derived motor neurons from controls, TARDBP mutant, VCP mutant and VCP knock ins underwent subcellular fractionation into nuclear and cytoplasmic fractions. Cultures were treated with VCP D2 ATPase inhibitor ML240.

first: Jasmine

last: Harley

first: Rickie

last: Patani


title: RNA-seq of heart healthy and heart diseased SCGs and pineal glands

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

institute: Technical University of Munich

summary: Disruption of the physiologic sleep-wake cycle and low melatonin levels frequently accompany cardiac disease, yet the underlying mechanism has remained enigmatic. Immunostaining of sympathetic axons in optically cleared pineal glands from humans and mice with cardiac disease revealed their substantial denervation compared to controls. Spatial, single-cell, nuclear, and bulk RNA sequencing traced this defect back to the superior cervical ganglia (SCG), which responded to cardiac disease with accumulation of inflammatory macrophages, fibrosis, and the selective loss of pineal gland-innervating neurons. Depletion of macrophages in the SCG prevented disease-associated denervation of the pineal gland and restored physiological melatonin secretion. Our data identify the mechanism underlying the disturbance of diurnal rhythmicity in cardiac disease and suggest means for therapeutic intervention.

overall_design: SCGs and pineal glands from heart healthy and heart diseased mice were subjected to bulk RNA-seq.

first: Stefan

last: Engelhardt


title: spatial RNA-seq of SCG

overall_design: A cryosection of fresh-frozen SCG from a heart healthy mouse was subjected to spatial RNA-seq (Vizgen).


title: single-cell RNA-seq of healthy (ctrl) and heart diseased (TAC) SCGs

overall_design: SCGs from heart healthy and heart diseased mice were subjected to single-cell RNA-seq (10x Genomics).


title: Effect of SMNDC1 small molecule inhibition on gene expression

city: Vienna

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
To investigate the effect of treating alphaTC1 cells with a small molecule inhibitor against SMNDC1, we treated cells with DMSO (control) or compound (G786-1089) for 16h.
We then performed gene expression profiling analysis and splicing analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for alphaTC1 cells treated with SMNDC1 inhibitor or DMSO, 3 replicates for each condition.

first: Lennart

last: Enders

first: Michael

last: Schuster


title: Recapitulating human peri-gastrulation development via self-organization of extended pluripotent stem cells

city: Dallas

first: Jun

last: Wu

address: 5323 harry Hines Blvd.

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Stem cell models that replicate the gastrulation process in human embryos have been created, but they lack the essential extraembryonic cells needed for early embryonic development and patterning. Here, we introduce a robust and efficient method that prompts human extended pluripotent stem (EPS) cells to self-organize into embryo-like structures, called peri-gastruloids, which encompass both embryonic (epiblast) and extraembryonic (hypoblast) tissues. These peri-gastruloids simulate critical stages of human peri-gastrulation development, such as forming amniotic and yolk sac cavities, developing bilaminar and trilaminar embryonic discs, specifying primordial germ cells, initiating gastrulation, and early neurulation. Single-cell RNA sequencing unveiled transcriptomic characteristics of these human peri-gastruloids, which closely resemble the primary peri-gastrulation cell types found in human and non-human primates. Our results emphasize the remarkable self-organizing ability of EPS cells to generate advanced human embryo-like structures. This peri-gastruloid platform allows for further exploration beyond gastrulation and may potentially aid in the development of human fetal tissues for use in regenerative medicine.

overall_design: Peri-gastruloids were pooled and harvested after 11 days of development for scRNA-seq analysis

first: Lizhong

last: Liu

first: Lei

last: Wang


title: heart healthy and heart diseased SCGs

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

overall_design: Refer to individual Series


title: C. elegans germ granules regulate both germline and somatic RNAome

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

type: Non-coding RNA profiling by high throughput sequencing


title: C. elegans germ granules regulate both germline and somatic RNAome [RNA-Seq]

summary: Germ granules are membrane-less organelles essential for small RNA biogenesis and germline development. Among the conserved properties of germ granules is their association with the nuclear membrane. Recent studies demonstrated that LOTUS domain proteins, EGGD-1 and EGGD-2 (also known as MIP-1 and MIP-2 respectively), promote the formation of perinuclear germ granules in C. elegans. This finding presents a unique opportunity to evaluate the significance of perinuclear localization of germ granules. Here we show that loss of eggd-1 causes the coalescence of germ granules and formation of abnormal cytoplasmic aggregates. Impairment of perinuclear granules affects certain germline classes of small RNAs including Piwi-interacting RNAs. Transcriptome profiling reveals overexpression of spermatogenic and cuticle-related genes in eggd-1 hermaphrodites. We further demonstrate that disruption of germ granules activates HLH-30-mediated transcriptional program in somatic tissues. Collectively, our findings underscore the essential role of EGGD-1 in germ granule organization and reveal an unexpected germ granule-to-soma communication.

overall_design: Gene expression analysis of wild type and eggd-1 C. elegans mutants by mRNA sequencing

first: Ian

last: Price

first: Jillian

last: Wagner

last: Pastore

first: Hannah

middle: L

last: Hertz


title: RNA-seq of heart healthy and heart diseased SCGs

overall_design: SCGs from heart healthy and heart diseased donors were subjected to bulk RNA-seq.


title: LAST-seq:single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis

city: Bethesda

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

summary: Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.

overall_design: HEK293T  and eHAP1 cells were sorted by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Chongyi

last: Chen


title: Protective role of gut insulin action in the development of nonalcoholic steatohepatitis and hepatocellular carcinoma associated with diabetes in mice

city: Tokyo

first: Kotaro

last: Soeda

address: 1-21-1 toyama, shinjuku-ku

department: Department of Molecular Diabetic Medicine

country: Japan

institute: National Center for Global Health and Medicine

summary: Diabetes is known to increase the risk of nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). Here we treated STAM (STelic Animal Model) mice, which develop diabetes, NASH and HCC associated with dysbiosis upon low-dose streptozotocin and high-fat diet (HFD), with insulin or phlorizin. Although both treatments ameliorated hyperglycemia and NASH, insulin treatment alone led to suppression of HCC accompanied by improvement of dysbiosis through restoration of antimicrobial peptide production. Similar changes in microflora are observed in insulin-treated patients comorbid with diabetes and NASH. Insulin treatment, however, failed to suppress HCC in the STAM mice lacking insulin receptor specifically in intestinal epithelial cells (ieIRKO), which showed dysbiosis and impaired gut barrier function. Furthermore, ieIRKO mice were prone to develop HCC merely on HFD. These data suggest that impaired gut insulin signaling increases the risk of HCC which can be countered by restoration of insulin action in diabetes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ileum in intestinal epithelial insulin receptor knock-out STAM mice treated with insulin, its control genotype (floxed and non-Cre) STAM mice, and control genotype STAM mice without insulin treatment.

first: Kohjiro

last: Ueki


title: High-throughput RNA-seq analysis of mocetinostat- and DMSO-treated TC28a2 cells

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: We performed global gene expression analysis in mocetinostat- and DMSO-treated TC28a2 human chondrocyte cells, to study genes regulated by mocesinostat comprehensively.

overall_design: RNA samples from mocetinostat- and DMSO-treated TC28a2 cells were obtained (N = 3 replicates per condition; 6 samples in total). Then, high-throughput RNA-seq analysis was performed.

first: Manabu

last: Kawata

first: Martin

last: Lotz

first: Padmaja


title: RNA-Sequencing analysis of liver tissue from female Foxa3-Cre YAP1 knockout mice, Foxa3-Cre YAP1 KO TAZ heterozygous mice, and WT littermate controls, at 3-4 months of age

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

summary: We developed a mouse model of bile duct paucity by deleting Yes-associated protein 1 (YAP1) in foregut endoderm progenitors, using the Foxa3 promoter to drive Cre expression. YAP1 KO mice are viable postnatally and survive long-term despite a complete failure of  intrahepatic bile duct development, resembling the liver phenotype of Alagille syndrome. Adult YAP1 KO mice suffer from severe chronic cholestasis, but show minimal hepatocellular injury, suggesting that the hepatocytes have adapted to preserve liver function and reduce damage from the toxicity of bile acids and bilirubin. We next bred Foxa3-Cre YAP1 KO TAZ heterozygote and Foxa3-Cre YAP1 KO TAZ KO (DKO) mice to assess the role of TAZ in this model. DKO mice and male YAP KO TAZ heterozygotes died around time of birth. The survivors, YAP1 KO TAZ heterozygote females, were overall phenotypically similar to YAP1 KO mice, with absence of intrahepatic bile ducts and long-term survival. We used RNA-seq to analyze the gene expression patterns of whole liver tissue of female adult YAP1 KO mice compared to WT controls (C57BL/6 background), and female adult YAP1 KO TAZ heterozygote (YKTH) mice compared to WT controls (mixed C57BL/6 - FVB background). We found that both YAP1 KO and YAP1 KO TAZ heterozygote female mice were overall very similar and showed similar alterations in gene expression compared to WT. There were a few differences in pathways involved in cell cycling and monocyte recruitment.

overall_design: We analyzed 6 healthy WT female liver tissue samples (3 C57BL/6 background, 3 mixed C57BL/6-FVB background), 3 female YAP1 KO liver tissue samples (C57BL/6 background), and 3 female YAP1 KO TAZ heterozygote (YKTH) liver tissue samples (mixed C57BL/6-FVB background).

first: Laura

last: Molina

first: Silvia


title: Transcription factor hepatocyte nuclear factor 1β controls a transcriptional network regulating cell polarity in kidney cells

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

summary: Mutations or deletions in HNF1β cause autosomal dominant tubulointerstitial kidney disease (ADTKD)-HNF1β, a rare and heterogenous disease characterized by renal cysts and/or malformation, maturity-onset diabetes of the young, hypomagnesemia, hypokalemia and hypocalciuria. The electrolyte disturbances may develop in the distal part of the nephron, which is important for finetuning of Mg2+, Ca2+, K+ reabsorption. Moreover, this segment is a prevalent site of cyst formation in ADTKD-HNF1β patients. Therefore, we aim to study the transcriptional network directed by HNF1β in the distal part of the nephron. For this we combined HNF1β ChIP-seq and mRNA expression data to identify direct targets of HNF1β in a renal distal convoluted tubule cell line (mpkDCT).

overall_design: RNA sequencing of mpkDCT cells transfected with siMock and siHNF1B, combined with ChIP-seq data from GSM2051311

first: Lotte

last: Tholen

first: Jeroen

last: de Baaij


overall_design: Gene expression in liver of six STAM mice or three normal mice was measured at 20 weeks of age. Three of STAM mice were treated with insulin, and the other STAM mice were non-treated control.


title: Breast cancer mutations HER2V777L and PIK3CAH1047R activate the p21-CDK4/6 –Cyclin D1 axis driving tumorigenesis and drug resistance.

city: St. Louis

first: Yirui

last: Sun

address: 660 S Euclid Ave

institute: Washington University in St. Louis

summary: In metastatic breast cancer, HER2 activating mutations frequently co-occur with mutations in the PIK3CA, TP53, or E-cadherin genes. Of these co-occurring mutations, HER2 and PIK3CA mutations are the most prevalent gene pair, with approximately 40% of HER2 mutated breast cancers also having activating mutations in PIK3CA. To study the effects of co-occurring HER2 and PIK3CA mutations, we bred genetically engineered mice with the HER2V777L; PIK3CAH1047R transgenes (HP mice) and studied the resulting breast cancers both in vivo as well as ex vivo using cancer organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT mice and PIK3CA single mutated mice, HER2 single mutated mice, and PIK3CA/HER2 double mutated mice.

first: Xiaoqing

last: Cheng

first: Maureen

last: Highkin

first: John

middle: R

last: Edwards

first: Ron

last: Bose


title: The effect of spleen tyrosine kinase on bone marrow monocytes in atherosclerosis

city: itabashi-ku

first: Daisuke

last: Tsukui

state: tokyo

institute: Teikyo University

summary: Spleen tyrosine kinase (Syk)del/del mice suppressed atherosclerosis and Sykdeldel macrophages showed cell migration impairment. To investigate the Syk-associated genes in cell migration, we analyzed RNA-Seq of bone marrow monocytes.

overall_design: Bone marrow monocytes were purified from mice fed with a high-fat diet for eight weeks and compared Syk+/+Rosa26CreER(T2)+/+ and Sykdel/delRosa26CreER(T2)+/+. Each sample was in triplicate.

first: Yoshitaka

last: Kimura

first: Kono

last: Hajime


title: Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain [RNA-seq]

city: Saint Louis

first: Benpeng

last: Miao

address: 4480 Clayton Avenue

department: Developmental Biology

summary: We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after the METH overdose, 15.6% of genes changed expression and 27.6% of open-chromatin regions altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes (DEGs) and differentially accessible regions (DARs) were simultaneously affected. Among the four rat brain regions analyzed, 149 transcription factors (TFs) and 31 epigenetic factors were significantly affected by the METH overdose. The METH overdose also resulted in reversed regulation patterns of both gene and chromatin accessibility in the dentate gyrus and Ammon’s horn. About 70% of METH-induced chromatin accessibility alterations are highly enriched in neurological processes and shared conserved sequences to the human genome. Many of these conserved regions were active brain-specific enhancers and harbored the SNPs associated with human neurological functions and diseases. Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with a METH overdose. Overall, our study provides clues to a better understanding of the molecular responses to METH overdose in the human brain.

overall_design: Adult male Sprague-Dawley rats with saline injection (Control sample) and Methamphetamine hydrochloride injection (METH-overdose sample)

first: Xiaoyun

last: Xing

first: Viktoriia

last: Bazylianska

first: Pamela

last: Madden

first: Anna

last: Moszczynska

first: Bo

last: Zhang


title: Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain [ATAC-seq]


title: Role of Gdf15 in neonatal hyperoxic lung injury

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

summary: Growth Differentiation Factor 15 (GDF15) is a divergent member of the TGF-β superfamily, and its expression increases under various stress conditions, including inflammation, hyperoxia, and senescence. GDF15 expression is increased in neonatal murine BPD models, and GDF15 loss exacerbates oxidative stress and decreases viability in vitro in pulmonary epithelial and endothelial cells. Our overall hypothesis is that the loss of GDF15 will exacerbate hyperoxic lung injury in the neonatal lung in vivo. We exposed neonatal Gdf15-/- mice and wild-type (WT) controls on a similar background to room air or hyperoxia (95% O2) for 5 days after birth. The mice were euthanized on PND 21. Gdf15 -/- mice had higher mortality and lower body weight than WT mice after exposure to hyperoxia. Upon exposure to hyperoxia, female mice had higher alveolar simplification in the Gdf15-/- group than the female WT group. Gdf15-/- and WT mice showed no difference in the degree of the arrest in angiogenesis upon exposure to hyperoxia. Gdf15-/- mice showed lower macrophage count in the lungs compared to WT mice. Our results suggest that Gdf15 deficiency decreases the tolerance to hyperoxic lung injury with evidence of sex-specific differences.

overall_design: We exposed neonatal Gdf15-/- mice and wild-type (WT) controls both C57BL6 background on a similar background to room air or hyperoxia (95% O2) for 5 days after birth. The mice were euthanized on PND 21.

first: Krithika

last: Lingappan


title: Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain

state: Missouri


title: SYNCRIP is the Molecular Brake of APOBEC-driven Mutagenesis, Tumor Heterogeneity and Therapy Resistance

first: Tao

last: Wang

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: Intratumoral genetic heterogeneity and mutational burden have been suggested to be the fuel and the source of resistance for many molecularly targeted therapies throughout a multitude of cancers. Emerging evidence indicates that tumor cells could hijack the powerful mutagenesis machinery mediated by the DNA deaminase APOBEC family proteins to intensify mutagenesis, promote intratumoral heterogeneity, and foster therapy resistance through a cell-autonomous mechanism. However, this mechanism has yet to be characterized. Utilizing prostate cancer (PCa) as a relevant model, we have identified the Synaptotagmin Binding Cytoplasmic RNA Interacting Protein (SYNCRIP) as a molecular brake for APOBEC-driven mutagenesis, intratumoral heterogeneity, and resistance to Androgen Receptor (AR) targeted therapies. Through a multi-disciplinary approach integrating bulk and single cell RNA-Seq (scRNA-Seq), whole-genome exome-sequencing (WES), and CRISPR library screening, we identified eight mutated resistance driver genes and revealed unparalleled details of how these heterogeneously aberrant subclones fuel the evolution of AR therapy resistance. For the first time, these findings exposed a cell-autonomous mechanism activating APOBEC-driven mutagenesis, consequently fueling mutational burden, genetic heterogeneity, and therapy resistance, and suggested that APOBEC proteins could be the potential therapeutic targets for preventing or overcoming resistance in PCa.

overall_design: 1) Examination of transcriptomic changes in LNCaP/AR prostate cancer cell lines with modifications of SYNCRIP genes. There is total 4 different conditions with 3 biological replicates each. 2) Examination of whole gxome changes in LNCaP/AR prostate cancer cell lines with modifications of SYNCRIP genes. There is total 4 different conditions with 3 biological replicates each. 3) Single cell RNA-seq examine the transcrptomic changes in LNCaP/AR prostate cancer cell lines with various shRNAs targeting SYNCRIP and treated with enzalutamide or vehicle. There is total 6 different conditions, with around 6,000 cells being sequenced each.  4) Examination of whole genome changes in LNCaP/AR prostate cancer cell line single clones. There is total 21 single clones. 5) Examination of whole genome changes in LNCaP/AR SREX and NREX cells. There is total 19 cell lines.

first: Ping

last: Mu


title: Epigenetic Features of HIV-Induced T-Cell Exhaustion Persist Despite Early Antiretroviral Therapy

status: Public on Jul 19 2023

city: Charlestown

first: Debattama

last: Sen

state: MA

department: Cancer Center

institute: MGH/Harvard

summary: T cell dysfunction occurs early following HIV infection, impacting the emergence of non-AIDS morbidities and limiting curative efforts. ART initiated during primary HIV infection (PHI) can reverse this dysfunction, but the extent of recovery is unknown. We studied 66 HIV-infected individuals treated from early PHI with up to three years of ART. Compared with HIV-uninfected controls, CD4 and CD8 T cells from early HIV infection were characterised by T cell activation and increased expression of the immune checkpoint receptors (ICRs) PD1, Tim-3 and TIGIT. Three years of ART lead to partial – but not complete – normalisation of ICR expression, the dynamics of which varied for individual ICRs. For HIV-specific cells, epigenetic profiling of tetramer-sorted CD8 T cells revealed that epigenetic features of exhaustion typically seen in chronic HIV infection were already present early in PHI, and that ART initiation during PHI resulted in only a partial shift of the epigenome to one with more favourable memory characteristics. These findings suggest that although ART initiation during PHI results in significant immune reconstitution, there may be only partial resolution of HIV-related phenotypic and epigenetic changes.

overall_design: ATAC-seq analysis of HIV tetramer-specific CD8+ T cells at early and late timepoints from patients who were either treated early or late with antiretroviral therapy (ART)/

first: Genevieve

middle: E

last: Martin

first: Matthew

last: Pace

first: Nicola

last: Robinson

first: Jodi

last: Meyerowitz

first: Emily

last: Adland

last: Thornhill

first: Mathew

last: Jones

first: Ane

last: Ogbe

first: Lucia

last: Parolini

first: Natalia

last: Olejniczak

first: Panagiota

last: Zacharopoulou

first: Helen

last: Brown

first: Christian

last: Willberg

first: Nneka

last: Nwokolo

first: Julie

last: Fox

first: Sarah

last: Fidler

first: W

middle: N

last: Haining

last: Frater


title: Control of Embryonic Brown Adipocyte Development by GATA6 [ChIP-Seq]

first: Patrick

last: Seale

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

summary: Brown adipose tissue (BAT) is a thermogenic organ that protects animals against hypothermia and obesity. BAT derives from the multipotent paraxial mesoderm; however, the identity of embryonic brown fat progenitor cells and regulators of adipogenic commitment are unclear.  We identified the transcription factor GATA6 as a selective marker of brown adipogenic progenitor cells. Deletion of Gata6 in the brown fat lineage resulted in a striking loss of BAT. To gain insight into the mechanism by which GATA6 supports BAT development, we performed ChIP-seq for GATA6 from the BAT of embryonic day 15.5 embryos.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for GATA6 in E15.5 BAT.

first: Angela

middle: H

last: Weller

first: Seoyoung

last: Jun

first: Kirill

last: Batmanov

first: Ethan

middle: C

last: Fein


title: Control of Embryonic Brown Adipocyte Development by GATA6 II

summary: Brown adipose tissue (BAT) is a thermogenic organ that protects animals against hypothermia and obesity. BAT derives from the multipotent paraxial mesoderm; however, the identity of embryonic brown fat progenitor cells and regulators of adipogenic commitment are unclear.  Here, we performed single cell gene expression analyses of mesenchymal cells during mouse embryogenesis with a focus on BAT development.

overall_design: Live (DAPI(-)) cells from control and Gata6ΔMyf5 mutant embryos harvested at E14.5


title: Low-input Hi-C library construction

first: Yanyi

last: Huang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: To evaluate the robustness of CtG, we constructed Hi-C libraries of varying quantities of cell inputs utilizing a low-input Hi-C technique.

overall_design: Both HEK293 and HEK293T cells were used. Either 1,000 cells or 10,000 cells were extracted to a 0.5 mL Eppendorf Lobind Microcentrifuge tube. Hi-C experiments were performed followed the method described in Rao et al., 2014 (PMID: 25497547) with some modifications.

first: Lu

last: Liu


title: Canonical and nuclear mTOR specify distinct transcriptional programs in androgen-dependent prostate cancer cells [RNAseq_mTOR]

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

summary: mTOR is a serine/threonine kinase that controls prostate cancer (PCa) cell growth in part by regulating gene programs associated with metabolic and cell proliferation pathways. mTOR- mediated control of gene expression can be achieved via phosphorylation of transcription factors, leading to changes in their cellular localization and activities. mTOR also directly associates with chromatin in complex with transcriptional regulators, including the androgen receptor (AR). Nuclear mTOR (nmTOR) has been previously shown to act as a transcriptional integrator of the androgen signaling pathway in association with the chromatin remodeling machinery, AR, and FOXA1. However, the contribution of cytoplasmic mTOR (cmTOR) and nmTOR and the role played by FOXA1 in this process remains to be explored. Herein, we engineered cells expressing mTOR tagged with nuclear localization and export signals dictating mTOR localization. Transcriptome profiling in AR-positive PCa cells revealed that nmTOR generally downregulates a subset of the androgen response pathway independently of its kinase activity, while cmTOR upregulates a cell cycle-related gene signature in a kinase-dependent manner. Biochemical and genome-wide transcriptomic analyses demonstrate that nmTOR functionally interacts with AR and FOXA1. Ablation of FOXA1 reprograms the nmTOR cistrome and transcriptome of androgen responsive PCa cells. This works highlights a transcriptional regulatory pathway in which direct interactions between nmTOR, AR and FOXA1 dictate a combinatorial role for these factors in the control of specific gene programs in PCa cells.

overall_design: Triplicate RNA-seq experiments in LNCaP cells with shRNA-mediated knockdown of mTOR rescued with either WT-mTOR , NES-mTOR (nuclear export signal tagged), NLS-mTOR (nuclear localization signal tagged), NLS-mTOR D2357E (NLS-mTOR with a kinase dead mutation; NLS-mTORKD) or empty vector (EV) conrol treated with 10nM R1881 or vehicle (EtOH) control for 24h.

first: Yonghong

last: Chen

first: Catherine

last: Dufour


title: RNA-seq reveals transcriptome changes in primary hepatocytes  following Wdr6 knockout

city: Jinan

first: Zhenyu

last: Yao

state: Shandong Province

address: No.544, Jing 4 Road, Huaiyin District

department: Shandong Provincial Hospital

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: To explore the potential functions and molecular mechanisms of Wdr6 in liver, we generated a whole-body knockout of Wdr6 in mice.

overall_design: We then performed transcriptomic analysis of primary hepatocytes from WDR6-WKO and control mice (n = 3- 4 independent experiments)

first: Jiajun

last: Zhao

first: Ling

last: Gao

first: Tao

last: Bo

first: Ying

last: Gong


title: SMARCB1 maintains lineage fidelity in renal cancer.

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

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

overall_design: Refer to individual Series


title: SMARCB1 maintains lineage fidelity in renal cancer - ATAC-seq

summary: Transcriptional lineage factors are a prominent class of essential genes in cancer, but the mechanisms that maintain lineage fidelity in advanced cancer clones, and whether lineage factor pathways could be broadly exploited for cancer therapy remain poorly understood. Here, we have used clear cell renal cell carcinoma (ccRCC) as a model to characterise the mechanisms that underlie lineage factor dependence in cancer. Through CRISPR/Cas9 loss-of-function screening and functional validation we find that loss of SMARCB1, a member of the SWI/SNF chromatin remodelling complex, can confer an advantage to ccRCC cells upon inhibition of the essential renal lineage factor PAX8. PAX8 inhibition resistant cells formed tumours with a dramatically altered histology showing neuroendocrine differentiation. Based on ATAC-seq and RNA-seq analysis, SMARCB1 inactivation leads to large-scale loss of kidney-specific epigenetic programmes, acquisition of a cellular state resembling that of rhabdoid tumours, and eventual activation of proliferative pathways. We show that these pathways are supported by the adoption of new transcriptional dependencies on IRF2, BHLHE40, and ZNFX1, factors that represent rare essential genes across different lineage-specific and oncogenic pathways, a principle validated in a large-scale CRISPR/Cas9 screening data set comprising hundreds of cancer cell lines. Thus, lineage factor requirements in cancer can switch upon challenge. The rules governing such lineage switching should be considered when designing novel lineage factor-targeted cancer therapies.

overall_design: ATAC-seq profiling in experimental models of renal carcinoma.

first: Ludovic

last: Wesolowski

first: Shoko

last: Hirosue


title: SMARCB1 maintains lineage fidelity in renal cancer - RNA-seq

overall_design: mRNA profiling in experimental models of renal carcinoma.


title: Circadian time-series RNA-sequencing of  SKNAS neuroblastoma cells with inducible N-MYC-ER, Replicate #2

status: Public on Jul 18 2023

city: Rochester

first: Brian

middle: James

last: Altman

state: NY

address: 601 Elmwood Avenue Box 633

department: Biomedical Genetics

institute: University of Rochester

summary: The molecular circadian clock, which controls rhythmic 24-hour oscillation of genes, proteins, and metabolites, is disrupted across many human cancers.  Deregulated expression of MYC oncoprotein has been shown to alter expression of molecular clock genes, leading to a disruption of molecular clock oscillation across cancer types.  It remains unclear what benefit cancer cells gain from suppressing clock oscillation, and how this loss of molecular clock oscillation impacts global gene expression and metabolism in cancer.  We hypothesized that MYC suppresses oscillation of gene expression and metabolism to instead upregulate pathways involved in biosynthesis in a static, non-oscillatory fashion.  To test this, cells from distinct cancer types with inducible MYC or the closely related N-MYC were examined, using detailed time-series RNA-sequencing and metabolomics, to determine the extent to which MYC activation disrupts global oscillation of genes, gene expression, programs, and metabolites.  We focused our analyses on genes, pathways, and metabolites that changed in common across multiple cancer cell line models.  We report here that MYC disrupted over 85% of oscillating genes, while instead promoting enhanced ribosomal and mitochondrial biogenesis and suppressed cell attachment pathways.  Notably, when MYC is activated, biosynthetic programs that were formerly circadian flipped to being upregulated in an oscillation-free manner.  Further, activation of MYC ablates the oscillation of nutrient transporter proteins while greatly upregulating transporter expression, cell surface localization, and intracellular amino acid pools.  Finally, we report that MYC disrupts metabolite oscillations and the temporal segregation of amino acid metabolism from nucleotide metabolism.  Our results demonstrate that MYC disruption of the molecular circadian clock releases metabolic and biosynthetic processes from circadian control, which may provide a distinct advantage to cancer cells.

overall_design: We activated SKNAS N-MYC-ER in cells for 24 hours with 4-hydroxytamoxifen (4OHT, MYC-ON), or used vehicle control (MYC-OFF).  We then entrained cells circadian rhythms with dexamethasone.  24 hours after dexamethasone treatment, cells were then collected every 4 hours for up to 48 hours, and RNA was extracted.  CT refers to circadian time, ie, hours after dexamethasone entrainment.  RNA at approximately 66.67 ng/µL was submitted to the University of Rochester Genomics Research Center (GRC) was analyzed by TapeStation and determined to have an average RNA Integrity Number (RIN) of 9.3.  RNA-sequencing was performed on polyadenylated mRNAs using an Illumina NovaSeq 6000 as 100 base paired end sequencing,, yielding an average of 93.1 million reads per sample (when adding together both paired ends).  Reads were mapped with Salmon, and collapsed to gene level with Tximport.  This experiment is a biological replicate to the SKNAS time series in GSE221103.

first: Chi

last: Dang


title: Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

institute: Stanford University

summary: Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) provides an accurate way to depict the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. Here, we develop and validate Cellformer, a novel deep learning method, that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enhances the bulk ATAC-seq resolution and allows an efficient cell type specific open chromatin profiling on large size cohorts at a low cost. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms and putative mediators involved in resilient to Alzheimer’s disease (RAD), an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer’s disease (AD). Cell type-resolved chromatin profiling unveils cell type specific pathways and nominates potential epigenetic mediators underlying RAD that may illuminate therapeutic opportunities to limit the cognitive impact of this highly prevalent yet incurable disease. Cellformer has been made freely and publicly available to advance analysis of high-throughput bulk ATAC-seq in future investigations.

overall_design: Bulk ATAC-seq

first: M

last: Corces


title: Multi-omics profiling of cholangiocytes reveals chromatin state dynamics during hepatic cystogenesis in polycystic liver disease (ChIP-Seq female)

city: Tianjin

first: Jiayuan

state: State...

address: Heping

institute: Tianjin Medical University

summary: Through genome-wide profiling of chromatin dynamics, we revealed a profound increase of global chromatin accessibility and a switch from H3K9me3 to H3K9ac on cis-regulatory DNA elements of cyst-associated genes during cystogenesis. In an integrated epigenomic and transcriptomic analysis, we identified a transcription factor network associated with dynamic shifts in chromatin states. Functionally, we showed that inhibition of H3K9ac acetyltransferase or H3K9me3 demethylase restored chromatin states and gene expression program to slow cyst growth in PLD mice.

overall_design: ChIP-seq in primary WT and PLD cholangiocytes.

first: Rongjie

last: Ji


title: Multi-omics profiling of cholangiocytes reveals chromatin state dynamics during hepatic cystogenesis in polycystic liver disease (RNA-Seq female)

overall_design: RNA-seq in primary WT and PLD cholangiocytes.


title: Boosting NAD preferentially blunts TH17 inflammation via arginine biosynthesis and redox regulatory control in control and psoriasis subjects [NR or placebo]

first: Komudi

last: Singh

address: Building 10

institute: NIH

summary: To evaluate whether NAD+-boosting modulates adaptive immunity, primary CD4+ T cells from healthy control and psoriasis subjects were exposed to vehicle or nicotinamide riboside (NR) supplementation. NR blunts IFNg and IL-17 secretion with greater effects on TH17 polarization. RNA-seq analysis implicates NR blunting of sequestosome 1 (SQSTM1/p62)-coupled oxidative stress. NR administration increases SQSTM1 and reduces reactive oxygen species (ROS) levels. Furthermore NR activates NRF2, and genetic knockdown of NRF2 and of the NRF2-dependent gene, SQSTM1 diminish NR amelioratory effects. Metabolomic analysis identify that NAD+-boosting increases arginine and fumarate biosynthesis and genetic knockdown of argininosuccinate lyase ameliorates NR-effects on IL-17 production. Hence, NR via amino acid metabolites orchestrate NRF2 activation, augments CD4+ T cell antioxidant defenses and attenuates TH17 responsiveness. Oral NR supplementation in healthy volunteers similarly increase serum arginine, SQSTM1 and antioxidant enzyme gene expression and blunts TH17 immune responsiveness, supporting evaluation of NAD+-boosting in CD4+ T cell linked inflammation.

overall_design: CD4 T cells isolated were from human blood. RNA was extracted from CD4 T cells by miRNeasy Micro Kit (Qiagen). RNA was quantified using a Qubit 3.0 fluorometer (Thermo Fisher Scientific) and its integrity confirmed using an Agilent Technologies 2100 Bioanalyzer (Agilent).

first: Kim

last: Han

first: Michael

last: Sack


title: Comparative analysis of response to treatments and molecular features of tumor- derived organoids versus cell lines and PDX derived from the same clear cell ovarian adenocarcinoma

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: We analyse the molecular response of tumor cell lines in PDX or organoids teatments.

first: Lucie

last: Thorel

first: Louis-Bastien

last: Weiswald


title: Boosting NAD preferentially blunts TH17 inflammation via arginine biosynthesis and redox regulatory control in control and psoriasis subjects

city: Bethesda


title: Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans

city: Boston

first: Hannah

middle: Josephine

last: Smith

address: 665 Huntington Avenue, Building 1, Room 512

department: Molecular Metabolism

institute: Harvard University T.H. Chan School of Public Health

summary: mTORC1 (mechanistic target of rapamycin complex 1) is a metabolic sensor that promotes growth when nutrients are abundant. Ubiquitous inhibition of mTORC1 extends lifespan in multiple organisms but also disrupts several anabolic processes resulting in stunted growth, slowed development, reduced fertility, and disrupted metabolism. However, it is unclear if these pleotropic effects of mTORC1 inhibition can be uncoupled from longevity. Here, we utilize the auxin-inducible degradation (AID) system to restrict mTORC1 inhibition to C. elegans neurons. We find that neuron-specific degradation of RAGA-1, an upstream activator of mTORC1, or LET-363, the ortholog of mammalian mTOR, is sufficient to extend lifespan in C. elegans. Unlike raga-1 loss of function genetic mutations or somatic AID of RAGA-1, neuronal AID of RAGA-1 robustly extends lifespan without impairing body size, developmental rate, brood size or neuronal function. Moreover, while somatic degradation of RAGA-1 alters the expression of thousands of genes, demonstrating the widespread effects of mTORC1 inhibition, neuronal degradation of RAGA-1 only results in around 200 differentially expressed genes with a specific enrichment in metabolism and stress response. Notably, our work demonstrates that targeting mTORC1 specifically in the nervous system in C. elegans uncouples longevity from growth and reproductive impairments, and that many canonical effects of low mTORC1 activity are not required to promote healthy aging. These data challenge previously held ideas about the mechanisms of mTORC1 lifespan extension and underscore the potential of promoting longevity by neuron-specific mTORC1 modulation.

overall_design: To compare the effects of knocking down RAGA-1 in either the neurons or all somatic tissues, we generated C. elegans strains in which endogenous raga-1 was tagged with an auxin-inducible degron tag. We then expressed the degrading enzyme, TIR1, in either the neurons (1250) or all somatic (1438) tissues using the rab-3 and eft-3 promoters, respectively. In these two strains along with wild type worms (N2), we began auxin treatment at day 1 of adulthood to induce RAGA-1 degradation in either the neurons or in all somatic tissues and then harvested RNA from whole worm lysate 2 days later. We then performed RNA sequencing and differential gene expression analysis to compare gene expression changes between auxin-treated (A) and untreated samples (C) from each genotype. 4 replicates of all 6 samples were performed.

first: Anne

last: Lanjuin

first: Arpit

last: Sharma

first: William

last: Mair


title: mRNA expression in mouse oviduct and Dicer1 tumors

city: Vancouver

first: Yemin

last: Wang

state: BC

address: 2660 Oak Street

institute: University of British Columbia

summary: We developed a genetically engineered conditional compound heterozygous Dicer1 mouse strain that fully recapitulates the bi-allelic mutations of DICER1 in DICER1 syndrome-associated cancers. Embryonic activation of bi-allelic Dicer1 mutations, driven by the anti-Müllerian hormone receptor 2 (Amhr2)-driven Cre strain (Amhr2+/cre),  drove cancer development from oviduct. mRNA sequencing was performed to compare the mRNA expression profiles between tumor and normal oviduct.

overall_design: mRNAs from five control oviduct and 4 Dicer1 tumors were included for sequencing

first: Huntsman

last: David


title: Regulation of human germline commitment by DMRT1 [CUT&RUN]

city: Cambridge

first: SUN MIN

last: LEE

state: Cambridgeshire

address: Gurdon Institute, Tennis Court Road

institute: Gurdon Institute

summary: Nascent human primordial germ cell-like cells (PGCLCs) can be specified with BMP2 or BMP4 together with SCF and EGF from germline competent embryonic stem cells which are maintained in the presence of inhibitors for GSK3, MEK, p38 and JNK together with FGF2, TGFβ and LIF (4i ESC). Here we discovered that Activin A and retinoic acid treatment after PGC specification induced genes expressed in migrating and gonadal PGCs in vivo, including DMRT1 and CDH5. Ectopic expression of DMRT1 and SOX17 resulted in repression of pluripotent genes as well as induction of DAZL and a subset of mitotic arrest PGC genes. Our findings provide novel insights on the roles of DMRT1 for the transition from nascent PGCs towards germline determination and molecular mechanisms of early human germline development.

overall_design: CUT&RUN-sequencing for DMRT1 and rabbit IgG in d8 DZ+PGCLC

first: Sun

middle: M

last: Lee

first: Naoko

last: Irie

first: Azim

last: Surani


title: Regulation of human germline commitment by DMRT1 [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: Three samples for TAPSbeta and CAPS

first: Chunxiao

last: Song


title: Renal cancer secretome induces migration of mesenchymal stromal cells

city: Warsaw

first: Agnieszka

last: Piekiełko-Witkowska

address: Marymoncka 99/103

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Centre of Postgraduate Medical Education

summary:
Background: Advanced Renal cell carcinoma (RCC) is therapeutically challenging. RCC progression is facilitated by mesenchymal stem/stromal cells (MSCs) that exert remarkable tumor tropism. The specific mechanisms mediating MSCs’ migration to RCC remain unknown. Here, we comprehensively analyzed RCC secretome to identify MSCs attractants.   Methods: Conditioned media (CM) were collected from five RCC-derived cell lines (Caki-1, 786-O, A498, KIJ265T, KIJ308T) and non-tumorous control cell line (RPTEC/TERT1) and analyzed using cytokine arrays targeting 274 cytokines in addition to global CM proteomics. MSCs were isolated from bone marrow of patients undergoing standard orthopedic surgeries. RCC CM and the selected recombinant cytokines were used to analyze their influence on MSCs migration and microarray-targeted gene expression. The expression of genes encoding cytokines was evaluated in 100 matched-paired control-RCC tumor samples.  Results: When compared with normal cells, CM from advanced RCC cell lines (Caki-1, KIJ265T) were the strongest stimulators of MSCs migration. Targeted analysis of 274 cytokines and global proteomics of RCC CM revealed decreased DPP4 and EGF, as well as increased AREG, FN1, and MMP1, with consistently altered gene expression in RCC cell lines and tumors. AREG and FN1 stimulated, while DPP4 attenuated MSCs migration. RCC CM induced MSCs’ transcriptional reprogramming, stimulating the expression of CD44, PTX3, and RAB27B. RCC cells secreted hyaluronic acid (HA), a CD44 ligand mediating MSCs’ homing to the kidney. AREG emerged as an upregulator of MSCs’ transcription.   Conclusions: advanced RCC cells secrete AREG, FN1 and HA to induce MSCs migration, while DPP4 loss prevents its inhibitory effect on MSCs homing. RCC secretome induces MSCs’ transcriptional reprograming to facilitate their migration. The identified components of RCC secretome represent potential therapeutic targets.
We used microarrays to determine the effect of the conditioned media (CM)  collected from two RCC-derived cell lines (Caki-1, KIJ265T) and non-tumorous control cell line (RPTEC/TERT1) on the transcriptome change in mesenchymal stem/stromal cells (MSCs).

overall_design: Conditioned media (CM) were collected from renal cancer-derived cell lines (Caki-1, KIJ265T) and non-tumorous control cell line (RPTEC/TERT1). Per each cell line, CM was collected from cells independently cultured in three separate cell culture flasks. Mesenchymal stromal cells were isolated from bone-marrow collected during standard orthopedic surgeries with the agreement of the Local Bioethics Committee (approval no. KB/115/2016) and written informed consent of patients and used for treatment of mesenchymal stromal cells (MSCs). For the CM treaments, 50,000 MSC cells were seeded on a well of 12-well plate, cultured for 24h, rinsed twice with DMEM (low glucose, no glutamine, no phenol red) (Gibco/Thermo Fisher Scientific, Paisley, UK) supplemented with GLUTAMAX (Gibco/Thermo Fisher Scientific, Paisley, UK), and cultured for 24h in medium without FBS. Next, the cells were rinsed once with PBS and four times with DMEM supplemented with GLUTAMAX and cultured for 24h in CM from RPTEC/TERT1, Caki-1 or KIJ265T cells.   MSCs were treated with CM collected from Caki-1 (n=3), KIJ265T (n=3), and RPTEC/TERT1 (n=3).  RNA was isolated from the treated MSCs and subjected to microarray analysis using Microarray analysis was performed using Affymetrix Gene Atlas System.

first: Piotr

last: Popławski

first: Weronika

last: Zarychta-Wiśniewska

first: Anna

last: Burdzińska

first: Joanna

last: Bogusławska

last: Adamiok-Ostrowska

first: Karolina

last: Hanusek

first: Beata

last: Rybicka

first: Alex

last: Białas

first: Helena

last: Kossowska

first: Roksana

last: Iwanicka-Rokicka

first: Marta

last: Koblowska

first: Leszek

last: Pączek


title: RNA-seq reveals transcriptome changes  which could be responsible to insulin in insulin resistance states

first: Zhenyu

last: Yao

summary: To explore genes that could be responsible to insulin in insulin resistance states (IR), we generated the IR mice models (mice after 6 weeks of high-fat feeding).

overall_design: We carried out liver transcriptome analysis between IR mice treated with exogenous insulin and such mice injected with a bovine serum albumin (BSA) vehicle control. For the insulin-treatment, the mice were fasted overnight (16h) and stimulated with insulin (0.75 units/kg body weight, i.p.) or its vehicle BSA for 6 h.

first: Jiajun

last: Zhao

first: Ling

last: Gao

first: Tao

last: Bo

first: Ying

last: Gong

first: Yunyun

last: Xu


title: Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates

city: Paris

first: Caroline

last: Tonnerre-Doncarli

address: 15 rue Hélène Brion

institute: Institut Jacques Monod, CNRS UMR7592, Université Paris cité

summary: Replication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce assembly of an efficient minimal replication origin without inducing transcription. Dimeric pG4s in replication origins trigger formation of an NFR next to precisely positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest a crucial role for dimeric pG4s in the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes.

sample_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: A Wt DT40 chicken cell line and clonal heterozygous or homozygous cell lines containing mutated version of the βA-globin fused to the IL2R gene and SV40 PolyA sequence, flanked with two USF binding sites inserted into a mid-late replicating region of chromosome one (chr1:71,981,290-73,532,377 bp, galGal5) were analyzed. Profiles of the histone variant H2AZ enrichments were obtained by chromatin immunoprecipitation DNA-sequencing (ChIP-seq).  NFR and Nucleosome coverage profiles were obtained from MNAse-Seq and ATAC-seq experiments respectively. Isolated and clustered pG4 profiles were obtained from datas published in Zheng et al. 2020 under the accession number GSE133379 (supplementary files). We also considered G4s detected by ChIPSeq with a G4P protein (Zheng et al. 2020, GSE133379) for human 293T cells (GSM3907020,GSM3907021, GSM3907022, GSM3907023); human A549 cells (GSM3907012, GSM3907013, GSM3907014, GSM3907015); human H1975 cells (GSM3907016, GSM3907017, GSM3907018, GSM3907019); human HeLa-S3 cells (GSM3907024, GSM3907025), chicken DF-1 cells (GSM3907028, GSM3907029) and mouse 3T3 cells (GSM3907026, GSM3907027). Human ChIP-G4s were combined. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.

first: Jeremy

last: Poulet-Benedetti

first: Anne-Laure

last: Valton

first: Marc

last: Laurent

first: Marie

last: Gérard

first: Natalja

last: Barinova

first: Nikolaos

last: Parisis

first: Floran

last: Massip

first: Franck

last: Picard

first: Marie-Noëlle

last: Prioleau


title: Regulation of human germline commitment by DMRT1 [scRNA-Seq]

first: SUN MIN

last: LEE

overall_design: 10x RNA profiles of 4i ESC, NANOS3+ PGCLCs, DMRT1+ PGCLCs, and d8 DAZL+ PGCLCs.

first: Sun

last: Lee

first: Naoko

last: Irie

first: Carmen

last: Sancho Serra

first: Roser

last: Vento-Tormo

first: Azim

last: Surani


title: Re-examination of differential microRNA expressions in cacner associated fibroblasts

city: Akita City

first: Sei

last: Kuriyama

department: Molecular Medicine & Biochemistry

institute: Akita University

summary: we reexamined microRNA expressions in cancer associated fibroblasts

overall_design: Comparison of differential microRNA gene expressions from normal fibroblasts taken from same patient's non-cancerous tissue to cancer associated fibroblasts of stomach cacner


title: Multi-omics profiling of cholangiocytes reveals chromatin state dynamics during hepatic cystogenesis in polycystic liver disease (ATAC-Seq female)

first: Jiayuan

last: Chen

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in primary WT and PLD cholangiocytes.

first: Rongjie

last: Ji


title: Expression in mouse oviduct and Dicer1 tumors

first: Yemin

last: Wang

overall_design: Refer to individual Series


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells [NHEJ_BaseE]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Emerging base and prime editing may provide safer and more precise genetic engineering than nuclease-based approaches bypassing the dependence on DNA double strand breaks (DSBs). However, little is known about cellular responses and genotoxicity. Here, we comparatively assessed state-of-the-art base and prime editors (B/PE) versus Cas9 in human hematopoietic stem/progenitor cells (HSPCs). BE and PE induced detrimental transcriptional responses constraining editing efficiency and/or HSPC repopulation in xenotransplants, albeit to a lesser extent than Cas9. DNA DSBs and their genotoxic byproducts, including deletions and translocations, were less frequent but not abrogated by BE and PE, particularly for cytidine BE due to suboptimal inhibition of base excision repair. Tailoring timing and B/PE expression enabled highly efficient and precise editing of long-term repopulating HSPCs. However, we uncovered a genome-wide effect of BEs on the mutational landscape of HSPCs, raising concerns for a potential genotoxic impact and calling for further investigations and improvements in view of clinical application.

overall_design: Targeted deep sequencing performed on samples from CB or mPB HSPC donors, treated with different editing conditions, namely, mock electroporation (mock electro), Cas9, BE4max, and ABE8.20-m, in different organs and time points (9 and 15 weeks) or after 7 days of in vitro culture

first: Martina

last: Fiumara

first: Samuele

last: Ferrari

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells [RNAseq_PrimeEd]

overall_design: Whole transcriptomic analyses on human HSPC cells from a pool of 6 mPB donors, comparing mock electroporation (UTelectro) samples with Prime Edited ones.


title: αKG treatment prevent maturation and stimulate proliferation of neonatal cardiomyocytes

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: In the heart, metabolic profile switches from glycolysis to fatty acid oxidation (FAO) rapidly after birth accompanied by chromatin reconfiguration, cell cycle exit and cardiomyocyte (CM) maturation, suggesting a synergistic rewiring of transcriptional networks regulated by epigenetic mechanisms in accordance with environmental and metabolic signals. To gain a better insight into the interconnection between epigenetic processes and metabolic pathways during cardiac development, maturation and heart regeneration, we induced a metabolic reprogramming by depleting CPT1b, a crucial enzyme for FAO, specifically in CM.  Cpt1b inactivation led to cardiomegaly and attenuated cardiac damage in response to myocardial injury primarily attributed to augmented CM proliferation and enhanced resistance to ischemic injury.

overall_design: Transcriptome profiles of P0-1 neonatal cardiomyocyte treated with DMSO and aKG for 96 hours

first: Xiang

last: Li

first: Stefan

last: Guenther

first: Thomas

last: Braun


title: Gene expression analysis of myonectin-regulated genes in atrophic skeletal muscle.

city: Nagoya

first: Koji

last: Ohashi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University

summary: To investigate the role of myonectin in muscle atrophy, myonectin-KO and wild type (C57BL/6J) mice were subjected to sciatic nerve denervation, leading to gastrocnemius muscle atrophy.

overall_design: We then performed gene expression profiling analysis using data obained from RNA-seq of 8 gastrocnemius muscle tissues (Myonectin-KO 4, wild type 4).

first: Yuta

last: Ozaki

first: Katsuhiro

last: Kato

first: Noriyuki

last: Ouchi


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells [NHEJ_PrimeE]

overall_design: Targeted deep sequencing on mPB HSPC donors, treated with different editing conditions, namely, mock electroporation (mock electro) or Prime Editing in bone marrow and peripheral blood collected at different time points (9 and 15 weeks) from xenotransplanted mice or after 7 days of in vitro culture


title: Single cell sequencing of WT and hb-egfaKO zebrafish spinal cord, at 1 week after sham or transection injury.

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: We identified hb-egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb-egfa mechanism of action, we perforemd single cell sequencing of WT and hb-egfaKO zebrafish spinal cord.

overall_design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 week post injury. Spinal cord of sham-injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing (4 samples in total, WT 1 wpi, WT sham, hb-egfaKO 1 wpi, hb-egfaKO sham).

first: Valentina

last: Cigliola

first: Adam

last: Shoffner

first: Nutishia

last: Lee

first: Jianhong

last: Ou

first: Clay

last: Becker

first: Jiaul

last: Hoque

first: Trevor

last: Gonzalez

first: Yanchao

last: Han

first: Grace

last: Sheng

first: Timothy

last: Faw

first: Muhammad

last: Abd-El-Barr

first: Shyni

last: Varghese

first: Aravind

last: Asokan

first: Kenneth

middle: D

last: Poss


title: Discovery of a Highly Potent and Selective HDAC3 and HDAC8 PROTAC Dual Degrader

city: Gainesville

first: Daiqing

last: Liao

state: Florida

address: 2033 Mowry Road

department: Anatomy and Cell Biology

institute: University of Florida

summary: HDAC3 and HDAC8 are members of class I deacetylases involved in several biological mechanisms and represent a highly sought-after therapeutic target for drug development. It is historically challenging to develop selective deacetylase inhibitors due to their conserved catalytic domains. HDAC3 also has deacetylase-independent activity, which cannot be blocked by conventional enzymatic inhibitors. Recent advance in proteolysis-targeting chimeras (PROTACs) provides an opportunity to eliminate the whole protein selectively, abolishing both enzymatic and scaffolding function. Here, we report a novel HDAC3/8 dual degrader YX968 that induces highly potent, rapid, and selective degradation of both HDAC3 and HDAC8 without trigging pan-HDAC inhibitory effects. Unbiased quantitative proteomics experiments further confirmed its high selectivity. This dual-specific degrader specifically ablates cellular pathways attributed to HDAC3 and HDAC8 and exhibits high potency in killing cancer cells. YX968 represents a new probe for dissecting the complex biological functions of HDAC3 and HDAC8.

overall_design: MDA-MB-231 cells were cultured in 6-well plate and treated with DMSO, 3, or 30 nM of YX968 for 14 h. Total RNAs were isolated using the RNeasy mini kit (Qiagen). Total RNAs were used for RNA-seq Poly A library constructions and sequencing was done with 20M raw reads/sample using the Illumina NovaSeq 6000 S4 2x150 platform at the Interdisciplinary Center for Biotechnology Research, University of Florida.

first: Yufeng

last: Xiao

first: Seth

last: Hale

first: Nikee

last: Awasthee

first: Xuan

last: Zhang

first: Yi

last: Liu

first: Zhiguang

last: Huo

first: Dongwen

last: Lv

first: Weizhou

last: Zhnag

first: Mei

last: He

first: Guangrong

last: Zheng


title: Genotoxic effects of base and prime editing in human hematopoietic stem cells

first: Stefano

last: Beretta

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


title: Iron Drives Anabolic Metabolism Through Active Histone Demethylation and mTORC1

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: All living cells require a minimal iron threshold to sustain anabolic metabolism. However, the mechanisms by which cells sense iron to regulate anabolic processes are unclear. Here, we report a universal eukaryotic pathway for iron sensing in which molecular iron is required to sustain active histone demethylation and maintain the expression of critical components of the pro-anabolic mTORC1 pathway. Specifically, we identify the iron-binding histone-demethylase KDM3B as an intrinsic iron sensor that regulates mTORC1 activity by demethylating H3K9me2 at enhancers of genes encoding high-affinity leucine transporters and RAPTOR. By directly suppressing leucine availability and RAPTOR levels, iron deficiency (ID) supersedes other nutrient inputs into mTORC1. This process occurs in vivo, and is not an indirect effect by canonical iron-utilizing pathways. Elevated expression of KDM3B targets is associated with reduced survival in a subset of human cancers and ID represses mTORC1 in patient-derived tumor cells and sensitizes cancer cells to chemotherapy. These data demonstrate a novel mechanism of eukaryotic iron sensing through dynamic chromatin remodeling and repression of mTORC1 mediated anabolism. Due to ancestral eukaryotes sharing homologues of KDMs and mTORC1 core components, this pathway likely predated the emergence of the other kingdom-specific nutrient sensors for mTORC1

overall_design:
293T cells treated with Vehicle (H2O) or 150uM DFO for 12 hours

Grant ID: NRSA 5F30DK109608-02
Name: Jason Solomon Shapiro

Grant ID: NRSA T32-DK007169
Name: Jason Solomon Shapiro

first: Jason

last: Shapiro

first: Hossein

last: Ardehali


title: microRNA expression in mouse oviduct and Dicer1 tumors

first: Yemin

last: Wang

summary: We developed a genetically engineered conditional compound heterozygous Dicer1 mouse strain that fully recapitulates the bi-allelic mutations of DICER1 in DICER1 syndrome-associated cancers. Embryonic activation of bi-allelic Dicer1 mutations, driven by the anti-Müllerian hormone receptor 2 (Amhr2)-driven Cre strain (Amhr2+/cre),  drove cancer development from oviduct. Small RNA sequencing was performed to compare the microRNA expression profiles between tumor and normal oviduct.

overall_design: Toal RNA from five control oviduct and 4 Dicer1 tumors were included for sequencing

first: Huntsman

last: David